Chemical elements
  Sodium
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      1uxu
      1uxv
      1uy0
      1uy1
      1uy2
      1uy3
      1uy4
      1uyp
      1uyz
      1v0h
      1v1r
      1v47
      1v4s
      1v4t
      1v54
      1v55
      1v6p
      1v6s
      1v70
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      1vkg
      1vlm
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      1vmh
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      1vq4
      1vq5
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      1vq7
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      1vq9
      1vqk
      1vql
      1vqm
      1vqn
      1vqo
      1vqp
      1vr5
      1vzq
    PDB 1w15-1xc6
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Sodium in the structure of The Structure Of The Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb 1vqm)






The binding sites of Sodium atom in the structure of The Structure Of The Transition State Analogue "Dan" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 1vqm). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 1vqm structure was solved by T.M.SCHMEING, T.A.STEITZ, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)50.0-2.3
Space groupC2221
a (A)211.445
b (A)298.564
c (A)574.493
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)21.4
Rfree (%)24.7


Sodium Binding Sites:

Sodium binding site 1 out of 75 in 1vqm


Sodium binding site 1 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 1 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: C1068, 0: C1069, 0: A1070, 0: G1072, 0: G1087, 0: Hoh3775, 0: Hoh3806, 0: Hoh4141, 0: Hoh5535, 0: Hoh9694,

conact list:


AtomAtomDistance (A)
NaC3' 0:C10684.59
NaO3' 0:C10684.49
NaC5' 0:C10684.53
NaOP1 0:C10694.46
NaP 0:C10693.79
NaOP2 0:C10692.41
NaO5' 0:C10694.88
NaN6 0:A10704.91
NaN9 0:G10724.75
NaC8 0:G10723.74
NaC6 0:G10723.50
NaN1 0:G10724.81
NaC5 0:G10723.34
NaN7 0:G10722.67
NaC4 0:G10724.56
NaO6 0:G10723.09
NaC6 0:G10874.17
NaN1 0:G10874.79
NaO6 0:G10873.27
NaO 0:Hoh37752.86
NaO 0:Hoh38062.83
NaO 0:Hoh41414.18
NaO 0:Hoh55352.65
NaO 0:Hoh96943.58

interactive model:


Sodium binding site 2 out of 75 in 1vqm


Sodium binding site 2 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 2 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G1119, 0: U1120, 0: G1121, 0: U1122, 0: Mg8025, 0: Hoh4759, 0: Hoh5121, 0: Hoh6238, 0: Hoh8323,

conact list:


AtomAtomDistance (A)
NaC3' 0:G11194.29
NaC1' 0:G11194.67
NaO3' 0:G11193.20
NaC2' 0:G11194.31
NaO2' 0:G11193.44
NaOP1 0:U11204.77
NaP 0:U11203.66
NaOP2 0:U11202.87
NaC5' 0:U11204.62
NaO5' 0:U11204.67
NaC8 0:G11213.91
NaC6 0:G11213.89
NaC5 0:G11213.69
NaN7 0:G11212.86
NaC4 0:G11214.94
NaOP2 0:G11214.89
NaO6 0:G11213.42
NaC5 0:U11224.22
NaC4 0:U11224.17
NaO4 0:U11223.60
NaMG 0:Mg80254.03
NaO 0:Hoh47593.16
NaO 0:Hoh51213.97
NaO 0:Hoh62384.24
NaO 0:Hoh83232.82

interactive model:


Sodium binding site 3 out of 75 in 1vqm


Sodium binding site 3 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 3 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: A629, 0: A630, 0: A631, 0: A632, 0: G2070, 0: G2072, 0: A2074, 0: Hoh3037, 0: Hoh3690, 0: Hoh4680, 0: Hoh5273, 0: Hoh6337,

conact list:


AtomAtomDistance (A)
NaC2 0:A6294.65
NaN1 0:A6294.44
NaN9 0:A6304.03
NaN3 0:A6302.64
NaC3' 0:A6304.60
NaC2 0:A6303.46
NaN1 0:A6304.78
NaC5 0:A6304.97
NaC1' 0:A6303.58
NaO3' 0:A6304.13
NaO4' 0:A6304.82
NaC4 0:A6303.66
NaC2' 0:A6303.72
NaO2' 0:A6302.71
NaC3' 0:A6313.99
NaO3' 0:A6314.27
NaC2' 0:A6313.61
NaO2' 0:A6312.90
NaOP1 0:A6324.15
NaP 0:A6324.67
NaN2 0:G20703.99
NaC2 0:G20704.74
NaOP2 0:G20724.39
NaP 0:A20744.88
NaOP2 0:A20743.41
NaO 0:Hoh30374.43
NaO 0:Hoh36904.80
NaO 0:Hoh46802.47
NaO 0:Hoh52732.55
NaO 0:Hoh63372.22

interactive model:


Sodium binding site 4 out of 75 in 1vqm


Sodium binding site 4 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 4 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G2092, 0: G2093, 0: G2094, 0: A2612, 0: A2649, 0: Hoh9752,

conact list:


AtomAtomDistance (A)
NaN9 0:G20924.66
NaN3 0:G20923.22
NaN2 0:G20923.49
NaC2 0:G20923.62
NaN1 0:G20924.75
NaC1' 0:G20924.48
NaO3' 0:G20924.98
NaC4 0:G20924.15
NaC2' 0:G20924.41
NaO2' 0:G20923.22
NaN9 0:G20934.73
NaC8 0:G20933.94
NaC6 0:G20933.61
NaN1 0:G20934.74
NaC5 0:G20933.47
NaN7 0:G20933.07
NaC4 0:G20934.50
NaO6 0:G20933.38
NaC8 0:G20943.98
NaC6 0:G20943.56
NaN1 0:G20944.93
NaC5 0:G20943.50
NaN7 0:G20942.83
NaC4 0:G20944.81
NaO6 0:G20942.99
NaC6 0:A26124.48
NaN1 0:A26124.58
NaN6 0:A26124.33
NaN3 0:A26494.48
NaC2 0:A26493.23
NaC6 0:A26493.95
NaN1 0:A26492.84
NaN6 0:A26494.29
NaO 0:Hoh97522.96

interactive model:


Sodium binding site 5 out of 75 in 1vqm


Sodium binding site 5 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 5 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G39, 0: C40, 0: G41, 0: A442, 0: C443, 0: Hoh6415,

conact list:


AtomAtomDistance (A)
NaN2 0:G393.90
NaC2 0:G394.56
NaN1 0:G394.80
NaN3 0:C404.85
NaC3' 0:C404.68
NaC2 0:C403.64
NaN1 0:C403.95
NaC1' 0:C403.27
NaO2 0:C402.61
NaO4' 0:C404.48
NaC2' 0:C403.17
NaO2' 0:C402.65
NaN9 0:G414.52
NaC8 0:G414.90
NaC1' 0:G414.21
NaO4' 0:G413.39
NaC5' 0:G414.71
NaC4' 0:G414.50
NaC2 0:A4423.85
NaC6 0:A4424.20
NaN1 0:A4423.32
NaN6 0:A4424.37
NaN3 0:C4434.30
NaC2 0:C4433.68
NaN1 0:C4434.59
NaC1' 0:C4434.67
NaO2 0:C4432.73
NaO 0:Hoh64154.07

interactive model:


Sodium binding site 6 out of 75 in 1vqm


Sodium binding site 6 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 6 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: C1394, 0: U1432, 0: G1433, 0: U1724, 0: C1725, 0: Sr9473, 0: Hoh4015, 0: Hoh5404, 0: Hoh6019, 0: Hoh7640,

conact list:


AtomAtomDistance (A)
NaN3 0:C13944.29
NaC2 0:C13943.50
NaN1 0:C13944.40
NaC1' 0:C13944.36
NaO2 0:C13942.32
NaC2' 0:C13944.10
NaO2' 0:C13944.01
NaN3 0:U14324.19
NaC5 0:U14324.77
NaC4 0:U14323.59
NaO4 0:U14322.42
NaC6 0:G14333.91
NaN1 0:G14334.33
NaC5 0:G14334.79
NaO6 0:G14333.33
NaN3 0:U17244.17
NaC2 0:U17243.34
NaN1 0:U17244.29
NaC1' 0:U17244.26
NaO2 0:U17242.15
NaC2' 0:U17244.43
NaO2' 0:U17244.30
NaO2' 0:C17254.95
NaSR 0:Sr94732.99
NaO 0:Hoh40152.71
NaO 0:Hoh54044.25
NaO 0:Hoh60194.79
NaO 0:Hoh76404.27

interactive model:


Sodium binding site 7 out of 75 in 1vqm


Sodium binding site 7 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 7 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: U2554, 0: C2556, 0: A2577, 0: G2578, 0: G2579, 0: G2580, 0: Hoh5081, 0: Hoh6818, 0: Hoh8270,

conact list:


AtomAtomDistance (A)
NaN3 0:U25544.80
NaN4 0:C25564.57
NaN9 0:A25774.25
NaN3 0:A25773.00
NaC2 0:A25773.73
NaN1 0:A25774.96
NaC1' 0:A25773.83
NaO4' 0:A25773.12
NaC4 0:A25773.91
NaC5' 0:A25774.93
NaC4' 0:A25774.04
NaN9 0:G25784.89
NaC8 0:G25784.07
NaC6 0:G25783.53
NaN1 0:G25784.70
NaC5 0:G25783.49
NaN7 0:G25783.09
NaC4 0:G25784.61
NaO6 0:G25783.19
NaC8 0:G25794.23
NaC6 0:G25793.34
NaN1 0:G25794.66
NaC5 0:G25793.48
NaN7 0:G25793.03
NaC4 0:G25794.81
NaO6 0:G25792.67
NaO6 0:G25804.90
NaO 0:Hoh50813.16
NaO 0:Hoh68184.16
NaO 0:Hoh82703.62

interactive model:


Sodium binding site 8 out of 75 in 1vqm


Sodium binding site 8 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 8 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: C2493, 0: U2523, 0: G2524, 0: G2525, 0: Hoh4178, 0: Hoh4220, 0: Hoh5223, 0: Hoh6888, 0: Hoh9808,

conact list:


AtomAtomDistance (A)
NaO2' 0:C24934.61
NaN3 0:U25234.33
NaC2 0:U25234.83
NaC6 0:U25234.12
NaN1 0:U25234.71
NaC5 0:U25233.60
NaC4 0:U25233.74
NaOP2 0:U25234.65
NaO4 0:U25233.96
NaN9 0:G25244.82
NaC8 0:G25243.56
NaC6 0:G25244.21
NaC5 0:G25243.76
NaN7 0:G25242.69
NaC4 0:G25244.92
NaOP2 0:G25244.40
NaO6 0:G25243.90
NaC6 0:G25253.75
NaN1 0:G25254.57
NaC5 0:G25254.53
NaN7 0:G25254.72
NaO6 0:G25252.89
NaO 0:Hoh41782.62
NaO 0:Hoh42204.30
NaO 0:Hoh52232.74
NaO 0:Hoh68884.14
NaO 0:Hoh98083.28

interactive model:


Sodium binding site 9 out of 75 in 1vqm


Sodium binding site 9 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 9 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: U2389, 0: U2390, 0: A2398, 0: G2399, 0: G2400, 0: Hoh3563, 0: Hoh3993, 0: Hoh4429, 0: Hoh5632, 0: Hoh5680, 0: Hoh6595, 0: Hoh6680, 0: Hoh6810,

conact list:


AtomAtomDistance (A)
NaN3 0:U23894.81
NaO4 0:U23894.54
NaO2 0:U23904.83
NaN7 0:A23984.71
NaOP2 0:A23983.90
NaN9 0:G23994.90
NaC8 0:G23993.90
NaC6 0:G23993.24
NaN1 0:G23994.61
NaC5 0:G23993.26
NaN7 0:G23992.70
NaC4 0:G23994.59
NaO6 0:G23992.65
NaC6 0:G24004.64
NaC5 0:G24004.68
NaN7 0:G24004.19
NaO6 0:G24004.09
NaO 0:Hoh35632.49
NaO 0:Hoh39934.48
NaO 0:Hoh44292.37
NaO 0:Hoh56322.46
NaO 0:Hoh56802.83
NaO 0:Hoh65953.76
NaO 0:Hoh66804.75
NaO 0:Hoh68104.46

interactive model:


Sodium binding site 10 out of 75 in 1vqm


Sodium binding site 10 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 10 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: U2539, 0: U2541, 0: U2607, 0: C2608, 0: U2610, B: Trp242, 0: Hoh3111, 0: Hoh3737, 0: Hoh5259, 0: Hoh8324, 0: Hoh9715, 0: Hoh9780, 0: Hoh9957,

conact list:


AtomAtomDistance (A)
NaO2 0:U25394.79
NaOP1 0:U25412.85
NaP 0:U25413.89
NaOP2 0:U25414.06
NaO5' 0:U25414.61
NaN3 0:U26074.61
NaC3' 0:U26074.96
NaC2 0:U26073.66
NaN1 0:U26074.26
NaC1' 0:U26074.12
NaO2 0:U26072.77
NaO3' 0:U26074.57
NaC2' 0:U26073.98
NaO2' 0:U26072.79
NaP 0:C26084.90
NaOP2 0:C26084.04
NaOP1 0:U26104.33
NaCE3 B:Trp2424.37
NaCZ3 B:Trp2423.45
NaCH2 B:Trp2423.92
NaO 0:Hoh31114.60
NaO 0:Hoh37372.42
NaO 0:Hoh52593.98
NaO 0:Hoh83244.72
NaO 0:Hoh97154.87
NaO 0:Hoh97804.32
NaO 0:Hoh99572.78

interactive model:


Sodium binding site 11 out of 75 in 1vqm


Sodium binding site 11 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 11 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G164, 0: A165, 0: A166, 0: A167, 0: C168, 0: G898, 0: G2110, 0: Mg8079, 0: Hoh3155, 0: Hoh3309, 0: Hoh4211, 0: Hoh4229, 0: Hoh5866, 0: Hoh6841, 0: Hoh9870,

conact list:


AtomAtomDistance (A)
NaOP1 0:G1644.60
NaP 0:G1644.79
NaOP2 0:G1644.33
NaO5' 0:G1644.93
NaOP1 0:A1654.33
NaP 0:A1653.90
NaOP2 0:A1652.68
NaO5' 0:A1654.54
NaN9 0:A1664.92
NaC3' 0:A1663.71
NaC1' 0:A1663.87
NaO3' 0:A1662.64
NaO4' 0:A1664.71
NaC2' 0:A1663.67
NaC4' 0:A1664.63
NaO2' 0:A1662.91
NaOP1 0:A1672.85
NaP 0:A1673.32
NaOP2 0:A1674.69
NaC5' 0:A1673.58
NaC4' 0:A1674.96
NaO5' 0:A1673.89
NaOP2 0:C1684.92
NaO6 0:G8984.99
NaOP1 0:G21104.84
NaMG 0:Mg80793.80
NaO 0:Hoh31554.05
NaO 0:Hoh33092.96
NaO 0:Hoh42113.30
NaO 0:Hoh42293.73
NaO 0:Hoh58664.75
NaO 0:Hoh68414.88
NaO 0:Hoh98703.68

interactive model:


Sodium binding site 12 out of 75 in 1vqm


Sodium binding site 12 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 12 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: U163, 0: G164, 0: A766, 0: C896, 0: A897, 0: Hoh3309, 0: Hoh3318, 0: Hoh6841, 0: Hoh8226, 0: Hoh9655,

conact list:


AtomAtomDistance (A)
NaOP1 0:U1634.67
NaOP1 0:G1644.79
NaN6 0:A7664.51
NaC3' 0:C8964.79
NaC2 0:C8964.03
NaN1 0:C8964.42
NaC1' 0:C8963.78
NaO2 0:C8962.99
NaC2' 0:C8963.32
NaO2' 0:C8962.73
NaN9 0:A8974.43
NaC8 0:A8974.52
NaC1' 0:A8973.95
NaO4' 0:A8972.96
NaC5' 0:A8974.10
NaC4' 0:A8973.93
NaO5' 0:A8974.68
NaO 0:Hoh33093.81
NaO 0:Hoh33183.33
NaO 0:Hoh68412.35
NaO 0:Hoh82263.09
NaO 0:Hoh96553.32

interactive model:


Sodium binding site 13 out of 75 in 1vqm


Sodium binding site 13 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 13 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G1416, 0: G1417, 0: C1686, 2: His41, 2: Trp42, 2: Arg43, 2: Asn45, 2: Asp46, 0: Hoh3284, 0: Hoh5715, 0: Hoh9902, 2: Hoh5293,

conact list:


AtomAtomDistance (A)
NaC3' 0:G14163.93
NaO3' 0:G14162.71
NaC2' 0:G14164.29
NaC4' 0:G14164.38
NaO2' 0:G14163.54
NaOP1 0:G14172.63
NaP 0:G14173.29
NaOP2 0:G14174.53
NaC5' 0:G14173.92
NaO5' 0:G14174.12
NaOP1 0:C16864.49
NaO 2:His414.87
NaC 2:Trp423.60
NaCA 2:Trp424.56
NaO 2:Trp422.38
NaO 2:Arg434.05
NaN 2:Arg434.46
NaC 2:Arg434.50
NaCA 2:Arg434.44
NaO 2:Asn452.43
NaN 2:Asn454.79
NaC 2:Asn453.58
NaCA 2:Asn454.75
NaN 2:Asp464.25
NaCB 2:Asp464.80
NaCA 2:Asp464.06
NaO 0:Hoh32843.96
NaO 0:Hoh57152.82
NaO 0:Hoh99022.41
NaO 2:Hoh52933.65

interactive model:


Sodium binding site 14 out of 75 in 1vqm


Sodium binding site 14 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 14 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 14 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G2543, 0: G2544, 0: U2545, 0: Na9120, 0: Hoh3022, 0: Hoh3358, 0: Hoh4068, 0: Hoh4524, 0: Hoh5819, 0: Hoh7971, 0: Hoh8326, 0: Hoh9683, 0: Hoh9837, 0: Hoh9865,

conact list:


AtomAtomDistance (A)
NaC8 0:G25434.19
NaC6 0:G25434.29
NaC5 0:G25434.07
NaN7 0:G25433.26
NaOP2 0:G25434.74
NaO6 0:G25433.85
NaC8 0:G25444.47
NaC6 0:G25443.91
NaC5 0:G25443.94
NaN7 0:G25443.38
NaO6 0:G25443.30
NaO4 0:U25454.74
NaNA 0:Na91202.98
NaO 0:Hoh30223.91
NaO 0:Hoh33584.16
NaO 0:Hoh40683.40
NaO 0:Hoh45242.30
NaO 0:Hoh58194.95
NaO 0:Hoh79713.00
NaO 0:Hoh83264.13
NaO 0:Hoh96834.32
NaO 0:Hoh98373.09
NaO 0:Hoh98654.31

interactive model:


Sodium binding site 15 out of 75 in 1vqm


Sodium binding site 15 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 15 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 15 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: C2542, 0: G2543, 0: G2544, 0: G2611, 0: C2614, 0: U2615, 0: Na9118, 0: Hoh3358, 0: Hoh7971, 0: Hoh9683, 0: Hoh9713, 0: Hoh9865,

conact list:


AtomAtomDistance (A)
NaC5 0:C25424.49
NaC4 0:C25424.59
NaN4 0:C25424.02
NaC6 0:G25433.87
NaC5 0:G25434.41
NaN7 0:G25434.18
NaO6 0:G25432.82
NaC6 0:G25444.26
NaN1 0:G25444.95
NaC5 0:G25444.88
NaO6 0:G25443.68
NaN9 0:G26114.83
NaC8 0:G26114.20
NaC6 0:G26114.93
NaC5 0:G26114.41
NaN7 0:G26113.91
NaC4 0:G26114.96
NaN4 0:C26144.12
NaN3 0:U26154.04
NaC4 0:U26153.92
NaO4 0:U26152.98
NaNA 0:Na91182.98
NaO 0:Hoh33582.85
NaO 0:Hoh79714.17
NaO 0:Hoh96833.11
NaO 0:Hoh97133.42
NaO 0:Hoh98654.64

interactive model:


Sodium binding site 16 out of 75 in 1vqm


Sodium binding site 16 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 16 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 16 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G885, 0: G2111, 0: A2112, 0: G2113, 0: C2475, 0: C2476, 0: Hoh3321, 0: Hoh3341, 0: Hoh4255, 0: Hoh5056,

conact list:


AtomAtomDistance (A)
NaC2' 0:G8854.82
NaO2' 0:G8853.43
NaN2 0:G21113.86
NaC2 0:G21114.67
NaN1 0:G21114.89
NaN9 0:A21124.18
NaN3 0:A21122.57
NaC2 0:A21123.24
NaN1 0:A21124.57
NaC5 0:A21124.96
NaC1' 0:A21123.86
NaC4 0:A21123.69
NaC2' 0:A21123.78
NaO2' 0:A21123.66
NaN9 0:G21133.81
NaN3 0:G21134.78
NaC8 0:G21134.11
NaC5 0:G21134.83
NaC1' 0:G21133.81
NaN7 0:G21134.74
NaO4' 0:G21133.65
NaC4 0:G21134.31
NaN3 0:C24753.54
NaC2 0:C24754.80
NaC5 0:C24754.98
NaC4 0:C24753.61
NaN4 0:C24752.76
NaN3 0:C24764.34
NaC2 0:C24763.85
NaN1 0:C24764.69
NaC1' 0:C24764.89
NaO2 0:C24763.16
NaO 0:Hoh33214.87
NaO 0:Hoh33414.48
NaO 0:Hoh42553.64
NaO 0:Hoh50562.51

interactive model:


Sodium binding site 17 out of 75 in 1vqm


Sodium binding site 17 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 17 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 17 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: A45, 0: C130, 0: A132, 0: A145, 0: U146, 0: G147, 0: Hoh3118, 0: Hoh4719, 0: Hoh7646, 0: Hoh7828,

conact list:


AtomAtomDistance (A)
NaC2' 0:A454.87
NaO2' 0:A453.69
NaN3 0:C1304.73
NaC2 0:C1303.94
NaN1 0:C1304.59
NaC1' 0:C1304.47
NaO2 0:C1303.08
NaO2' 0:C1304.99
NaN6 0:A1324.53
NaC5 0:A1454.87
NaN6 0:A1454.55
NaN7 0:A1454.26
NaN3 0:U1464.76
NaC5 0:U1463.92
NaC4 0:U1463.52
NaO4 0:U1462.55
NaC6 0:G1474.32
NaO6 0:G1473.18
NaO 0:Hoh31182.74
NaO 0:Hoh47192.90
NaO 0:Hoh76462.83
NaO 0:Hoh78283.89

interactive model:


Sodium binding site 18 out of 75 in 1vqm


Sodium binding site 18 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 18 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 18 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: A776, 0: U777, 0: C778, 0: U779, 0: A780, 0: U864, 0: G865, 0: U866, 0: Mg8031, 0: Sr9441, 0: Hoh3247, 0: Hoh3578, 0: Hoh3881, 0: Hoh4274, 0: Hoh8202,

conact list:


AtomAtomDistance (A)
NaN9 0:A7764.38
NaC3' 0:A7762.97
NaC1' 0:A7763.23
NaO3' 0:A7762.12
NaO4' 0:A7764.06
NaC2' 0:A7762.90
NaC4' 0:A7763.99
NaO2' 0:A7762.32
NaOP1 0:U7773.47
NaP 0:U7772.97
NaOP2 0:U7773.03
NaO5' 0:U7774.43
NaOP2 0:C7784.82
NaN3 0:U7794.71
NaC5 0:U7794.56
NaC4 0:U7793.74
NaO4 0:U7792.57
NaN6 0:A7803.90
NaO4 0:U8644.87
NaO6 0:G8654.26
NaO4 0:U8664.25
NaMG 0:Mg80314.76
NaSR 0:Sr94413.47
NaO 0:Hoh32472.18
NaO 0:Hoh35783.86
NaO 0:Hoh38812.80
NaO 0:Hoh42744.44
NaO 0:Hoh82023.02

interactive model:


Sodium binding site 19 out of 75 in 1vqm


Sodium binding site 19 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 19 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 19 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: C1946, 0: G1971, 0: G2009, 0: A2010, 0: U2012, 0: Hoh3203, 0: Hoh5203, 0: Hoh8122,

conact list:


AtomAtomDistance (A)
NaC5 0:C19464.76
NaN4 0:C19464.89
NaC6 0:G19713.97
NaN1 0:G19714.12
NaO6 0:G19713.02
NaOP1 0:G20093.96
NaC3' 0:G20094.88
NaP 0:G20093.81
NaO3' 0:G20094.76
NaOP2 0:G20093.21
NaO5' 0:G20093.91
NaOP1 0:A20104.36
NaP 0:A20104.06
NaOP2 0:A20102.91
NaN3 0:U20124.58
NaC5 0:U20123.97
NaC4 0:U20123.41
NaO4 0:U20122.34
NaO 0:Hoh32033.03
NaO 0:Hoh52033.46
NaO 0:Hoh81223.73

interactive model:


Sodium binding site 20 out of 75 in 1vqm


Sodium binding site 20 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 20 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 20 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G820, 0: U821, 0: C822, 0: C853, 0: G854, 0: U1831, 0: G1832, 0: Sr9457, 0: Hoh3345, 0: Hoh3810, 0: Hoh4218, 0: Hoh6677, 0: Hoh9662, 0: Hoh9932,

conact list:


AtomAtomDistance (A)
NaO3' 0:G8204.24
NaOP1 0:U8213.44
NaP 0:U8213.57
NaO3' 0:U8214.90
NaOP2 0:U8212.91
NaOP1 0:C8223.58
NaP 0:C8224.29
NaOP2 0:C8224.13
NaC3' 0:C8534.81
NaO3' 0:C8533.50
NaOP1 0:G8542.67
NaP 0:G8543.62
NaOP2 0:G8544.31
NaO5' 0:G8544.97
NaC3' 0:U18313.83
NaC1' 0:U18314.87
NaO3' 0:U18313.13
NaO4' 0:U18314.79
NaC5' 0:U18314.76
NaC2' 0:U18313.96
NaC4' 0:U18313.84
NaO2' 0:U18313.00
NaOP1 0:G18324.15
NaP 0:G18324.33
NaSR 0:Sr94574.05
NaO 0:Hoh33452.79
NaO 0:Hoh38102.56
NaO 0:Hoh42184.62
NaO 0:Hoh66774.40
NaO 0:Hoh96623.68
NaO 0:Hoh99324.47

interactive model:


Sodium binding site 21 out of 75 in 1vqm


Sodium binding site 21 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 21 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 21 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G56, 0: A59, 0: A60, 0: G61, 0: C62, 0: Hoh5774, 0: Hoh6996,

conact list:


AtomAtomDistance (A)
NaC6 0:G563.67
NaN1 0:G564.73
NaC5 0:G564.38
NaN7 0:G564.39
NaO6 0:G562.61
NaN9 0:A593.98
NaN3 0:A592.71
NaC2 0:A593.26
NaC6 0:A594.87
NaN1 0:A594.31
NaC5 0:A594.52
NaC1' 0:A593.91
NaO3' 0:A594.94
NaC4 0:A593.48
NaC2' 0:A594.52
NaO2' 0:A593.85
NaC8 0:A604.48
NaC6 0:A603.94
NaN1 0:A604.85
NaC5 0:A603.88
NaN6 0:A603.72
NaN7 0:A603.69
NaC4 0:A604.78
NaC8 0:G614.09
NaC6 0:G613.67
NaC5 0:G613.63
NaN7 0:G612.94
NaC4 0:G614.94
NaO6 0:G613.07
NaC4 0:C624.75
NaN4 0:C623.93
NaO 0:Hoh57742.76
NaO 0:Hoh69963.02

interactive model:


Sodium binding site 22 out of 75 in 1vqm


Sodium binding site 22 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 22 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 22 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: C65, 0: G66, 0: A106, 0: U107, 0: U108, 0: Hoh3704, 0: Hoh7095,

conact list:


AtomAtomDistance (A)
NaO3' 0:C654.64
NaOP1 0:G663.17
NaP 0:G663.65
NaOP2 0:G663.20
NaO5' 0:G664.93
NaN6 0:A1064.81
NaN3 0:U1074.13
NaC4 0:U1074.01
NaO4 0:U1073.10
NaN3 0:U1084.22
NaC2 0:U1083.85
NaN1 0:U1084.95
NaO2 0:U1082.99
NaO 0:Hoh37044.46
NaO 0:Hoh70952.90

interactive model:


Sodium binding site 23 out of 75 in 1vqm


Sodium binding site 23 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 23 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 23 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G140, 0: C141, 0: G142, 0: C143, 0: Hoh4436, 0: Hoh4630, 0: Hoh9861,

conact list:


AtomAtomDistance (A)
NaN3 0:G1403.98
NaN2 0:G1403.43
NaC2 0:G1403.80
NaN1 0:G1404.57
NaC4 0:G1404.87
NaC2' 0:G1404.99
NaN3 0:C1414.56
NaC3' 0:C1414.73
NaC2 0:C1413.62
NaN1 0:C1414.08
NaC1' 0:C1413.73
NaO2 0:C1412.80
NaP 0:C1414.78
NaO3' 0:C1414.93
NaO4' 0:C1412.64
NaOP2 0:C1413.67
NaC5' 0:C1413.96
NaC2' 0:C1414.96
NaC4' 0:C1413.44
NaO5' 0:C1414.61
NaC8 0:G1424.17
NaC6 0:G1423.62
NaN1 0:G1424.99
NaC5 0:G1423.63
NaN7 0:G1422.99
NaC4 0:G1424.96
NaO6 0:G1422.97
NaN4 0:C1434.66
NaO 0:Hoh44364.23
NaO 0:Hoh46304.90
NaO 0:Hoh98612.89

interactive model:


Sodium binding site 24 out of 75 in 1vqm


Sodium binding site 24 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 24 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 24 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: U170, 0: C171, 0: C218, 0: G219, 0: G221, 0: A222, 0: Hoh3175, 0: Hoh5502, 0: Hoh9647, 0: Hoh9925, 3: Hoh9441,

conact list:


AtomAtomDistance (A)
NaN3 0:U1704.18
NaC2 0:U1703.72
NaN1 0:U1704.80
NaO2 0:U1702.81
NaC2' 0:U1704.58
NaO2' 0:U1704.72
NaC3' 0:C1714.81
NaC1' 0:C1713.81
NaO4' 0:C1713.23
NaC5' 0:C1714.52
NaC2' 0:C1714.47
NaC4' 0:C1713.69
NaO2' 0:C1714.00
NaC3' 0:C2183.74
NaC1' 0:C2184.37
NaO3' 0:C2183.32
NaO4' 0:C2184.24
NaC5' 0:C2184.63
NaC2' 0:C2183.71
NaC4' 0:C2183.55
NaO2' 0:C2182.71
NaOP1 0:G2194.87
NaP 0:G2194.60
NaC5' 0:G2194.22
NaO5' 0:G2194.75
NaC6 0:G2214.16
NaC5 0:G2214.95
NaN7 0:G2214.93
NaO6 0:G2212.97
NaC6 0:A2224.99
NaN1 0:A2224.93
NaN6 0:A2224.37
NaO 0:Hoh31752.88
NaO 0:Hoh55024.62
NaO 0:Hoh96474.94
NaO 0:Hoh99252.64
NaO 3:Hoh94414.98

interactive model:


Sodium binding site 25 out of 75 in 1vqm


Sodium binding site 25 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 25 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 25 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G386, 0: G387, 0: G388, 0: C401, 0: U402, 0: C403, 0: Hoh5947, 0: Hoh6760, 0: Hoh7569, 0: Hoh7707,

conact list:


AtomAtomDistance (A)
NaC6 0:G3863.97
NaN1 0:G3864.77
NaC5 0:G3864.74
NaN7 0:G3864.95
NaO6 0:G3863.12
NaC6 0:G3873.58
NaN1 0:G3874.77
NaC5 0:G3874.17
NaN7 0:G3874.02
NaO6 0:G3872.50
NaC6 0:G3883.80
NaN1 0:G3884.66
NaC5 0:G3884.45
NaN7 0:G3884.59
NaO6 0:G3883.04
NaC4 0:C4014.57
NaN4 0:C4013.57
NaN3 0:U4023.62
NaC2 0:U4024.86
NaC4 0:U4023.63
NaO4 0:U4022.84
NaC4 0:C4034.82
NaN4 0:C4034.03
NaO 0:Hoh59473.89
NaO 0:Hoh67604.09
NaO 0:Hoh75692.94
NaO 0:Hoh77074.96

interactive model:


Sodium binding site 26 out of 75 in 1vqm


Sodium binding site 26 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 26 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 26 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: C1894, 0: A1895, 0: G1896, 0: U1897, 0: A1942, 0: Sr9490, 0: Hoh5808, 0: Hoh6812, 0: Hoh8442,

conact list:


AtomAtomDistance (A)
NaN3 0:C18944.51
NaC3' 0:C18944.87
NaC2 0:C18943.55
NaN1 0:C18944.01
NaC1' 0:C18943.65
NaO2 0:C18942.70
NaO3' 0:C18944.80
NaO4' 0:C18942.98
NaC5' 0:C18944.80
NaC2' 0:C18945.00
NaC4' 0:C18943.87
NaN9 0:A18954.82
NaC8 0:A18953.96
NaC6 0:A18954.26
NaC5 0:A18953.88
NaN6 0:A18954.10
NaN7 0:A18953.29
NaC4 0:A18954.78
NaC8 0:G18964.01
NaC6 0:G18963.48
NaN1 0:G18964.84
NaC5 0:G18963.47
NaN7 0:G18962.83
NaC4 0:G18964.79
NaO6 0:G18962.87
NaN3 0:U18974.98
NaC5 0:U18974.67
NaC4 0:U18974.11
NaO4 0:U18973.34
NaN6 0:A19424.11
NaSR 0:Sr94904.11
NaO 0:Hoh58082.45
NaO 0:Hoh68124.09
NaO 0:Hoh84422.42

interactive model:


Sodium binding site 27 out of 75 in 1vqm


Sodium binding site 27 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 27 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 27 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: C621, 0: G622, 0: U623, 0: 1ma628, 0: A629, 0: A630, 0: A632, 0: C633, Y: Leu150, 0: Hoh3487, 0: Hoh5983,

conact list:


AtomAtomDistance (A)
NaN3 0:C6214.78
NaC6 0:C6214.67
NaC5 0:C6213.66
NaC4 0:C6213.76
NaN4 0:C6213.40
NaC8 0:G6224.64
NaC6 0:G6223.57
NaN1 0:G6224.89
NaC5 0:G6223.83
NaN7 0:G6223.41
NaO6 0:G6222.74
NaN3 0:U6234.63
NaC5 0:U6234.30
NaC4 0:U6233.70
NaO4 0:U6232.86
NaO3' 0:1ma6284.85
NaC2' 0:1ma6284.47
NaO2' 0:1ma6283.06
NaO3' 0:A6294.59
NaOP1 0:A6303.25
NaP 0:A6303.77
NaOP2 0:A6303.39
NaC6 0:A6325.00
NaN6 0:A6323.79
NaN4 0:C6334.82
NaCD1 Y:Leu1504.49
NaO 0:Hoh34872.75
NaO 0:Hoh59834.49

interactive model:


Sodium binding site 28 out of 75 in 1vqm


Sodium binding site 28 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 28 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 28 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G1704, 0: C1705, 0: G1706, 0: G1707, 0: A1710, 0: Hoh3515, 0: Hoh3538, 0: Hoh4662, 0: Hoh5148, 0: Hoh5894, 0: Hoh7826, 0: Hoh8229,

conact list:


AtomAtomDistance (A)
NaOP2 0:G17044.57
NaOP2 0:C17054.34
NaC6 0:G17063.61
NaN1 0:G17064.79
NaC5 0:G17064.16
NaN7 0:G17063.99
NaO6 0:G17062.59
NaC6 0:G17073.62
NaN1 0:G17073.93
NaC5 0:G17074.92
NaO6 0:G17072.62
NaOP1 0:A17104.90
NaOP2 0:A17104.14
NaO 0:Hoh35153.86
NaO 0:Hoh35382.62
NaO 0:Hoh46623.65
NaO 0:Hoh51484.19
NaO 0:Hoh58942.46
NaO 0:Hoh78262.75
NaO 0:Hoh82292.46

interactive model:


Sodium binding site 29 out of 75 in 1vqm


Sodium binding site 29 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 29 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 29 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G2540, 0: G2611, 0: C2614, 0: U2615, 0: G2616, 0: U2645, 0: Mg8088, 0: Hoh3636, 0: Hoh4876, 0: Hoh9689, 0: Hoh9831, 0: Hoh9922, 0: Hoh9989,

conact list:


AtomAtomDistance (A)
NaC6 0:G25403.69
NaN1 0:G25403.96
NaO6 0:G25402.68
NaN9 0:G26114.22
NaC8 0:G26114.17
NaC1' 0:G26113.82
NaC2' 0:G26113.88
NaO2' 0:G26113.14
NaOP1 0:C26145.00
NaOP2 0:C26144.31
NaOP2 0:U26154.83
NaC6 0:G26164.22
NaN1 0:G26164.26
NaO6 0:G26163.36
NaC2 0:U26454.30
NaN1 0:U26454.45
NaC1' 0:U26454.46
NaO2 0:U26454.07
NaC2' 0:U26454.92
NaO2' 0:U26454.12
NaMG 0:Mg80882.35
NaO 0:Hoh36362.80
NaO 0:Hoh48763.10
NaO 0:Hoh96894.82
NaO 0:Hoh98314.63
NaO 0:Hoh99222.79
NaO 0:Hoh99894.27

interactive model:


Sodium binding site 30 out of 75 in 1vqm


Sodium binding site 30 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 30 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 30 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: U1740, 0: U1741, 0: G2033, 0: A2038, 0: A2039, 0: Hoh3645, 0: Hoh4956, 0: Hoh5915, 0: Hoh6805, 0: Hoh7328,

conact list:


AtomAtomDistance (A)
NaC5 0:U17404.70
NaC4 0:U17404.10
NaO4 0:U17403.05
NaN3 0:U17414.79
NaC5 0:U17414.21
NaC4 0:U17413.69
NaO4 0:U17412.76
NaC2' 0:G20334.10
NaO2' 0:G20333.14
NaN6 0:A20384.31
NaN6 0:A20394.27
NaO 0:Hoh36453.08
NaO 0:Hoh49564.65
NaO 0:Hoh59153.84
NaO 0:Hoh68053.02
NaO 0:Hoh73282.96

interactive model:


Sodium binding site 31 out of 75 in 1vqm


Sodium binding site 31 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 31 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 31 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: C663, 0: G681, 0: A682, 0: G683, 0: Sr9465, 0: Hoh4610, 0: Hoh8435,

conact list:


AtomAtomDistance (A)
NaN4 0:C6634.45
NaN9 0:G6814.80
NaC3' 0:G6814.00
NaC1' 0:G6813.73
NaO3' 0:G6813.06
NaO4' 0:G6814.47
NaC2' 0:G6813.75
NaC4' 0:G6814.85
NaO2' 0:G6812.98
NaP 0:A6824.04
NaOP2 0:A6823.68
NaO5' 0:A6824.78
NaC8 0:G6834.33
NaC6 0:G6833.52
NaN1 0:G6834.86
NaC5 0:G6833.65
NaN7 0:G6833.13
NaC4 0:G6835.00
NaO6 0:G6832.80
NaSR 0:Sr94654.64
NaO 0:Hoh46102.57
NaO 0:Hoh84352.36

interactive model:


Sodium binding site 32 out of 75 in 1vqm


Sodium binding site 32 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 32 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 32 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: U308, 0: G334, 0: U335, 0: A339, 0: C342, T: Ser94, T: Asn95, T: Hoh1124,

conact list:


AtomAtomDistance (A)
NaN3 0:U3084.96
NaC5 0:U3084.68
NaC4 0:U3083.96
NaO4 0:U3082.84
NaN2 0:G3344.00
NaC2 0:G3344.92
NaC2 0:U3354.07
NaN1 0:U3354.61
NaC1' 0:U3354.04
NaO2 0:U3352.95
NaC2' 0:U3353.90
NaO2' 0:U3353.21
NaC6 0:A3394.77
NaN6 0:A3393.63
NaN3 0:C3424.76
NaC2 0:C3423.93
NaN1 0:C3424.69
NaC1' 0:C3424.50
NaO2 0:C3422.82
NaO2' 0:C3424.77
NaO T:Ser943.08
NaCB T:Ser943.51
NaOG T:Ser942.67
NaC T:Ser943.49
NaCA T:Ser944.15
NaN T:Asn954.02
NaCB T:Asn954.57
NaND2 T:Asn954.39
NaOD1 T:Asn952.71
NaCG T:Asn953.66
NaCA T:Asn954.25
NaO T:Hoh11242.42

interactive model:


Sodium binding site 33 out of 75 in 1vqm


Sodium binding site 33 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 33 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 33 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: A914, 0: C915, 0: C1043, 0: C1044, 0: G1045, 0: Hoh6143, 0: Hoh9648, 0: Hoh9844,

conact list:


AtomAtomDistance (A)
NaC3' 0:A9143.65
NaC1' 0:A9144.93
NaO3' 0:A9142.62
NaC2' 0:A9143.62
NaC4' 0:A9144.39
NaO2' 0:A9142.76
NaOP1 0:C9154.60
NaP 0:C9153.43
NaOP2 0:C9152.96
NaC5' 0:C9154.19
NaO5' 0:C9154.29
NaC3' 0:C10434.31
NaO3' 0:C10433.21
NaC5' 0:C10434.78
NaC2' 0:C10434.96
NaC4' 0:C10434.33
NaO2' 0:C10434.33
NaC3' 0:C10444.27
NaP 0:C10443.97
NaO3' 0:C10444.51
NaOP2 0:C10443.56
NaC5' 0:C10443.76
NaC4' 0:C10444.20
NaO5' 0:C10444.36
NaOP1 0:G10454.76
NaP 0:G10453.65
NaOP2 0:G10452.34
NaC5' 0:G10453.83
NaO5' 0:G10453.94
NaO 0:Hoh61433.07
NaO 0:Hoh96484.88
NaO 0:Hoh98444.57

interactive model:


Sodium binding site 34 out of 75 in 1vqm


Sodium binding site 34 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 34 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 34 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: U623, 0: U624, 0: C633, 0: U900, 0: G901, 0: G902, 0: Hoh3066, 0: Hoh5652, 0: Hoh7465, 0: Hoh8287,

conact list:


AtomAtomDistance (A)
NaC3' 0:U6235.00
NaC2 0:U6234.13
NaN1 0:U6234.56
NaC1' 0:U6233.90
NaO2 0:U6233.09
NaC2' 0:U6233.53
NaO2' 0:U6232.81
NaC6 0:U6244.98
NaN1 0:U6244.53
NaC1' 0:U6243.75
NaO4' 0:U6242.93
NaC5' 0:U6244.28
NaC2' 0:U6244.93
NaC4' 0:U6243.83
NaO5' 0:U6244.91
NaO2 0:C6334.34
NaO3' 0:U9004.68
NaOP1 0:G9012.47
NaP 0:G9013.76
NaO3' 0:G9014.79
NaOP2 0:G9014.84
NaC5' 0:G9013.66
NaC4' 0:G9014.82
NaO5' 0:G9013.99
NaOP1 0:G9024.86
NaOP2 0:G9024.80
NaO 0:Hoh30663.74
NaO 0:Hoh56524.07
NaO 0:Hoh74652.66
NaO 0:Hoh82874.07

interactive model:


Sodium binding site 35 out of 75 in 1vqm


Sodium binding site 35 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 35 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 35 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: C162, 0: U768, 0: C769, 0: G2111, 0: A2112, 0: Hoh3520, 0: Hoh5390, 0: Hoh8138, 0: Hoh8301,

conact list:


AtomAtomDistance (A)
NaC5' 0:C1624.36
NaC4' 0:C1624.85
NaC2 0:U7684.51
NaC1' 0:U7684.63
NaO2 0:U7683.34
NaC2' 0:U7683.82
NaO2' 0:U7683.07
NaC1' 0:C7694.25
NaO4' 0:C7693.26
NaC5' 0:C7694.18
NaC4' 0:C7693.84
NaC3' 0:G21114.53
NaO3' 0:G21113.35
NaC5' 0:G21114.64
NaC4' 0:G21114.65
NaOP1 0:A21122.92
NaP 0:A21123.73
NaOP2 0:A21124.62
NaO5' 0:A21124.97
NaO 0:Hoh35204.26
NaO 0:Hoh53902.74
NaO 0:Hoh81382.99
NaO 0:Hoh83014.35

interactive model:


Sodium binding site 36 out of 75 in 1vqm


Sodium binding site 36 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 36 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 36 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G1119, 0: C1243, 0: U1244, J: Ile46, J: Thr47, 0: Hoh3499, 0: Hoh4051, 0: Hoh5382,

conact list:


AtomAtomDistance (A)
NaC8 0:G11194.47
NaC6 0:G11193.40
NaN1 0:G11194.73
NaC5 0:G11193.64
NaN7 0:G11193.22
NaC4 0:G11195.00
NaO6 0:G11192.59
NaOP1 0:C12434.60
NaC3' 0:C12434.49
NaC6 0:C12433.69
NaN1 0:C12434.55
NaC5 0:C12433.69
NaP 0:C12433.91
NaC4 0:C12434.60
NaOP2 0:C12433.13
NaC5' 0:C12434.85
NaO5' 0:C12433.61
NaC6 0:U12444.54
NaC5 0:U12444.26
NaOP2 0:U12444.21
NaCD1 J:Ile464.47
NaC J:Ile464.92
NaCG1 J:Ile463.92
NaO J:Thr473.27
NaN J:Thr474.19
NaCB J:Thr474.56
NaC J:Thr474.11
NaCA J:Thr474.48
NaO 0:Hoh34993.51
NaO 0:Hoh40513.79
NaO 0:Hoh53822.31

interactive model:


Sodium binding site 37 out of 75 in 1vqm


Sodium binding site 37 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 37 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 37 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: C920, 0: U2277, 0: U2278, 0: G2279, 0: A2463, 0: A2467, 0: Hoh3080, 0: Hoh7044, 0: Hoh7365,

conact list:


AtomAtomDistance (A)
NaN3 0:C9203.02
NaC2 0:C9203.50
NaN1 0:C9204.88
NaO2 0:C9203.19
NaC4 0:C9204.11
NaN4 0:C9204.33
NaO3' 0:U22774.13
NaOP1 0:U22782.40
NaP 0:U22783.63
NaOP2 0:U22784.93
NaC5' 0:U22783.38
NaC4' 0:U22784.64
NaO5' 0:U22783.88
NaN9 0:G22794.79
NaC1' 0:G22794.01
NaO4' 0:G22793.21
NaC5' 0:G22794.59
NaC4' 0:G22794.14
NaC2 0:A24634.18
NaC6 0:A24634.70
NaN1 0:A24633.63
NaN6 0:A24634.81
NaC8 0:A24674.82
NaC6 0:A24674.28
NaC5 0:A24674.31
NaN6 0:A24673.61
NaN7 0:A24673.81
NaO 0:Hoh30802.96
NaO 0:Hoh70443.99
NaO 0:Hoh73654.01

interactive model:


Sodium binding site 38 out of 75 in 1vqm


Sodium binding site 38 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 38 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 38 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G941, 0: U942, 0: C1023, 0: G1024, 0: C1025, 0: Hoh3351, 0: Hoh4590, 0: Hoh6804, 0: Hoh6993, 0: Hoh7958,

conact list:


AtomAtomDistance (A)
NaC6 0:G9413.71
NaN1 0:G9414.68
NaC5 0:G9414.44
NaN7 0:G9414.52
NaO6 0:G9412.71
NaN3 0:U9423.85
NaC5 0:U9424.86
NaC4 0:U9423.54
NaO4 0:U9422.51
NaC5 0:C10235.00
NaN4 0:C10234.51
NaC6 0:G10244.11
NaC5 0:G10244.72
NaN7 0:G10244.53
NaO6 0:G10243.00
NaC4 0:C10254.84
NaN4 0:C10253.83
NaO 0:Hoh33513.95
NaO 0:Hoh45904.06
NaO 0:Hoh68042.34
NaO 0:Hoh69933.75
NaO 0:Hoh79583.51

interactive model:


Sodium binding site 39 out of 75 in 1vqm


Sodium binding site 39 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 39 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 39 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G2094, 0: U2610, 0: G2611, 0: A2612, B: Trp242, 0: Mg8009, 0: Hoh3111, 0: Hoh4335, 0: Hoh4464, 0: Hoh5259, 0: Hoh7899, 0: Hoh8321, 0: Hoh9929, 0: Hoh9959,

conact list:


AtomAtomDistance (A)
NaOP1 0:G20944.04
NaOP1 0:U26104.60
NaO3' 0:U26104.26
NaC5' 0:U26104.18
NaC4' 0:U26104.75
NaOP1 0:G26112.81
NaN2 0:G26114.02
NaP 0:G26113.82
NaOP2 0:G26114.15
NaOP1 0:A26124.52
NaCD2 B:Trp2424.44
NaCE3 B:Trp2423.57
NaCZ3 B:Trp2423.46
NaCH2 B:Trp2424.26
NaMG 0:Mg80092.64
NaO 0:Hoh31112.70
NaO 0:Hoh43353.04
NaO 0:Hoh44643.83
NaO 0:Hoh52594.07
NaO 0:Hoh78994.02
NaO 0:Hoh83212.99
NaO 0:Hoh99294.44
NaO 0:Hoh99592.72

interactive model:


Sodium binding site 40 out of 75 in 1vqm


Sodium binding site 40 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 40 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 40 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G898, 0: A922, 0: A923, 0: G924, 0: A2108, 0: U2109, 0: Hoh3794, 0: Hoh6208,

conact list:


AtomAtomDistance (A)
NaN9 0:G8984.63
NaN3 0:G8983.43
NaN2 0:G8984.00
NaC3' 0:G8984.92
NaC2 0:G8984.07
NaC1' 0:G8984.15
NaO3' 0:G8984.21
NaC4 0:G8984.33
NaC2' 0:G8984.35
NaO2' 0:G8983.49
NaOP1 0:A9222.88
NaP 0:A9224.14
NaOP2 0:A9224.63
NaC5' 0:A9224.85
NaO5' 0:A9224.75
NaC3' 0:A9234.66
NaC2' 0:A9233.82
NaO2' 0:A9233.02
NaN9 0:G9244.69
NaC8 0:G9244.88
NaC1' 0:G9244.13
NaO4' 0:G9243.28
NaC5' 0:G9244.56
NaC4' 0:G9244.30
NaO5' 0:G9244.87
NaO3' 0:A21084.93
NaC4' 0:A21084.92
NaOP1 0:U21094.28
NaP 0:U21093.92
NaOP2 0:U21092.66
NaO5' 0:U21094.89
NaO 0:Hoh37943.27
NaO 0:Hoh62083.13

interactive model:


Sodium binding site 41 out of 75 in 1vqm


Sodium binding site 41 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 41 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 41 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: A453, 0: U454, 0: C461, 0: C478, 0: G479, 0: Sr9423, 0: Hoh4120, 0: Hoh4301, 0: Hoh6201, 0: Hoh6495, 0: Hoh6780,

conact list:


AtomAtomDistance (A)
NaN3 0:A4534.57
NaC3' 0:A4533.87
NaC1' 0:A4534.05
NaO3' 0:A4532.85
NaO4' 0:A4534.97
NaC2' 0:A4533.75
NaC4' 0:A4534.96
NaO2' 0:A4532.88
NaOP1 0:U4544.26
NaP 0:U4543.30
NaOP2 0:U4542.60
NaC5' 0:U4544.68
NaO5' 0:U4544.51
NaN4 0:C4614.39
NaOP1 0:C4782.81
NaP 0:C4783.63
NaOP2 0:C4783.81
NaC5' 0:C4784.73
NaO5' 0:C4784.02
NaOP1 0:G4794.36
NaP 0:G4794.27
NaOP2 0:G4793.20
NaSR 0:Sr94233.65
NaO 0:Hoh41204.74
NaO 0:Hoh43014.33
NaO 0:Hoh62014.70
NaO 0:Hoh64952.31
NaO 0:Hoh67804.66

interactive model:


Sodium binding site 42 out of 75 in 1vqm


Sodium binding site 42 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 42 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 42 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: U837, 0: C838, 0: C839, B: Gln230, B: Gly231, B: Trp232, 0: Hoh3956, 0: Hoh5162, 0: Hoh5472, 0: Hoh5660, 0: Hoh7329, 0: Hoh9896, B: Hoh9646,

conact list:


AtomAtomDistance (A)
NaOP1 0:U8373.31
NaP 0:U8374.18
NaOP2 0:U8374.07
NaOP2 0:C8384.77
NaN4 0:C8394.98
NaO B:Gln2302.55
NaC B:Gln2303.65
NaCA B:Gln2304.94
NaN B:Gly2314.11
NaC B:Gly2314.76
NaCA B:Gly2313.62
NaCE3 B:Trp2324.55
NaCZ3 B:Trp2323.80
NaCH2 B:Trp2324.10
NaO 0:Hoh39564.57
NaO 0:Hoh51623.03
NaO 0:Hoh54723.32
NaO 0:Hoh56602.68
NaO 0:Hoh73292.96
NaO 0:Hoh98963.80
NaO B:Hoh96464.52

interactive model:


Sodium binding site 43 out of 75 in 1vqm


Sodium binding site 43 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 43 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 43 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: A167, 0: C168, 0: U2109, 0: G2110, 0: G2111, 0: U2276, 0: U2277, 0: Hoh5010, 0: Hoh5866, 0: Hoh9709,

conact list:


AtomAtomDistance (A)
NaC3' 0:A1674.31
NaO3' 0:A1673.19
NaC2' 0:A1674.53
NaC4' 0:A1674.72
NaO2' 0:A1673.68
NaOP1 0:C1683.22
NaP 0:C1683.90
NaC5' 0:C1684.49
NaO5' 0:C1684.72
NaO3' 0:U21094.86
NaOP1 0:G21104.52
NaP 0:G21103.79
NaO3' 0:G21104.39
NaOP2 0:G21102.40
NaC5' 0:G21104.80
NaO5' 0:G21104.46
NaOP1 0:G21113.06
NaP 0:G21113.95
NaOP2 0:G21114.14
NaO3' 0:U22764.88
NaOP1 0:U22772.88
NaP 0:U22774.07
NaOP2 0:U22774.37
NaO 0:Hoh50104.79
NaO 0:Hoh58663.14
NaO 0:Hoh97093.58

interactive model:


Sodium binding site 44 out of 75 in 1vqm


Sodium binding site 44 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 44 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 44 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: A635, 0: G636, 0: U1359, 0: C1360, C: Gly66, 0: Hoh3319, 0: Hoh4081, 0: Hoh6374, 0: Hoh7544, 0: Hoh9838, C: Hoh9111,

conact list:


AtomAtomDistance (A)
NaOP1 0:A6354.76
NaOP1 0:G6364.65
NaOP2 0:G6364.86
NaC3' 0:U13594.44
NaO3' 0:U13593.78
NaC2' 0:U13593.92
NaO2' 0:U13593.13
NaOP1 0:C13602.50
NaP 0:C13603.52
NaOP2 0:C13604.03
NaO5' 0:C13604.90
NaO C:Gly664.33
NaO 0:Hoh33193.21
NaO 0:Hoh40812.52
NaO 0:Hoh63743.25
NaO 0:Hoh75442.52
NaO 0:Hoh98383.84
NaO C:Hoh91114.26

interactive model:


Sodium binding site 45 out of 75 in 1vqm


Sodium binding site 45 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 45 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 45 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: A1367, 0: C2056, 0: U2057, 0: G2058, 0: Hoh3216, 0: Hoh3430, 0: Hoh6158, 0: Hoh6663, 0: Hoh7162,

conact list:


AtomAtomDistance (A)
NaN6 0:A13674.85
NaOP1 0:C20564.25
NaP 0:C20563.89
NaOP2 0:C20562.70
NaO5' 0:C20564.68
NaC5 0:U20574.03
NaC4 0:U20573.89
NaO4 0:U20573.10
NaO6 0:G20584.52
NaO 0:Hoh32164.36
NaO 0:Hoh34302.37
NaO 0:Hoh61583.79
NaO 0:Hoh66633.67
NaO 0:Hoh71624.35

interactive model:


Sodium binding site 46 out of 75 in 1vqm


Sodium binding site 46 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 46 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 46 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G390, 0: U391, 0: U392, 0: U398, 0: C399, M: Lys193, M: Ala194,

conact list:


AtomAtomDistance (A)
NaN2 0:G3904.02
NaC2 0:G3904.73
NaN1 0:G3904.90
NaN3 0:U3914.96
NaC3' 0:U3914.89
NaC2 0:U3913.77
NaN1 0:U3914.23
NaC1' 0:U3913.62
NaO2 0:U3912.70
NaO4' 0:U3914.85
NaC2' 0:U3913.40
NaO2' 0:U3912.82
NaC6 0:U3924.77
NaN1 0:U3924.34
NaC1' 0:U3923.76
NaO4' 0:U3923.11
NaC5' 0:U3924.71
NaC4' 0:U3924.21
NaN3 0:U3984.08
NaC2 0:U3984.03
NaO2 0:U3983.17
NaN3 0:C3994.20
NaC2 0:C3993.55
NaN1 0:C3994.20
NaC1' 0:C3994.27
NaO2 0:C3992.92
NaO M:Lys1933.42
NaC M:Lys1934.40
NaO M:Ala1944.06
NaN M:Ala1944.82
NaC M:Ala1943.75
NaCA M:Ala1944.33
NaOXT M:Ala1943.61

interactive model:


Sodium binding site 47 out of 75 in 1vqm


Sodium binding site 47 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 47 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 47 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G544, 0: G545, 0: C546, 0: G610, 0: U611, 0: U612, 0: Hoh3273, 0: Hoh3481, 0: Hoh3501, 0: Hoh4415, 0: Hoh4475, 0: Hoh4710, 0: Hoh4798,

conact list:


AtomAtomDistance (A)
NaC6 0:G5444.01
NaN1 0:G5445.00
NaC5 0:G5444.57
NaN7 0:G5444.55
NaO6 0:G5443.19
NaC6 0:G5453.64
NaN1 0:G5454.88
NaC5 0:G5454.14
NaN7 0:G5453.91
NaO6 0:G5452.62
NaC4 0:C5464.78
NaN4 0:C5463.83
NaC6 0:G6104.48
NaO6 0:G6103.45
NaN3 0:U6114.03
NaC4 0:U6114.15
NaO4 0:U6113.38
NaN3 0:U6124.41
NaC4 0:U6124.75
NaO4 0:U6124.34
NaO 0:Hoh32734.96
NaO 0:Hoh34813.45
NaO 0:Hoh35012.92
NaO 0:Hoh44152.70
NaO 0:Hoh44752.72
NaO 0:Hoh47104.16
NaO 0:Hoh47984.19

interactive model:


Sodium binding site 48 out of 75 in 1vqm


Sodium binding site 48 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 48 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 48 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G458, 0: G464, 0: C474, 0: G475, 0: A476, C: Arg55, C: Thr56, 0: Hoh3443, 0: Hoh5055, 0: Hoh5175, C: Hoh9142,

conact list:


AtomAtomDistance (A)
NaC8 0:G4584.97
NaO4' 0:G4584.83
NaC6 0:G4644.00
NaN1 0:G4644.35
NaO6 0:G4642.98
NaO3' 0:C4744.98
NaOP1 0:G4754.00
NaP 0:G4753.59
NaOP2 0:G4752.54
NaO5' 0:G4754.03
NaOP2 0:A4763.98
NaO C:Arg552.87
NaCB C:Arg554.43
NaC C:Arg554.01
NaCA C:Arg554.89
NaN C:Thr564.88
NaCA C:Thr564.88
NaO 0:Hoh34432.75
NaO 0:Hoh50552.77
NaO 0:Hoh51753.18
NaO C:Hoh91424.67

interactive model:


Sodium binding site 49 out of 75 in 1vqm


Sodium binding site 49 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 49 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 49 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: A796, 0: A797, 0: G798, 0: C799, 0: G814, 0: U815, 0: G816, 0: Hoh3799, 0: Hoh3961, 0: Hoh4479,

conact list:


AtomAtomDistance (A)
NaOP2 0:A7964.47
NaOP2 0:A7974.44
NaC6 0:G7984.20
NaC5 0:G7984.85
NaN7 0:G7984.69
NaO6 0:G7983.07
NaC4 0:C7994.84
NaN4 0:C7993.89
NaC6 0:G8144.03
NaN1 0:G8144.89
NaC5 0:G8144.84
NaO6 0:G8143.07
NaN3 0:U8153.70
NaC2 0:U8154.99
NaC5 0:U8154.90
NaC4 0:U8153.55
NaO4 0:U8152.64
NaN3 0:G8164.88
NaN2 0:G8163.98
NaC2 0:G8164.12
NaC6 0:G8164.79
NaN1 0:G8164.03
NaO 0:Hoh37994.22
NaO 0:Hoh39613.55
NaO 0:Hoh44793.54

interactive model:


Sodium binding site 50 out of 75 in 1vqm


Sodium binding site 50 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 50 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 50 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: U1831, 0: G1832, 0: C2021, 0: A2022, 0: Hoh4371, 0: Hoh4693, 0: Hoh5725, 0: Hoh7077, 0: Hoh7107, 0: Hoh8299, 0: Hoh9729,

conact list:


AtomAtomDistance (A)
NaOP1 0:U18313.59
NaP 0:U18314.21
NaOP2 0:U18314.02
NaO5' 0:U18314.74
NaP 0:G18324.97
NaOP2 0:G18323.51
NaC3' 0:C20214.64
NaC1' 0:C20214.96
NaO3' 0:C20214.12
NaO4' 0:C20214.09
NaC5' 0:C20214.80
NaC4' 0:C20213.84
NaOP1 0:A20223.40
NaP 0:A20224.17
NaOP2 0:A20224.52
NaO 0:Hoh43712.33
NaO 0:Hoh46933.18
NaO 0:Hoh57253.55
NaO 0:Hoh70774.65
NaO 0:Hoh71074.77
NaO 0:Hoh82994.01
NaO 0:Hoh97292.93

interactive model:


Sodium binding site 51 out of 75 in 1vqm


Sodium binding site 51 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 51 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 51 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G2491, 0: U2492, 0: C2493, 0: U2528, 0: G2529, 0: C2530, 0: Hoh3248, 0: Hoh3766, 0: Hoh4148,

conact list:


AtomAtomDistance (A)
NaC6 0:G24914.47
NaO6 0:G24913.39
NaN3 0:U24924.02
NaC4 0:U24923.83
NaO4 0:U24922.86
NaC5 0:C24934.62
NaC4 0:C24934.59
NaN4 0:C24933.91
NaC5 0:U25284.87
NaC4 0:U25284.42
NaO4 0:U25283.63
NaC6 0:G25293.95
NaC5 0:G25294.55
NaN7 0:G25294.38
NaO6 0:G25292.85
NaC4 0:C25304.89
NaN4 0:C25303.98
NaO 0:Hoh32483.07
NaO 0:Hoh37663.83
NaO 0:Hoh41483.32

interactive model:


Sodium binding site 52 out of 75 in 1vqm


Sodium binding site 52 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 52 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 52 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G918, 0: U919, 0: G921, 0: A922, 0: G924, 0: C925, 0: Hoh3785, 0: Hoh7779, 0: Hoh9898,

conact list:


AtomAtomDistance (A)
NaO6 0:G9184.47
NaN3 0:U9194.37
NaC4 0:U9194.23
NaO4 0:U9193.28
NaC2' 0:G9214.91
NaO2' 0:G9213.56
NaN3 0:A9224.04
NaC2 0:A9224.75
NaC1' 0:A9224.50
NaO4' 0:A9223.86
NaC4 0:A9224.93
NaC5' 0:A9224.86
NaC4' 0:A9224.44
NaC6 0:G9244.03
NaC5 0:G9244.46
NaN7 0:G9244.14
NaO6 0:G9243.03
NaN4 0:C9254.31
NaO 0:Hoh37854.24
NaO 0:Hoh77793.62
NaO 0:Hoh98983.24

interactive model:


Sodium binding site 53 out of 75 in 1vqm


Sodium binding site 53 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 53 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 53 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G1576, 0: U1577, 0: C1578, 0: G1618, 0: G1619, 0: C1620, 0: Hoh3331, 0: Hoh3864, 0: Hoh4278, 0: Hoh7782,

conact list:


AtomAtomDistance (A)
NaC6 0:G15764.23
NaN1 0:G15764.97
NaO6 0:G15763.18
NaN3 0:U15774.05
NaC4 0:U15774.09
NaO4 0:U15773.28
NaN4 0:C15784.26
NaC6 0:G16183.40
NaN1 0:G16184.27
NaC5 0:G16184.00
NaN7 0:G16184.16
NaO6 0:G16182.74
NaC6 0:G16193.71
NaN1 0:G16194.96
NaC5 0:G16194.17
NaN7 0:G16193.88
NaO6 0:G16192.72
NaC4 0:C16204.64
NaN4 0:C16203.71
NaO 0:Hoh33314.10
NaO 0:Hoh38643.16
NaO 0:Hoh42783.19
NaO 0:Hoh77822.80

interactive model:


Sodium binding site 54 out of 75 in 1vqm


Sodium binding site 54 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 54 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 54 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: A194, 0: C195, 0: G196, 0: A415, 0: G416, 0: G426, 0: Hoh3512, 0: Hoh4872,

conact list:


AtomAtomDistance (A)
NaP 0:A1944.84
NaOP2 0:A1944.08
NaO5' 0:A1944.77
NaC6 0:C1954.39
NaC5 0:C1954.03
NaP 0:C1954.64
NaOP2 0:C1953.32
NaO5' 0:C1954.81
NaC8 0:G1964.13
NaC6 0:G1963.60
NaN1 0:G1964.95
NaC5 0:G1963.60
NaN7 0:G1962.98
NaC4 0:G1964.91
NaO6 0:G1962.99
NaN9 0:A4154.77
NaN3 0:A4153.55
NaC2 0:A4154.35
NaC1' 0:A4154.08
NaC4 0:A4154.54
NaC2' 0:A4153.77
NaO2' 0:A4152.99
NaN9 0:G4164.89
NaC1' 0:G4164.30
NaO4' 0:G4163.37
NaC5' 0:G4164.53
NaC4' 0:G4164.23
NaN3 0:G4264.69
NaN2 0:G4264.92
NaO 0:Hoh35122.98
NaO 0:Hoh48724.42

interactive model:


Sodium binding site 55 out of 75 in 1vqm


Sodium binding site 55 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 55 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 55 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G868, 0: G869, 0: A886, 0: G887, 0: Hoh3721, 0: Hoh4263, 0: Hoh4495, 0: Hoh5707, 0: Hoh5784, 0: Hoh9889, 0: Hoh9981,

conact list:


AtomAtomDistance (A)
NaN3 0:G8684.41
NaC3' 0:G8684.27
NaC1' 0:G8684.33
NaO3' 0:G8683.18
NaC2' 0:G8684.15
NaO2' 0:G8683.29
NaN9 0:G8694.72
NaC8 0:G8693.35
NaC5 0:G8694.39
NaP 0:G8693.95
NaN7 0:G8693.04
NaOP2 0:G8693.44
NaO5' 0:G8694.62
NaN3 0:A8864.84
NaC3' 0:A8864.84
NaC1' 0:A8864.53
NaO3' 0:A8864.06
NaC2' 0:A8864.35
NaO2' 0:A8863.22
NaP 0:G8874.06
NaOP2 0:G8872.88
NaO5' 0:G8874.96
NaO 0:Hoh37214.30
NaO 0:Hoh42634.79
NaO 0:Hoh44953.61
NaO 0:Hoh57073.27
NaO 0:Hoh57844.90
NaO 0:Hoh98892.90
NaO 0:Hoh99814.05

interactive model:


Sodium binding site 56 out of 75 in 1vqm


Sodium binding site 56 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 56 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 56 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: C910, 0: G911, 0: U1293, 0: A1294, 0: G1295, 0: Hoh5793, 0: Hoh5917, 0: Hoh6866,

conact list:


AtomAtomDistance (A)
NaN4 0:C9104.11
NaN3 0:G9114.83
NaN2 0:G9113.50
NaC2 0:G9113.80
NaC6 0:G9114.44
NaN1 0:G9113.54
NaO6 0:G9114.74
NaOP1 0:U12933.88
NaP 0:U12933.70
NaOP2 0:U12932.69
NaO5' 0:U12934.44
NaOP2 0:A12943.97
NaC6 0:G12953.62
NaN1 0:G12954.83
NaC5 0:G12954.17
NaN7 0:G12953.98
NaO6 0:G12952.57
NaO 0:Hoh57934.10
NaO 0:Hoh59174.74
NaO 0:Hoh68662.29

interactive model:


Sodium binding site 57 out of 75 in 1vqm


Sodium binding site 57 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 57 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 57 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G644, 0: C762, 0: G902, 0: U903, L: Thr12, L: Ser17, L: His18, L: Lys19, L: Arg21, 0: Hoh3814, 0: Hoh3824, L: Hoh9426, L: Hoh9447,

conact list:


AtomAtomDistance (A)
NaO6 0:G6444.95
NaN3 0:C7624.74
NaC4 0:C7624.30
NaN4 0:C7623.37
NaC6 0:G9024.11
NaN1 0:G9024.80
NaO6 0:G9023.07
NaN3 0:U9033.57
NaC2 0:U9034.86
NaC5 0:U9034.69
NaC4 0:U9033.38
NaO4 0:U9032.52
NaCB L:Thr124.94
NaCG2 L:Thr124.74
NaCA L:Thr124.94
NaO L:Ser174.25
NaC L:Ser174.74
NaO L:His183.15
NaN L:His184.38
NaCB L:His183.64
NaC L:His183.47
NaCG L:His184.76
NaCA L:His183.18
NaN L:Lys194.61
NaO L:Arg214.73
NaN L:Arg214.48
NaCB L:Arg214.33
NaCD L:Arg214.96
NaCG L:Arg215.00
NaCA L:Arg214.88
NaO 0:Hoh38142.62
NaO 0:Hoh38243.78
NaO L:Hoh94262.14
NaO L:Hoh94472.79

interactive model:


Sodium binding site 58 out of 75 in 1vqm


Sodium binding site 58 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 58 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 58 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: U831, 0: U832, 0: G833, 0: Hoh4311, 0: Hoh5004, 0: Hoh5573, 0: Hoh7543, 0: Hoh9986,

conact list:


AtomAtomDistance (A)
NaC1' 0:U8314.80
NaO2 0:U8314.20
NaO3' 0:U8314.45
NaC2' 0:U8314.39
NaO2' 0:U8313.07
NaN3 0:U8323.90
NaC2 0:U8324.60
NaC6 0:U8323.68
NaN1 0:U8324.45
NaC5 0:U8322.87
NaC4 0:U8322.99
NaOP2 0:U8324.89
NaO5' 0:U8324.93
NaO4 0:U8323.01
NaN9 0:G8334.91
NaC8 0:G8333.74
NaC6 0:G8333.92
NaC5 0:G8333.63
NaN7 0:G8332.72
NaC4 0:G8334.86
NaOP2 0:G8334.82
NaO6 0:G8333.51
NaO 0:Hoh43112.99
NaO 0:Hoh50043.19
NaO 0:Hoh55732.87
NaO 0:Hoh75434.10
NaO 0:Hoh99864.78

interactive model:


Sodium binding site 59 out of 75 in 1vqm


Sodium binding site 59 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 59 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 59 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G2585, 0: U2586, 0: Omu2587, 0: G2592, 0: C2593, 0: Hoh4076, 0: Hoh4288, 0: Hoh6646, 0: Hoh7571, 0: Hoh9916, 0: Hoh9955,

conact list:


AtomAtomDistance (A)
NaC6 0:G25853.56
NaN1 0:G25854.40
NaC5 0:G25854.12
NaN7 0:G25854.28
NaO6 0:G25852.95
NaN3 0:U25864.53
NaC6 0:U25864.93
NaC5 0:U25863.59
NaC4 0:U25863.25
NaO4 0:U25862.32
NaN3 0:Omu25874.18
NaC4 0:Omu25874.17
NaO4 0:Omu25873.48
NaC6 0:G25923.95
NaN1 0:G25924.24
NaO6 0:G25922.92
NaN4 0:C25934.14
NaO 0:Hoh40764.31
NaO 0:Hoh42882.73
NaO 0:Hoh66464.58
NaO 0:Hoh75713.15
NaO 0:Hoh99163.21
NaO 0:Hoh99552.71

interactive model:


Sodium binding site 60 out of 75 in 1vqm


Sodium binding site 60 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 60 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 60 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G2772, 0: G2773, 0: U2774, 0: A2799, 0: A2801, 0: C2802, 0: Hoh4949,

conact list:


AtomAtomDistance (A)
NaC8 0:G27724.99
NaC6 0:G27723.22
NaN1 0:G27724.21
NaC5 0:G27723.76
NaN7 0:G27723.85
NaC4 0:G27724.94
NaO6 0:G27722.54
NaC8 0:G27734.77
NaC6 0:G27733.43
NaN1 0:G27734.69
NaC5 0:G27733.80
NaN7 0:G27733.52
NaO6 0:G27732.57
NaO4 0:U27744.96
NaOP2 0:A27994.69
NaN6 0:A28014.50
NaN4 0:C28024.59
NaO 0:Hoh49493.10

interactive model:


Sodium binding site 61 out of 75 in 1vqm


Sodium binding site 61 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 61 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 61 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: C197, 0: G229, 0: C230, 0: Hoh4275, 0: Hoh5811, 0: Hoh7088,

conact list:


AtomAtomDistance (A)
NaN3 0:C1973.07
NaC2 0:C1973.79
NaO2 0:C1973.63
NaC4 0:C1974.02
NaN4 0:C1974.05
NaO2' 0:G2294.29
NaO4' 0:C2304.72
NaC5' 0:C2303.98
NaC4' 0:C2304.11
NaO 0:Hoh42754.01
NaO 0:Hoh58112.78
NaO 0:Hoh70883.21

interactive model:


Sodium binding site 62 out of 75 in 1vqm


Sodium binding site 62 out of 75 in 1vqm
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stereopicture of Sodium binding site 62 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 62 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G618, 0: G1076, 0: G1077, 0: A1078, 0: A1079, 0: C1080, 0: Hoh5754, 0: Hoh8222,

conact list:


AtomAtomDistance (A)
NaOP1 0:G6184.53
NaOP2 0:G10764.80
NaN7 0:G10774.74
NaO3' 0:A10784.89
NaOP1 0:A10792.53
NaP 0:A10793.91
NaOP2 0:A10794.79
NaC5' 0:A10794.45
NaO5' 0:A10794.38
NaOP2 0:C10804.38
NaO 0:Hoh57542.89
NaO 0:Hoh82222.42

interactive model:


Sodium binding site 63 out of 75 in 1vqm


Sodium binding site 63 out of 75 in 1vqm
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stereopicture of Sodium binding site 63 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 63 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 9: C3040, D: Arg51, D: Lys53, D: Pro68,

conact list:


AtomAtomDistance (A)
NaN3 9:C30403.34
NaC2 9:C30404.20
NaO2 9:C30404.14
NaC4 9:C30404.16
NaN4 9:C30403.99
NaCB D:Arg513.66
NaCD D:Arg514.76
NaCG D:Arg513.88
NaCE D:Lys534.41
NaCG D:Pro684.64

interactive model:


Sodium binding site 64 out of 75 in 1vqm


Sodium binding site 64 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 64 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 64 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: A955, 0: G956, 9: C3081, 9: U3082, 0: Hoh5815, 0: Hoh6457, 0: Hoh6842, 0: Hoh7121,

conact list:


AtomAtomDistance (A)
NaC3' 0:A9554.25
NaO3' 0:A9553.62
NaC2' 0:A9554.17
NaC4' 0:A9554.30
NaO2' 0:A9553.02
NaOP1 0:G9564.60
NaP 0:G9564.80
NaC3' 9:C30814.68
NaO3' 9:C30813.41
NaC4' 9:C30814.97
NaOP1 9:U30822.75
NaP 9:U30823.69
NaOP2 9:U30824.72
NaC5' 9:U30824.93
NaO5' 9:U30824.82
NaO 0:Hoh58153.50
NaO 0:Hoh64574.63
NaO 0:Hoh68424.13
NaO 0:Hoh71212.93

interactive model:


Sodium binding site 65 out of 75 in 1vqm


Sodium binding site 65 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 65 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 65 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 9: G3021, 9: G3022, 9: U3055, 9: A3057, 9: G3058, 9: C3059, 9: Hoh3535, 9: Hoh7361,

conact list:


AtomAtomDistance (A)
NaC2 9:G30214.88
NaC6 9:G30213.69
NaN1 9:G30213.81
NaC5 9:G30214.77
NaO6 9:G30213.18
NaC6 9:G30224.21
NaN1 9:G30224.95
NaO6 9:G30223.02
NaN3 9:U30554.83
NaC2 9:U30553.83
NaN1 9:U30554.52
NaC1' 9:U30554.19
NaO2 9:U30552.72
NaO3' 9:U30554.78
NaC2' 9:U30554.88
NaO2' 9:U30554.36
NaN3 9:A30573.76
NaC2 9:A30572.76
NaC6 9:A30574.05
NaN1 9:A30572.92
NaC5 9:A30574.83
NaN6 9:A30574.75
NaC4 9:A30574.63
NaOP2 9:A30574.84
NaC8 9:G30584.37
NaC6 9:G30583.97
NaC5 9:G30583.95
NaN7 9:G30583.26
NaO6 9:G30583.32
NaN3 9:C30594.15
NaC4 9:C30594.33
NaN4 9:C30593.91
NaO 9:Hoh35354.77
NaO 9:Hoh73613.82

interactive model:


Sodium binding site 66 out of 75 in 1vqm


Sodium binding site 66 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 66 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 66 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: C: Asp45, C: Thr94, C: Glu95, C: Lys96, C: Asp97, C: Arg98, C: Hoh9110, C: Hoh9199, C: Hoh9228,

conact list:


AtomAtomDistance (A)
NaCB C:Asp454.20
NaOD2 C:Asp453.10
NaOD1 C:Asp452.18
NaCG C:Asp452.90
NaO C:Thr942.99
NaC C:Thr944.16
NaO C:Glu953.88
NaN C:Glu954.75
NaC C:Glu953.85
NaCA C:Glu954.38
NaO C:Lys962.49
NaN C:Lys964.04
NaC C:Lys963.41
NaCA C:Lys964.32
NaN C:Asp974.15
NaCA C:Asp974.21
NaN C:Arg984.76
NaO C:Hoh91102.85
NaO C:Hoh91994.26
NaO C:Hoh92284.54

interactive model:


Sodium binding site 67 out of 75 in 1vqm


Sodium binding site 67 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 67 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 67 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G2286, 0: C2287, 0: G2288, H: Arg114,

conact list:


AtomAtomDistance (A)
NaO6 0:G22864.99
NaN3 0:C22874.45
NaC4 0:C22874.60
NaN4 0:C22873.75
NaN3 0:G22884.31
NaN2 0:G22884.34
NaC2 0:G22884.17
NaC6 0:G22885.00
NaN1 0:G22884.50
NaC4 0:G22884.71
NaCD H:Arg1143.65
NaCZ H:Arg1143.95
NaCG H:Arg1144.91
NaNE H:Arg1144.20
NaNH1 H:Arg1142.97

interactive model:


Sodium binding site 68 out of 75 in 1vqm


Sodium binding site 68 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 68 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 68 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: A2677, J: Arg60, J: Val61, J: Asp62, J: Ile63, J: Gly64, J: Tyr69, J: Phe70, J: Tyr71, 0: Hoh3110, J: Hoh4949,

conact list:


AtomAtomDistance (A)
NaOP1 0:A26773.99
NaO J:Arg602.57
NaC J:Arg603.61
NaCA J:Arg604.95
NaO J:Val612.67
NaN J:Val614.00
NaCB J:Val614.80
NaC J:Val613.16
NaCG1 J:Val615.00
NaCA J:Val613.44
NaO J:Asp624.99
NaN J:Asp624.12
NaC J:Asp624.38
NaCA J:Asp624.70
NaO J:Ile632.60
NaN J:Ile633.95
NaCB J:Ile634.62
NaC J:Ile633.68
NaCA J:Ile634.30
NaN J:Gly644.74
NaCA J:Gly644.97
NaO J:Tyr692.78
NaCB J:Tyr694.34
NaCD2 J:Tyr694.13
NaC J:Tyr693.98
NaCG J:Tyr694.71
NaCA J:Tyr694.81
NaN J:Phe704.91
NaC J:Phe704.95
NaCA J:Phe704.98
NaN J:Tyr714.10
NaCB J:Tyr714.13
NaCA J:Tyr714.74
NaO 0:Hoh31102.66
NaO J:Hoh49492.38

interactive model:


Sodium binding site 69 out of 75 in 1vqm


Sodium binding site 69 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 69 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 69 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: M: Ser106, M: Arg107, M: Phe109, M: Pro110, M: Asn111, M: Leu112, M: Arg113, M: Cl9318, M: Hoh9429,

conact list:


AtomAtomDistance (A)
NaO M:Ser1062.60
NaCB M:Ser1063.75
NaOG M:Ser1062.65
NaC M:Ser1063.49
NaCA M:Ser1063.77
NaN M:Arg1074.67
NaO M:Phe1092.78
NaC M:Phe1093.61
NaCA M:Phe1094.82
NaO M:Pro1103.21
NaN M:Pro1103.96
NaCB M:Pro1104.99
NaC M:Pro1103.44
NaCA M:Pro1103.56
NaN M:Asn1114.26
NaC M:Asn1114.63
NaCA M:Asn1114.92
NaO M:Leu1122.52
NaN M:Leu1124.00
NaCB M:Leu1124.98
NaC M:Leu1123.68
NaCA M:Leu1124.39
NaN M:Arg1134.72
NaCA M:Arg1134.94
NaCL M:Cl93184.57
NaO M:Hoh94292.96

interactive model:


Sodium binding site 70 out of 75 in 1vqm


Sodium binding site 70 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 70 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 70 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: C2366, Q: Asn16, Q: Asp20, Q: Arg21, Q: Gly22, Q: Thr23, Q: Ser24, Q: Arg28, Q: Asp44, Q: Ser46, Q: Hoh1795, Q: Hoh5427, Q: Hoh7505,

conact list:


AtomAtomDistance (A)
NaOP1 0:C23664.22
NaND2 Q:Asn164.69
NaOD1 Q:Asn163.59
NaCG Q:Asn164.41
NaO Q:Asp202.38
NaCB Q:Asp204.88
NaC Q:Asp203.54
NaCA Q:Asp204.59
NaO Q:Arg214.24
NaN Q:Arg214.33
NaC Q:Arg213.92
NaCA Q:Arg214.32
NaO Q:Gly222.35
NaN Q:Gly223.87
NaC Q:Gly223.52
NaCA Q:Gly224.27
NaO Q:Thr234.34
NaN Q:Thr234.54
NaC Q:Thr234.12
NaCA Q:Thr234.73
NaN Q:Ser243.95
NaCB Q:Ser244.08
NaOG Q:Ser243.00
NaCA Q:Ser244.07
NaNH2 Q:Arg284.99
NaOD1 Q:Asp444.32
NaN Q:Ser464.97
NaCB Q:Ser463.42
NaOG Q:Ser462.62
NaCA Q:Ser464.78
NaO Q:Hoh17952.49
NaO Q:Hoh54272.87
NaO Q:Hoh75053.77

interactive model:


Sodium binding site 71 out of 75 in 1vqm


Sodium binding site 71 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 71 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 71 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: G2660, R: Lys69, R: Ser70, R: Lys71, R: Val72, R: Asp73, R: Na9138, R: Hoh9427, R: Hoh9429, R: Hoh9438, R: Hoh9439, R: Hoh9472, R: Hoh9488,

conact list:


AtomAtomDistance (A)
NaOP1 0:G26604.04
NaO R:Lys694.72
NaO R:Ser702.33
NaC R:Ser703.52
NaCA R:Ser704.47
NaO R:Lys714.35
NaN R:Lys714.36
NaC R:Lys713.97
NaCA R:Lys714.28
NaO R:Val722.44
NaN R:Val723.96
NaC R:Val723.42
NaCA R:Val724.37
NaN R:Asp734.16
NaCB R:Asp734.92
NaOD1 R:Asp734.50
NaCA R:Asp734.12
NaNA R:Na91382.65
NaO R:Hoh94274.34
NaO R:Hoh94294.65
NaO R:Hoh94382.47
NaO R:Hoh94392.23
NaO R:Hoh94722.94
NaO R:Hoh94883.64

interactive model:


Sodium binding site 72 out of 75 in 1vqm


Sodium binding site 72 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 72 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 72 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: U2659, 0: G2660, R: Lys69, R: Ser70, R: Val72, R: Asp73, R: Gly74, R: Trp75, R: Asp76, R: Na9137, 0: Hoh4696, R: Hoh9427, R: Hoh9438, R: Hoh9439, R: Hoh9488,

conact list:


AtomAtomDistance (A)
NaC3' 0:U26594.21
NaO3' 0:U26593.02
NaC5' 0:U26594.56
NaC4' 0:U26594.24
NaO2' 0:U26594.67
NaOP1 0:G26602.94
NaP 0:G26603.66
NaOP2 0:G26604.66
NaO5' 0:G26604.77
NaO R:Lys694.05
NaO R:Ser703.79
NaC R:Ser704.59
NaCA R:Ser704.99
NaO R:Val722.20
NaN R:Val724.38
NaCB R:Val724.34
NaC R:Val723.35
NaCG1 R:Val724.56
NaCA R:Val724.25
NaN R:Asp734.25
NaC R:Asp734.67
NaCA R:Asp734.31
NaN R:Gly744.44
NaN R:Trp754.40
NaC R:Trp753.96
NaCA R:Trp754.90
NaO R:Trp752.76
NaN R:Asp764.80
NaCA R:Asp764.69
NaNA R:Na91372.65
NaO 0:Hoh46964.32
NaO R:Hoh94272.43
NaO R:Hoh94383.61
NaO R:Hoh94392.21
NaO R:Hoh94884.56

interactive model:


Sodium binding site 73 out of 75 in 1vqm


Sodium binding site 73 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 73 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 73 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: U12, 0: G13, R: Lys60, R: Gln61, R: His62, R: Asn63, R: Trp75, R: Sr9418,

conact list:


AtomAtomDistance (A)
NaC3' 0:U123.96
NaO3' 0:U123.05
NaC5' 0:U124.79
NaC2' 0:U124.33
NaC4' 0:U124.03
NaO2' 0:U123.53
NaOP1 0:G133.80
NaP 0:G134.09
NaOP2 0:G134.95
NaO R:Lys602.60
NaC R:Lys603.58
NaCA R:Lys604.92
NaO R:Gln613.23
NaN R:Gln613.90
NaCB R:Gln614.33
NaC R:Gln613.63
NaCG R:Gln614.55
NaCA R:Gln613.26
NaN R:His624.89
NaND2 R:Asn633.56
NaOD1 R:Asn633.61
NaCG R:Asn633.87
NaCZ2 R:Trp754.93
NaSR R:Sr94182.80

interactive model:


Sodium binding site 74 out of 75 in 1vqm


Sodium binding site 74 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 74 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 74 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: S: His7, S: Ala27, S: Glu61, S: Hoh9483,

conact list:


AtomAtomDistance (A)
NaNE2 S:His72.93
NaCD2 S:His73.71
NaCE1 S:His73.99
NaCG S:His74.95
NaCB S:Ala274.89
NaOE1 S:Glu613.00
NaOE2 S:Glu612.44
NaCD S:Glu613.06
NaCG S:Glu614.54
NaO S:Hoh94832.78

interactive model:


Sodium binding site 75 out of 75 in 1vqm


Sodium binding site 75 out of 75 in 1vqm
Click to enlarge
stereopicture of Sodium binding site 75 out of 75 in 1vqm
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 75 of Sodium in the PDB 1vqm. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: 0: U391, 0: U392, 0: A395, 3: Arg42, 3: Asn43, 0: Sr9461, 0: Hoh3278, 0: Hoh3366, 0: Hoh7089, 0: Hoh7597, 3: Hoh9442,

conact list:


AtomAtomDistance (A)
NaC4 0:U3914.53
NaO4 0:U3913.74
NaN3 0:U3924.47
NaC5 0:U3924.85
NaC4 0:U3923.77
NaO4 0:U3922.55
NaOP1 0:A3954.16
NaP 0:A3954.99
NaO 3:Arg423.47
NaCB 3:Arg424.30
NaCD 3:Arg424.16
NaC 3:Arg424.08
NaCG 3:Arg424.35
NaCA 3:Arg424.69
NaN 3:Asn434.74
NaOD1 3:Asn433.39
NaCG 3:Asn434.53
NaCA 3:Asn434.85
NaSR 0:Sr94613.32
NaO 0:Hoh32783.48
NaO 0:Hoh33662.93
NaO 0:Hoh70893.91
NaO 0:Hoh75972.28
NaO 3:Hoh94424.21

interactive model:




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