Nickel in PDB 8omx: Ni,Fe-Codh -600MV State : 1 Min Dioxygen Exposure

All present enzymatic activity of Ni,Fe-Codh -600MV State : 1 Min Dioxygen Exposure:
1.2.7.4;

The structure of Ni,Fe-Codh -600MV State : 1 Min Dioxygen Exposure, PDB code: 8omx was solved by Y.Basak, J.-H.Jeoung, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.82 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.74, 75.501, 71.503, 90, 111.77, 90
R / Rfree (%)	15.5 / 19.3

The structure of Ni,Fe-Codh -600MV State : 1 Min Dioxygen Exposure also contains other interesting chemical elements:

Iron

(Fe)

11 atoms

The binding sites of Nickel atom in the Ni,Fe-Codh -600MV State : 1 Min Dioxygen Exposure (pdb code 8omx). 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 -600MV State : 1 Min Dioxygen Exposure, PDB code: 8omx:

Nickel binding site 1 out of 1 in the Ni,Fe-Codh -600MV State : 1 Min Dioxygen Exposure


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 -600MV State : 1 Min Dioxygen Exposure within 5.0Å range: probe atom residue distance (Å) B Occ X:Ni1003 b:23.1 occ:0.55 NI1 X:NFS1003 0.0 23.1 0.6 O X:HOH1524 2.1 22.1 0.3 O X:HOH1568 2.2 23.6 0.3 S5 X:NFS1003 2.2 21.7 0.7 SG X:CYS526 2.2 18.9 0.7 S3 X:NFS1003 2.3 22.4 0.7 FE X:FE21004 2.3 23.1 0.3 S2 X:NFS1003 2.4 25.5 0.6 FE X:FE21004 2.8 21.9 0.6 HB2 X:CYS526 2.8 21.2 0.3 FE3 X:NFS1003 2.9 20.9 0.7 SG X:CYS526 3.0 23.1 0.3 CB X:CYS526 3.3 17.0 0.7 FE2 X:NFS1003 3.3 20.3 0.6 CB X:CYS526 3.3 17.3 0.3 HB3 X:CYS526 3.4 20.9 0.7 HB2 X:CYS526 3.5 20.9 0.7 FE4 X:NFS1003 3.6 20.9 0.6 HZ2 X:LYS563 3.6 25.9 1.0 HB3 X:CYS526 3.8 21.2 0.3 S1 X:NFS1003 3.8 21.9 0.8 HG X:CYS526 3.8 28.5 0.3 HA2 X:GLY445 3.9 18.0 1.0 NE2 X:HIS261 4.2 26.0 1.0 SG X:CYS295 4.4 18.5 0.6 HE2 X:HIS93 4.4 23.3 1.0 NZ X:LYS563 4.4 21.5 1.0 HZ1 X:LYS563 4.4 25.9 1.0 HA3 X:GLY475 4.5 21.1 1.0 S4 X:NFS1003 4.5 21.3 0.7 HE3 X:LYS563 4.6 27.1 1.0 O X:HOH1267 4.6 18.2 1.0 H X:CYS476 4.6 21.8 1.0 SG X:CYS295 4.6 19.4 0.4 CA X:CYS526 4.6 16.9 0.3 HB2 X:LYS563 4.6 20.1 1.0 CA X:CYS526 4.7 16.9 0.7 HA X:CYS526 4.7 20.5 0.3 SG X:CYS446 4.7 18.2 1.0 CA X:GLY445 4.7 15.2 1.0 HA X:CYS526 4.8 20.5 0.7 HB3 X:LYS563 4.8 20.1 1.0 HB2 X:ALA564 4.8 22.0 1.0 H X:GLY445 4.8 18.1 1.0 C X:GLY445 4.9 18.2 1.0 H X:CYS526 4.9 18.2 0.7 H X:CYS526 4.9 18.2 0.3 HD12 X:ILE567 5.0 26.5 1.0 HD2 X:LYS563 5.0 21.4 1.0

Y.Basak, J.H.Jeoung, L.Domnik, H.Dobbek. Stepwise O 2 -Induced Rearrangement and Disassembly of the [Nife 4 (Oh)( Mu 3 -S) 4 ] Active Site Cluster of Co Dehydrogenase. Angew.Chem.Int.Ed.Engl. V. 62 05341 2023.
ISSN: ESSN 1521-3773
PubMed: 37279092
DOI: 10.1002/ANIE.202305341