Chemical elements
  Sodium
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      1o68
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    PDB 4ecn-4g8t
    PDB 4gdt-8icw
    PDB 8icx-9icy

Sodium in the structure of Deletion Mutant (Delta 141) of Molybdopterin Synthase (pdb 1nvj)






The binding sites of Sodium atom in the structure of Deletion Mutant (Delta 141) of Molybdopterin Synthase (pdb code 1nvj). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 1nvj structure was solved by M.J.RUDOLPH, M.M.WUEBBENS, O.TURQUE, K.V.RAJAGOPALAN, H.SCHINDELIN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)47.1-2.1
Space groupC2221
a (A)104.128
b (A)127.832
c (A)138.118
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)17.7
Rfree (%)22.7


Sodium Binding Sites:

Sodium binding site 1 out of 4 in 1nvj


Sodium binding site 1 out of 4 in 1nvj
Click to enlarge
stereopicture of Sodium binding site 1 out of 4 in 1nvj
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1nvj. 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: Ala23, A: Glu24, A: Asp26, B: Lys37, B: Gly91, B: Asp92, B: Glu93, A: Hoh161, A: Hoh166, A: Hoh169, A: Hoh175, A: Hoh176, B: Hoh169, B: Hoh188,

conact list:


AtomAtomDistance (A)
NaO A:Ala234.17
NaO A:Glu244.51
NaOD1 A:Asp264.29
NaCE B:Lys373.76
NaCD B:Lys374.72
NaCG B:Lys374.92
NaNZ B:Lys374.13
NaO B:Gly912.40
NaC B:Gly913.42
NaCA B:Gly913.99
NaN B:Asp924.47
NaCA B:Asp924.81
NaOE2 B:Glu934.96
NaCG B:Glu934.72
NaO A:Hoh1612.45
NaO A:Hoh1664.70
NaO A:Hoh1694.85
NaO A:Hoh1752.64
NaO A:Hoh1762.41
NaO B:Hoh1692.41
NaO B:Hoh1884.38

interactive model:


Sodium binding site 2 out of 4 in 1nvj


Sodium binding site 2 out of 4 in 1nvj
Click to enlarge
stereopicture of Sodium binding site 2 out of 4 in 1nvj
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1nvj. 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: Ala23, C: Glu24, C: Asp26, D: Lys37, D: Gly91, D: Asp92, D: Glu93, D: Na142, C: Hoh143, C: Hoh144, C: Hoh158, C: Hoh160, C: Hoh166, C: Hoh167, D: Hoh154, D: Hoh156, D: Hoh158, D: Hoh171, D: Hoh217,

conact list:


AtomAtomDistance (A)
NaO C:Ala233.93
NaO C:Glu244.51
NaOD1 C:Asp264.54
NaCE D:Lys373.74
NaCD D:Lys374.69
NaNZ D:Lys374.17
NaO D:Gly912.44
NaC D:Gly913.44
NaCA D:Gly913.92
NaN D:Asp924.52
NaCA D:Asp924.84
NaOE2 D:Glu934.38
NaCD D:Glu934.79
NaCG D:Glu934.50
NaNA D:Na1423.29
NaO C:Hoh1432.38
NaO C:Hoh1442.48
NaO C:Hoh1582.67
NaO C:Hoh1604.35
NaO C:Hoh1664.18
NaO C:Hoh1674.57
NaO D:Hoh1544.75
NaO D:Hoh1562.53
NaO D:Hoh1582.50
NaO D:Hoh1714.69
NaO D:Hoh2174.77

interactive model:


Sodium binding site 3 out of 4 in 1nvj


Sodium binding site 3 out of 4 in 1nvj
Click to enlarge
stereopicture of Sodium binding site 3 out of 4 in 1nvj
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1nvj. 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: Gly91, D: Na141, C: Hoh143, C: Hoh158, C: Hoh160, C: Hoh166, C: Hoh167, C: Hoh177, C: Hoh186, D: Hoh154, D: Hoh156, D: Hoh158, D: Hoh171, D: Hoh177, D: Hoh199, D: Hoh211, D: Hoh217,

conact list:


AtomAtomDistance (A)
NaO D:Gly914.83
NaNA D:Na1413.29
NaO C:Hoh1434.86
NaO C:Hoh1582.58
NaO C:Hoh1604.51
NaO C:Hoh1664.07
NaO C:Hoh1674.69
NaO C:Hoh1772.40
NaO C:Hoh1864.42
NaO D:Hoh1544.41
NaO D:Hoh1562.51
NaO D:Hoh1582.55
NaO D:Hoh1714.79
NaO D:Hoh1774.24
NaO D:Hoh1992.41
NaO D:Hoh2113.82
NaO D:Hoh2174.71

interactive model:


Sodium binding site 4 out of 4 in 1nvj


Sodium binding site 4 out of 4 in 1nvj
Click to enlarge
stereopicture of Sodium binding site 4 out of 4 in 1nvj
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 1nvj. 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: E: Ala23, E: Glu24, E: Asp26, F: Lys37, F: Gly91, F: Asp92, A: Hoh193, E: Hoh154, E: Hoh155, E: Hoh161, F: Hoh168, F: Hoh173, F: Hoh183,

conact list:


AtomAtomDistance (A)
NaO E:Ala234.20
NaO E:Glu244.34
NaOD1 E:Asp264.17
NaCE F:Lys373.84
NaCD F:Lys374.94
NaNZ F:Lys374.47
NaO F:Gly912.49
NaC F:Gly913.33
NaCA F:Gly913.64
NaN F:Asp924.46
NaCA F:Asp924.91
NaO A:Hoh1932.68
NaO E:Hoh1542.34
NaO E:Hoh1554.96
NaO E:Hoh1614.44
NaO F:Hoh1682.39
NaO F:Hoh1734.35
NaO F:Hoh1832.48

interactive model:




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