Nickel in PDB 7zy1: I567A Mutant of Recombinant Codh-II

All present enzymatic activity of I567A Mutant of Recombinant Codh-II:
1.2.7.4;

The structure of I567A Mutant of Recombinant Codh-II, PDB code: 7zy1 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)	34.24 / 1.43
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	111.669, 75.809, 71.5, 90, 111.11, 90
R / Rfree (%)	12.9 / 14.4

The structure of I567A Mutant of Recombinant Codh-II also contains other interesting chemical elements:

Iron

(Fe)

11 atoms

The binding sites of Nickel atom in the I567A Mutant of Recombinant Codh-II (pdb code 7zy1). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the I567A Mutant of Recombinant Codh-II, PDB code: 7zy1:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the I567A 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 I567A Mutant of Recombinant Codh-II within 5.0Å range: probe atom residue distance (Å) B Occ X:Ni703 b:18.4 occ:0.25 NI X:WCC703 0.0 18.4 0.2 NI X:WCC703 1.0 11.7 0.2 SG X:CYS526 2.1 15.7 0.7 S4 X:WCC703 2.2 13.5 0.7 O X:HOH911 2.2 14.8 0.7 S1 X:WCC703 2.4 14.9 0.8 FE X:FE2704 2.4 21.9 0.3 HB2 X:CYS526 2.6 32.0 0.3 FE X:FE2704 2.8 12.5 0.5 FE3 X:WCC703 2.9 13.3 0.7 FE1 X:WCC703 3.2 13.9 0.7 O X:HOH1431 3.3 36.7 1.0 CB X:CYS526 3.3 12.1 0.7 CB X:CYS526 3.3 26.8 0.3 SG X:CYS526 3.4 21.8 0.3 HB3 X:CYS526 3.5 14.3 0.7 HB2 X:CYS526 3.5 14.3 0.7 FE4 X:WCC703 3.5 14.5 0.8 HZ2 X:LYS563 3.5 18.6 1.0 HB3 X:CYS526 3.6 32.0 0.3 S3 X:WCC703 3.7 19.1 1.0 HG X:CYS295 3.8 15.5 0.6 HA2 X:GLY445 3.9 15.9 1.0 SG X:CYS295 4.2 12.8 0.6 NZ X:LYS563 4.3 15.8 1.0 HZ1 X:LYS563 4.4 18.6 1.0 SG X:CYS295 4.4 14.1 0.4 HA3 X:GLY475 4.5 14.2 1.0 HE3 X:LYS563 4.5 16.6 1.0 NE2 X:HIS261 4.5 16.6 1.0 S2 X:WCC703 4.5 16.5 0.9 H X:CYS476 4.5 15.4 1.0 HG X:CYS526 4.5 26.1 0.3 O X:HOH1063 4.6 15.1 1.0 CA X:CYS526 4.6 25.6 0.3 CA X:CYS526 4.7 10.9 0.7 HD2 X:LYS563 4.7 15.9 1.0 HB2 X:LYS563 4.7 14.6 1.0 HA X:CYS526 4.7 30.2 0.3 HA X:CYS526 4.8 12.7 0.7 H X:CYS526 4.8 15.2 0.7 H X:CYS526 4.8 15.2 0.3 SG X:CYS446 4.8 14.3 1.0 CA X:GLY445 4.8 13.2 1.0 HB3 X:LYS563 4.9 14.6 1.0 O X:HOH815 4.9 18.6 0.9 CE X:LYS563 4.9 14.0 1.0 H X:GLY445 4.9 15.6 1.0 HZ3 X:LYS563 4.9 18.6 1.0 SG X:CYS333 5.0 14.1 1.0

Nickel binding site 2 out of 2 in the I567A 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 2 of I567A Mutant of Recombinant Codh-II within 5.0Å range: probe atom residue distance (Å) B Occ X:Ni703 b:11.7 occ:0.22 NI X:WCC703 0.0 11.7 0.2 NI X:WCC703 1.0 18.4 0.2 SG X:CYS526 2.2 15.7 0.7 S1 X:WCC703 2.3 14.9 0.8 O X:HOH1431 2.5 36.7 1.0 S4 X:WCC703 2.5 13.5 0.7 HB2 X:CYS526 2.9 32.0 0.3 FE3 X:WCC703 2.9 13.3 0.7 HA2 X:GLY445 3.0 15.9 1.0 O X:HOH911 3.0 14.8 0.7 SG X:CYS526 3.1 21.8 0.3 FE X:FE2704 3.3 21.9 0.3 HB3 X:CYS526 3.4 14.3 0.7 CB X:CYS526 3.5 12.1 0.7 CB X:CYS526 3.5 26.8 0.3 FE X:FE2704 3.8 12.5 0.5 HB2 X:CYS526 3.9 14.3 0.7 CA X:GLY445 3.9 13.2 1.0 FE1 X:WCC703 4.0 13.9 0.7 HB3 X:CYS526 4.0 32.0 0.3 O X:HOH1063 4.0 15.1 1.0 FE4 X:WCC703 4.0 14.5 0.8 H X:GLY445 4.1 15.6 1.0 HZ2 X:LYS563 4.3 18.6 1.0 HG X:CYS526 4.3 26.1 0.3 HB2 X:ALA564 4.3 16.8 1.0 C X:GLY445 4.4 13.9 1.0 SG X:CYS446 4.4 14.3 1.0 HA3 X:GLY475 4.4 14.2 1.0 H X:CYS476 4.5 15.4 1.0 N X:GLY445 4.5 13.0 1.0 HA3 X:GLY445 4.5 15.9 1.0 S3 X:WCC703 4.6 19.1 1.0 HG X:CYS295 4.6 15.5 0.6 HA X:CYS526 4.6 30.2 0.3 HB2 X:LYS563 4.6 14.6 1.0 HA X:CYS526 4.6 12.7 0.7 HB3 X:LYS563 4.7 14.6 1.0 CA X:CYS526 4.7 25.6 0.3 CA X:CYS526 4.7 10.9 0.7 N X:CYS446 4.7 14.0 1.0 HE3 X:LYS563 4.8 16.6 1.0 O X:GLY445 4.9 17.0 1.0 S2 X:WCC703 4.9 16.5 0.9 H X:CYS446 4.9 16.5 1.0 HB3 X:HIS561 5.0 12.2 1.0 HA X:CYS446 5.0 16.6 1.0 SG X:CYS295 5.0 12.8 0.6 HA X:ALA564 5.0 14.9 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