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Nickel in the structure of Ni,Fe-Codh With N-Butylisocyanate State (pdb 2yiv)

The binding sites of Nickel atom in the structure of Ni,Fe-Codh With N-Butylisocyanate State (pdb code 2yiv). This binding sites where shown with 5.0 Angstroms radius around Nickel atom.
The 2yiv structure was solved by J.H.JEOUNG, H.DOBBEK, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)18.9-1.3
Space groupC121
a (A)112.700
b (A)75.240
c (A)71.220
alpha (°)90.00
beta (°)111.38
gamma (°)90.00
Rfactor (%)11.23
Rfree (%)14.33

Nickel Binding Sites:

Nickel binding site 1 out of 1 in 2yiv

Nickel binding site 1 out of 1 in 2yiv
Click to enlarge
stereopicture of Nickel binding site 1 out of 1 in 2yiv
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Nickel in the PDB 2yiv. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Nickel atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: X: His93, X: His261, X: Cys295, X: Gly445, X: Cys446, X: Gly475, X: Cys476, X: Cys526, X: Lys563, X: Ala564, X: Ile567, X: Wcc5002, X: Yiv5003, X: Fe5004, X: Hoh2691, X: Hoh5100,

conact list:

AtomAtomDistance (A)
NiHE2 X:His934.72
NiNE2 X:His2614.94
NiSG X:Cys2954.36
NiSG X:Cys2954.51
NiHA2 X:Gly4453.60
NiH X:Gly4454.75
NiC X:Gly4454.86
NiCA X:Gly4454.52
NiSG X:Cys4464.60
NiHA3 X:Gly4754.38
NiH X:Cys4764.52
NiHB2 X:Cys5263.46
NiCB X:Cys5263.28
NiHB3 X:Cys5263.35
NiHA X:Cys5264.72
NiSG X:Cys5262.09
NiH X:Cys5264.80
NiCA X:Cys5264.62
NiHB2 X:Lys5634.69
NiHZ3 X:Lys5634.05
NiHB3 X:Lys5634.80
NiHE3 X:Lys5634.60
NiHZ2 X:Lys5634.78
NiNZ X:Lys5634.76
NiHB3 X:Ala5644.95
NiHD13 X:Ile5674.71
NiS1 X:Wcc50022.32
NiNI X:Wcc50020.00
NiFE1 X:Wcc50023.56
NiFE3 X:Wcc50023.77
NiS4 X:Wcc50023.99
NiS2 X:Wcc50024.71
NiFE4 X:Wcc50022.86
NiS3 X:Wcc50022.17
NiN X:Yiv50032.86
NiH2A X:Yiv50034.55
NiC1 X:Yiv50033.21
NiO1 X:Yiv50032.77
NiH1A X:Yiv50032.68
NiC X:Yiv50031.95
NiC2 X:Yiv50034.52
NiH1 X:Yiv50033.67
NiFE X:Fe50043.10
NiFE X:Fe50042.19
NiO X:Hoh26914.41
NiO X:Hoh51003.10

interactive model:

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