Nickel in PDB 7zx5: I567T Mutant of Recombinant Codh-II

All present enzymatic activity of I567T Mutant of Recombinant Codh-II:
1.2.7.4;

The structure of I567T Mutant of Recombinant Codh-II, PDB code: 7zx5 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)	35.42 / 1.54
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.185, 75.424, 71.236, 90, 111.03, 90
R / Rfree (%)	17.6 / 21.3

The structure of I567T Mutant of Recombinant Codh-II also contains other interesting chemical elements:

Iron

(Fe)

11 atoms

The binding sites of Nickel atom in the I567T Mutant of Recombinant Codh-II (pdb code 7zx5). 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 I567T Mutant of Recombinant Codh-II, PDB code: 7zx5:

Nickel binding site 1 out of 1 in the I567T Mutant of Recombinant Codh-II


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of I567T Mutant of Recombinant Codh-II within 5.0Å range: probe atom residue distance (Å) B Occ X:Ni703 b:22.9 occ:0.57 NI X:WCC703 0.0 22.9 0.6 S4 X:WCC703 2.1 20.2 0.7 S1 X:WCC703 2.2 19.8 0.7 SG X:CYS526 2.2 17.5 0.7 O X:HOH953 2.4 19.7 1.0 FE X:FE2704 2.4 23.0 0.3 O X:HOH1234 2.5 24.8 0.3 HB2 X:CYS526 2.7 19.7 0.3 FE3 X:WCC703 2.8 18.5 0.8 HG X:CYS526 2.8 21.9 0.3 FE X:FE2704 2.9 20.4 0.7 FE1 X:WCC703 3.4 18.0 0.7 CB X:CYS526 3.4 19.7 0.3 CB X:CYS526 3.4 19.8 0.7 SG X:CYS526 3.4 21.9 0.3 HB3 X:CYS526 3.5 19.7 0.7 HB2 X:CYS526 3.5 19.7 0.7 FE4 X:WCC703 3.6 21.2 0.9 HZ2 X:LYS563 3.6 18.8 1.0 HB3 X:CYS526 3.6 19.7 0.3 HA2 X:GLY445 3.8 13.4 1.0 S3 X:WCC703 3.8 20.8 0.9 O X:HOH1207 4.0 29.2 1.0 HG X:CYS295 4.2 20.0 0.7 NZ X:LYS563 4.4 18.8 1.0 HZ1 X:LYS563 4.4 18.8 1.0 HE2 X:HIS93 4.4 17.7 1.0 SG X:CYS295 4.4 13.1 0.3 S2 X:WCC703 4.5 20.8 0.9 NE2 X:HIS261 4.5 26.5 1.0 HA3 X:GLY475 4.5 14.9 1.0 SG X:CYS295 4.5 20.0 0.7 H X:CYS476 4.6 16.5 1.0 HE3 X:LYS563 4.6 18.2 1.0 CA X:GLY445 4.6 13.4 1.0 SG X:CYS446 4.6 17.8 1.0 HB2 X:LYS563 4.7 10.9 1.0 O X:HOH864 4.7 16.5 1.0 CA X:CYS526 4.7 14.4 0.7 CA X:CYS526 4.7 14.5 0.3 HB3 X:LYS563 4.7 10.9 1.0 HA X:CYS526 4.8 14.5 0.7 C X:GLY445 4.8 15.5 1.0 HA X:CYS526 4.8 14.5 0.3 HD2 X:LYS563 4.8 14.1 1.0 H X:GLY445 4.8 12.5 1.0 H X:CYS526 4.8 13.9 0.3 H X:CYS526 4.8 13.9 0.7 HB3 X:HIS561 5.0 10.8 1.0 HB2 X:ALA564 5.0 13.1 1.0

Y.Basak, J.H.Jeoung, L.Domnik, J.Ruickoldt, H.Dobbek. Substrate Activation at the Ni,Fe Cluster of Co Dehydrogenases: the Influence of the Protein Matrix Acs Catalysis 2022.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.2C02922