Nickel in PDB 3i39: Ni,Fe-Codh-320 Mv+Cn State

All present enzymatic activity of Ni,Fe-Codh-320 Mv+Cn State:
1.2.99.2;

The structure of Ni,Fe-Codh-320 Mv+Cn State, PDB code: 3i39 was solved by J.-H.Jeoung, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.60 / 1.36
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	111.279, 75.834, 71.099, 90.00, 111.33, 90.00
R / Rfree (%)	15.4 / 19

The structure of Ni,Fe-Codh-320 Mv+Cn State also contains other interesting chemical elements:

Iron

(Fe)

11 atoms

The binding sites of Nickel atom in the Ni,Fe-Codh-320 Mv+Cn State (pdb code 3i39). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Ni,Fe-Codh-320 Mv+Cn State, PDB code: 3i39:

Nickel binding site 1 out of 1 in the Ni,Fe-Codh-320 Mv+Cn State


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Ni,Fe-Codh-320 Mv+Cn State within 5.0Å range: probe atom residue distance (Å) B Occ X:Ni5002 b:13.8 occ:0.72 NI X:WCC5002 0.0 13.8 0.7 C X:CYN5005 1.8 14.2 0.7 SG X:CYS526 2.1 12.4 1.0 S3 X:WCC5002 2.2 13.2 0.8 S1 X:WCC5002 2.3 11.6 0.8 FE X:FE25003 2.6 16.8 0.7 FE4 X:WCC5002 2.8 11.3 0.8 N X:CYN5005 2.9 13.4 0.7 FE X:FE25004 3.0 25.4 0.1 CB X:CYS526 3.3 10.7 1.0 FE1 X:WCC5002 3.4 10.9 0.8 FE3 X:WCC5002 3.7 13.1 0.8 S4 X:WCC5002 3.8 13.2 0.8 NE2 X:HIS261 4.1 17.4 1.0 SG X:CYS295 4.3 8.5 0.3 NZ X:LYS563 4.4 11.3 1.0 O X:HOH724 4.5 9.3 1.0 SG X:CYS295 4.6 12.3 0.7 CA X:GLY445 4.6 10.0 1.0 CA X:CYS526 4.6 9.7 1.0 S2 X:WCC5002 4.6 11.4 0.8 SG X:CYS446 4.6 11.1 1.0 C X:GLY445 4.9 9.8 1.0 CE1 X:HIS261 4.9 12.7 1.0 CD2 X:HIS261 5.0 16.5 1.0

J.H.Jeoung, H.Dobbek. Structural Basis of Cyanide Inhibition of Ni, Fe-Containing Carbon Monoxide Dehydrogenase J.Am.Chem.Soc. V. 131 9922 2009.
ISSN: ISSN 0002-7863
PubMed: 19583208
DOI: 10.1021/JA9046476