Chemical elements
  Sodium
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    Chemical Properties
    PDB 131d-1bli
    PDB 1bph-1d10
    PDB 1d11-1ej2
    PDB 1eja-1gb5
    PDB 1gb6-1goh
    PDB 1gq2-1ikp
    PDB 1ikq-1jz1
    PDB 1jz2-1kvs
    PDB 1kvt-1me8
    PDB 1mg2-1nsz
    PDB 1nta-1oyt
    PDB 1p0s-1qjs
    PDB 1qnj-1s5d
    PDB 1s5e-1tjp
    PDB 1tk6-1uxt
    PDB 1uxu-1vzq
    PDB 1w15-1xc6
    PDB 1xcu-1yf1
    PDB 1ygg-1zko
    PDB 1zkp-2afh
    PDB 2agv-2bhc
    PDB 2bhp-2cc6
    PDB 2cc7-2dec
    PDB 2deg-2ein
    PDB 2eit-2fjb
    PDB 2fld-2gg8
    PDB 2gg9-2h9j
    PDB 2h9k-2ien
    PDB 2ieo-2jih
    PDB 2jin-2omd
    PDB 2omg-2p77
    PDB 2p78-2q68
    PDB 2q69-2qz7
    PDB 2qzi-2v35
    PDB 2v3h-2vwo
    PDB 2vx4-2wig
    PDB 2wij-2x1z
    PDB 2x20-2xmk
    PDB 2xmm-2zfq
    PDB 2zfr-3a6s
    PDB 3a6t-3b1e
    PDB 3b2n-3bos
    PDB 3bov-3ccr
    PDB 3ccs-3d7r
    PDB 3d97-3e3y
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    PDB 3euw-3fgw
    PDB 3fh4-3g3r
    PDB 3g3s-3gxw
    PDB 3gyz-3hwt
    PDB 3hww-3ijp
    PDB 3imm-3k0g
    PDB 3k13-3l7x
    PDB 3l88-3max
    PDB 3mbb-3mr1
    PDB 3mty-3nu3
    PDB 3nu4-3ot1
    PDB 3ow2-3qwc
    PDB 3qx5-3tfr
    PDB 3tfs-3v6o
    PDB 3v72-4ag2
      3v72
      3vbf
      3vbh
      3vbo
      3vd3
      3vd4
      3vd5
      3vd7
      3vd9
      3vda
      3vdb
      3vdc
      3vh9
      3vi2
      3vif
      3vig
      3vih
      3vii
      3vij
      3vik
      3vil
      3vim
      3vin
      3vio
      3vip
      3vou
      3vsb
      3znb
      3zso
      420d
      434d
      435d
      437d
      464d
      466d
      4a1n
      4a3r
      4a41
      4a44
      4a45
      4a81
      4a87
      4aab
      4aax
      4acl
      4adn
      4ae4
      4aeb
      4af8
      4ag2
    PDB 4aga-4eae
    PDB 4ecn-4g8t
    PDB 4gdt-8icw
    PDB 8icx-9icy

Sodium in the structure of E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex With Iptg (pdb 3vd9)






The binding sites of Sodium atom in the structure of E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex With Iptg (pdb code 3vd9). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 3vd9 structure was solved by R.W.WHEATLEY, J.C.KAPPELHOFF, J.N.HAHN, M.L.DUGDALE, M.J.DUTKOSKI, S.D.TAMMAN, M.E.FRASER, R.E.HUBER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)86.2-2.0
Space groupP212121
a (A)151.537
b (A)162.550
c (A)203.440
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)16.9
Rfree (%)22.3


Sodium Binding Sites:

Sodium binding site 1 out of 16 in 3vd9


Sodium binding site 1 out of 16 in 3vd9
Click to enlarge
stereopicture of Sodium binding site 1 out of 16 in 3vd9
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3vd9. 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: A: Tyr100, A: Asp201, A: His540, A: Trp568, A: Phe601, A: Cys602, A: Asn604, A: Ipt2001, A: Hoh4051, A: Hoh4256,

conact list:


AtomAtomDistance (A)
NaCZ A:Tyr1004.83
NaOH A:Tyr1003.73
NaO A:Asp2014.51
NaCB A:Asp2014.49
NaOD2 A:Asp2012.40
NaOD1 A:Asp2013.59
NaCG A:Asp2013.26
NaNE2 A:His5404.70
NaCD1 A:Trp5684.98
NaCZ2 A:Trp5684.96
NaCE2 A:Trp5684.86
NaNE1 A:Trp5684.04
NaO A:Phe6012.37
NaCB A:Phe6014.70
NaC A:Phe6013.53
NaCA A:Phe6014.61
NaO A:Cys6024.85
NaN A:Cys6024.27
NaC A:Cys6024.51
NaCA A:Cys6024.13
NaCB A:Asn6044.70
NaND2 A:Asn6043.66
NaOD1 A:Asn6042.37
NaCG A:Asn6043.34
NaC6 A:Ipt20013.34
NaC5 A:Ipt20014.44
NaC4 A:Ipt20014.42
NaO4 A:Ipt20014.13
NaO6 A:Ipt20012.43
NaO A:Hoh40514.19
NaO A:Hoh42562.31

interactive model:


Sodium binding site 2 out of 16 in 3vd9


Sodium binding site 2 out of 16 in 3vd9
Click to enlarge
stereopicture of Sodium binding site 2 out of 16 in 3vd9
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3vd9. 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: A: Leu350, A: Phe556, A: Arg557, A: Tyr559, A: Pro560, A: Arg561, A: Leu562, A: Gln563, A: Hoh4261, A: Hoh4358, A: Hoh4490, A: Hoh4547,

conact list:


AtomAtomDistance (A)
NaCD1 A:Leu3504.68
NaO A:Phe5562.36
NaCB A:Phe5564.81
NaC A:Phe5563.51
NaCA A:Phe5564.22
NaO A:Arg5574.80
NaN A:Arg5574.55
NaC A:Arg5574.79
NaCA A:Arg5574.70
NaO A:Tyr5592.38
NaN A:Tyr5594.55
NaC A:Tyr5593.42
NaCA A:Tyr5594.54
NaO A:Pro5603.29
NaN A:Pro5604.04
NaC A:Pro5603.70
NaCA A:Pro5603.80
NaN A:Arg5614.62
NaC A:Arg5614.97
NaO A:Leu5622.37
NaN A:Leu5624.17
NaCB A:Leu5624.51
NaC A:Leu5623.41
NaCA A:Leu5624.24
NaN A:Gln5634.29
NaCG A:Gln5634.68
NaCA A:Gln5634.35
NaO A:Hoh42613.94
NaO A:Hoh43582.39
NaO A:Hoh44902.55
NaO A:Hoh45473.82

interactive model:


Sodium binding site 3 out of 16 in 3vd9


Sodium binding site 3 out of 16 in 3vd9
Click to enlarge
stereopicture of Sodium binding site 3 out of 16 in 3vd9
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3vd9. 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: A: Phe931, A: Pro932, A: Ser933, A: Leu967, A: Met968, A: Glu969, A: Thr970, A: Ser971, A: Hoh4195, A: Hoh4441, A: Hoh4607, A: Hoh4658,

conact list:


AtomAtomDistance (A)
NaCE2 A:Phe9313.97
NaCD1 A:Phe9314.34
NaCD2 A:Phe9314.57
NaCZ A:Phe9313.48
NaCE1 A:Phe9313.69
NaCG A:Phe9314.75
NaO A:Pro9322.73
NaN A:Pro9324.34
NaCB A:Pro9324.20
NaCD A:Pro9324.22
NaC A:Pro9323.72
NaCG A:Pro9324.66
NaCA A:Pro9324.33
NaN A:Ser9334.74
NaO A:Leu9672.58
NaC A:Leu9673.70
NaCA A:Leu9674.93
NaO A:Met9683.86
NaN A:Met9684.24
NaC A:Met9683.88
NaCA A:Met9683.82
NaN A:Glu9694.57
NaC A:Glu9694.98
NaO A:Thr9702.68
NaN A:Thr9704.27
NaC A:Thr9703.74
NaCA A:Thr9704.62
NaN A:Ser9714.58
NaCA A:Ser9714.55
NaO A:Hoh41952.85
NaO A:Hoh44413.51
NaO A:Hoh46072.49
NaO A:Hoh46584.68

interactive model:


Sodium binding site 4 out of 16 in 3vd9


Sodium binding site 4 out of 16 in 3vd9
Click to enlarge
stereopicture of Sodium binding site 4 out of 16 in 3vd9
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3vd9. 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: A: Pro596, A: Asn597, A: Asp598, A: Glu797, A: Hoh4389, A: Hoh4473, A: Hoh4671, A: Hoh4675, A: Hoh4797, A: Hoh4884, A: Hoh4894,

conact list:


AtomAtomDistance (A)
NaC A:Pro5964.97
NaO A:Asn5972.37
NaN A:Asn5973.95
NaND2 A:Asn5974.82
NaC A:Asn5973.56
NaOD1 A:Asn5974.50
NaCG A:Asn5974.61
NaCA A:Asn5974.37
NaN A:Asp5984.53
NaOD1 A:Asp5984.64
NaCA A:Asp5984.63
NaOE1 A:Glu7973.82
NaOE2 A:Glu7973.99
NaCD A:Glu7974.25
NaO A:Hoh43892.17
NaO A:Hoh44732.00
NaO A:Hoh46713.31
NaO A:Hoh46754.46
NaO A:Hoh47974.94
NaO A:Hoh48841.97
NaO A:Hoh48942.03

interactive model:


Sodium binding site 5 out of 16 in 3vd9


Sodium binding site 5 out of 16 in 3vd9
Click to enlarge
stereopicture of Sodium binding site 5 out of 16 in 3vd9
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 3vd9. 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: B: Tyr100, B: Asp201, B: His540, B: Trp568, B: Phe601, B: Cys602, B: Asn604, B: Ipt2001, B: Hoh4070, B: Hoh4282,

conact list:


AtomAtomDistance (A)
NaCZ B:Tyr1004.72
NaOH B:Tyr1003.60
NaO B:Asp2014.68
NaCB B:Asp2014.55
NaOD2 B:Asp2012.39
NaOD1 B:Asp2013.63
NaCG B:Asp2013.30
NaNE2 B:His5404.59
NaCZ2 B:Trp5684.81
NaCE2 B:Trp5684.81
NaNE1 B:Trp5684.09
NaO B:Phe6012.37
NaCB B:Phe6014.57
NaC B:Phe6013.50
NaCA B:Phe6014.54
NaN B:Cys6024.26
NaC B:Cys6024.64
NaCA B:Cys6024.18
NaCB B:Asn6044.72
NaND2 B:Asn6043.61
NaOD1 B:Asn6042.38
NaCG B:Asn6043.33
NaC6 B:Ipt20013.26
NaC5 B:Ipt20014.36
NaC4 B:Ipt20014.40
NaO4 B:Ipt20014.07
NaO6 B:Ipt20012.37
NaO B:Hoh40704.24
NaO B:Hoh42822.31

interactive model:


Sodium binding site 6 out of 16 in 3vd9


Sodium binding site 6 out of 16 in 3vd9
Click to enlarge
stereopicture of Sodium binding site 6 out of 16 in 3vd9
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 3vd9. 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: B: Leu350, B: Phe556, B: Arg557, B: Tyr559, B: Pro560, B: Arg561, B: Leu562, B: Gln563, B: Hoh4289, B: Hoh4397, B: Hoh4554, B: Hoh4652, B: Hoh4960,

conact list:


AtomAtomDistance (A)
NaCD1 B:Leu3504.68
NaO B:Phe5562.37
NaCB B:Phe5564.91
NaC B:Phe5563.55
NaCA B:Phe5564.32
NaO B:Arg5574.91
NaN B:Arg5574.56
NaC B:Arg5574.84
NaCA B:Arg5574.70
NaO B:Tyr5592.37
NaN B:Tyr5594.61
NaC B:Tyr5593.39
NaCA B:Tyr5594.54
NaO B:Pro5603.21
NaN B:Pro5603.97
NaC B:Pro5603.65
NaCA B:Pro5603.73
NaN B:Arg5614.61
NaC B:Arg5614.97
NaO B:Leu5622.37
NaN B:Leu5624.15
NaCB B:Leu5624.49
NaC B:Leu5623.41
NaCA B:Leu5624.23
NaN B:Gln5634.30
NaCG B:Gln5634.65
NaCA B:Gln5634.33
NaO B:Hoh42893.90
NaO B:Hoh43972.57
NaO B:Hoh45542.30
NaO B:Hoh46523.61
NaO B:Hoh49604.87

interactive model:


Sodium binding site 7 out of 16 in 3vd9


Sodium binding site 7 out of 16 in 3vd9
Click to enlarge
stereopicture of Sodium binding site 7 out of 16 in 3vd9
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 3vd9. 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: B: Phe931, B: Pro932, B: Ser933, B: Leu967, B: Met968, B: Glu969, B: Thr970, B: Ser971, B: Hoh4218, B: Hoh4502, B: Hoh4625, B: Hoh4844,

conact list:


AtomAtomDistance (A)
NaCE2 B:Phe9313.81
NaCD1 B:Phe9314.30
NaCD2 B:Phe9314.41
NaCZ B:Phe9313.38
NaC B:Phe9314.93
NaCE1 B:Phe9313.67
NaCG B:Phe9314.65
NaO B:Pro9322.38
NaN B:Pro9324.23
NaCB B:Pro9324.21
NaCD B:Pro9324.26
NaC B:Pro9323.49
NaCG B:Pro9324.68
NaCA B:Pro9324.19
NaN B:Ser9334.53
NaCA B:Ser9334.81
NaO B:Leu9672.54
NaC B:Leu9673.69
NaCA B:Leu9674.89
NaO B:Met9683.93
NaN B:Met9684.27
NaC B:Met9683.98
NaCA B:Met9683.88
NaN B:Glu9694.73
NaO B:Thr9702.86
NaN B:Thr9704.41
NaC B:Thr9703.94
NaCA B:Thr9704.78
NaN B:Ser9714.80
NaCA B:Ser9714.81
NaO B:Hoh42182.63
NaO B:Hoh45023.34
NaO B:Hoh46254.78
NaO B:Hoh48444.05

interactive model:


Sodium binding site 8 out of 16 in 3vd9


Sodium binding site 8 out of 16 in 3vd9
Click to enlarge
stereopicture of Sodium binding site 8 out of 16 in 3vd9
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Sodium in the PDB 3vd9. 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: B: Ser647, B: Asp648, B: Asn649, B: Glu650, B: Leu651, B: Leu670, B: Hoh5054,

conact list:


AtomAtomDistance (A)
NaO B:Ser6472.74
NaOG B:Ser6474.75
NaC B:Ser6473.82
NaO B:Asp6484.19
NaN B:Asp6484.30
NaC B:Asp6483.71
NaCA B:Asp6483.90
NaN B:Asn6493.70
NaC B:Asn6494.20
NaCA B:Asn6494.25
NaO B:Glu6502.75
NaN B:Glu6503.20
NaOE1 B:Glu6504.89
NaCB B:Glu6504.27
NaC B:Glu6503.62
NaCA B:Glu6503.85
NaN B:Leu6514.83
NaO B:Leu6702.91
NaN B:Leu6704.20
NaCB B:Leu6704.74
NaC B:Leu6704.02
NaCA B:Leu6704.53
NaO B:Hoh50542.87

interactive model:


Sodium binding site 9 out of 16 in 3vd9


Sodium binding site 9 out of 16 in 3vd9
Click to enlarge
stereopicture of Sodium binding site 9 out of 16 in 3vd9
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Sodium in the PDB 3vd9. 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: B: Pro596, B: Asn597, B: Asp598, B: Glu797, B: Hoh4235, B: Hoh4426, B: Hoh4540, B: Hoh4650, B: Hoh4994, B: Hoh5056,

conact list:


AtomAtomDistance (A)
NaCB B:Pro5964.96
NaC B:Pro5964.86
NaCA B:Pro5964.97
NaO B:Asn5972.38
NaN B:Asn5973.82
NaND2 B:Asn5974.76
NaC B:Asn5973.56
NaOD1 B:Asn5974.52
NaCG B:Asn5974.58
NaCA B:Asn5974.29
NaN B:Asp5984.60
NaOD1 B:Asp5984.77
NaCA B:Asp5984.76
NaOE1 B:Glu7973.74
NaOE2 B:Glu7974.10
NaCD B:Glu7974.32
NaO B:Hoh42352.85
NaO B:Hoh44262.10
NaO B:Hoh45402.77
NaO B:Hoh46503.83
NaO B:Hoh49944.96
NaO B:Hoh50562.25

interactive model:


Sodium binding site 10 out of 16 in 3vd9


Sodium binding site 10 out of 16 in 3vd9
Click to enlarge
stereopicture of Sodium binding site 10 out of 16 in 3vd9
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Sodium in the PDB 3vd9. 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: Tyr100, C: Asp201, C: His540, C: Trp568, C: Phe601, C: Cys602, C: Asn604, C: Ipt2001, C: Hoh4080, C: Hoh4297,

conact list:


AtomAtomDistance (A)
NaCZ C:Tyr1004.70
NaOH C:Tyr1003.56
NaO C:Asp2014.52
NaCB C:Asp2014.45
NaOD2 C:Asp2012.40
NaOD1 C:Asp2013.52
NaCG C:Asp2013.21
NaNE2 C:His5404.74
NaCZ2 C:Trp5684.87
NaCE2 C:Trp5684.84
NaNE1 C:Trp5684.10
NaO C:Phe6012.37
NaCB C:Phe6014.59
NaC C:Phe6013.53
NaCA C:Phe6014.57
NaN C:Cys6024.28
NaC C:Cys6024.68
NaCA C:Cys6024.21
NaCB C:Asn6044.73
NaND2 C:Asn6043.71
NaOD1 C:Asn6042.37
NaCG C:Asn6043.37
NaC6 C:Ipt20013.28
NaC5 C:Ipt20014.40
NaC4 C:Ipt20014.43
NaO4 C:Ipt20014.03
NaO6 C:Ipt20012.28
NaO C:Hoh40804.29
NaO C:Hoh42972.30

interactive model:


Sodium binding site 11 out of 16 in 3vd9


Sodium binding site 11 out of 16 in 3vd9
Click to enlarge
stereopicture of Sodium binding site 11 out of 16 in 3vd9
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Sodium in the PDB 3vd9. 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: Leu350, C: Phe556, C: Arg557, C: Tyr559, C: Pro560, C: Arg561, C: Leu562, C: Gln563, C: Hoh4303, C: Hoh4411, C: Hoh4757,

conact list:


AtomAtomDistance (A)
NaCD1 C:Leu3504.57
NaO C:Phe5562.37
NaCB C:Phe5564.85
NaC C:Phe5563.54
NaCA C:Phe5564.23
NaO C:Arg5574.85
NaN C:Arg5574.59
NaC C:Arg5574.85
NaCA C:Arg5574.78
NaO C:Tyr5592.37
NaN C:Tyr5594.56
NaC C:Tyr5593.37
NaCA C:Tyr5594.52
NaO C:Pro5603.19
NaN C:Pro5603.93
NaC C:Pro5603.56
NaCA C:Pro5603.66
NaN C:Arg5614.47
NaC C:Arg5614.89
NaO C:Leu5622.37
NaN C:Leu5624.04
NaCB C:Leu5624.46
NaC C:Leu5623.38
NaCA C:Leu5624.19
NaN C:Gln5634.26
NaCG C:Gln5634.65
NaCA C:Gln5634.32
NaO C:Hoh43033.84
NaO C:Hoh44112.72
NaO C:Hoh47572.42

interactive model:


Sodium binding site 12 out of 16 in 3vd9


Sodium binding site 12 out of 16 in 3vd9
Click to enlarge
stereopicture of Sodium binding site 12 out of 16 in 3vd9
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Sodium in the PDB 3vd9. 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: Phe931, C: Pro932, C: Ser933, C: Leu967, C: Met968, C: Glu969, C: Thr970, C: Ser971, C: Hoh4228, C: Hoh4521, C: Hoh4640,

conact list:


AtomAtomDistance (A)
NaCE2 C:Phe9313.95
NaCD1 C:Phe9314.30
NaCD2 C:Phe9314.54
NaCZ C:Phe9313.49
NaC C:Phe9315.00
NaCE1 C:Phe9313.68
NaCG C:Phe9314.70
NaO C:Pro9322.61
NaN C:Pro9324.25
NaCB C:Pro9324.18
NaCD C:Pro9324.22
NaC C:Pro9323.64
NaCG C:Pro9324.65
NaCA C:Pro9324.25
NaN C:Ser9334.68
NaO C:Leu9672.55
NaC C:Leu9673.71
NaCA C:Leu9674.94
NaO C:Met9683.81
NaN C:Met9684.28
NaC C:Met9683.92
NaCA C:Met9683.87
NaN C:Glu9694.67
NaO C:Thr9702.69
NaN C:Thr9704.33
NaC C:Thr9703.75
NaCA C:Thr9704.65
NaN C:Ser9714.57
NaCA C:Ser9714.51
NaO C:Hoh42282.91
NaO C:Hoh45213.61
NaO C:Hoh46402.85

interactive model:


Sodium binding site 13 out of 16 in 3vd9


Sodium binding site 13 out of 16 in 3vd9
Click to enlarge
stereopicture of Sodium binding site 13 out of 16 in 3vd9
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Sodium in the PDB 3vd9. 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: Ser647, C: Asp648, C: Asn649, C: Glu650, C: Leu651, C: Leu670, C: Hoh4858, C: Hoh5085,

conact list:


AtomAtomDistance (A)
NaO C:Ser6472.86
NaOG C:Ser6474.72
NaC C:Ser6473.90
NaO C:Asp6484.30
NaN C:Asp6484.36
NaC C:Asp6483.79
NaCA C:Asp6483.99
NaN C:Asn6493.73
NaC C:Asn6494.20
NaCA C:Asn6494.25
NaO C:Glu6502.72
NaN C:Glu6503.18
NaOE1 C:Glu6504.87
NaCB C:Glu6504.33
NaC C:Glu6503.55
NaCA C:Glu6503.82
NaN C:Leu6514.73
NaO C:Leu6702.94
NaN C:Leu6704.20
NaCB C:Leu6704.83
NaC C:Leu6704.07
NaCA C:Leu6704.60
NaO C:Hoh48583.04
NaO C:Hoh50852.90

interactive model:


Sodium binding site 14 out of 16 in 3vd9


Sodium binding site 14 out of 16 in 3vd9
Click to enlarge
stereopicture of Sodium binding site 14 out of 16 in 3vd9
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 14 of Sodium in the PDB 3vd9. 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: D: Tyr100, D: Asp201, D: His540, D: Trp568, D: Phe601, D: Cys602, D: Asn604, D: Ipt2001, D: Hoh4081, D: Hoh4177,

conact list:


AtomAtomDistance (A)
NaCZ D:Tyr1004.69
NaOH D:Tyr1003.57
NaO D:Asp2014.49
NaCB D:Asp2014.47
NaOD2 D:Asp2012.40
NaOD1 D:Asp2013.59
NaCG D:Asp2013.25
NaNE2 D:His5404.79
NaCZ2 D:Trp5684.84
NaCE2 D:Trp5684.80
NaNE1 D:Trp5684.05
NaO D:Phe6012.38
NaCB D:Phe6014.66
NaC D:Phe6013.52
NaCA D:Phe6014.60
NaO D:Cys6024.89
NaN D:Cys6024.24
NaC D:Cys6024.56
NaCA D:Cys6024.12
NaCB D:Asn6044.73
NaND2 D:Asn6043.75
NaOD1 D:Asn6042.37
NaCG D:Asn6043.39
NaC6 D:Ipt20013.31
NaC5 D:Ipt20014.41
NaC4 D:Ipt20014.42
NaO4 D:Ipt20014.11
NaO6 D:Ipt20012.51
NaO D:Hoh40814.11
NaO D:Hoh41772.33

interactive model:


Sodium binding site 15 out of 16 in 3vd9


Sodium binding site 15 out of 16 in 3vd9
Click to enlarge
stereopicture of Sodium binding site 15 out of 16 in 3vd9
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 15 of Sodium in the PDB 3vd9. 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: D: Leu350, D: Phe556, D: Arg557, D: Tyr559, D: Pro560, D: Arg561, D: Leu562, D: Gln563, D: Hoh4295, D: Hoh4390, D: Hoh4519, D: Hoh4589, D: Hoh4844,

conact list:


AtomAtomDistance (A)
NaCD1 D:Leu3504.63
NaO D:Phe5562.36
NaCB D:Phe5564.83
NaC D:Phe5563.52
NaCA D:Phe5564.24
NaO D:Arg5574.77
NaN D:Arg5574.56
NaC D:Arg5574.79
NaCA D:Arg5574.70
NaO D:Tyr5592.56
NaN D:Tyr5594.67
NaC D:Tyr5593.55
NaCA D:Tyr5594.68
NaO D:Pro5603.28
NaN D:Pro5604.12
NaC D:Pro5603.72
NaCA D:Pro5603.83
NaN D:Arg5614.67
NaC D:Arg5614.98
NaO D:Leu5622.38
NaN D:Leu5624.16
NaCB D:Leu5624.55
NaC D:Leu5623.41
NaCA D:Leu5624.24
NaN D:Gln5634.29
NaCG D:Gln5634.68
NaCA D:Gln5634.33
NaO D:Hoh42953.86
NaO D:Hoh43902.43
NaO D:Hoh45192.43
NaO D:Hoh45893.71
NaO D:Hoh48444.81

interactive model:


Sodium binding site 16 out of 16 in 3vd9


Sodium binding site 16 out of 16 in 3vd9
Click to enlarge
stereopicture of Sodium binding site 16 out of 16 in 3vd9
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 16 of Sodium in the PDB 3vd9. 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: D: Phe931, D: Pro932, D: Ser933, D: Leu967, D: Met968, D: Glu969, D: Thr970, D: Ser971, D: Hoh4474, D: Hoh4563, D: Hoh4663,

conact list:


AtomAtomDistance (A)
NaCE2 D:Phe9314.02
NaCD1 D:Phe9314.36
NaCD2 D:Phe9314.58
NaCZ D:Phe9313.57
NaC D:Phe9314.99
NaCE1 D:Phe9313.76
NaCG D:Phe9314.75
NaO D:Pro9322.66
NaN D:Pro9324.25
NaCB D:Pro9324.12
NaCD D:Pro9324.22
NaC D:Pro9323.62
NaCG D:Pro9324.65
NaCA D:Pro9324.23
NaN D:Ser9334.63
NaCA D:Ser9334.95
NaO D:Leu9672.52
NaC D:Leu9673.67
NaCA D:Leu9674.90
NaO D:Met9683.82
NaN D:Met9684.24
NaC D:Met9683.89
NaCA D:Met9683.82
NaN D:Glu9694.63
NaC D:Glu9694.99
NaO D:Thr9702.68
NaN D:Thr9704.16
NaC D:Thr9703.71
NaCA D:Thr9704.53
NaN D:Ser9714.57
NaCA D:Ser9714.60
NaO D:Hoh44743.41
NaO D:Hoh45632.22
NaO D:Hoh46632.88

interactive model:




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