Nickel in PDB 7zkj: Codh/Acs Complex of C. Hydrogenoformans

All present enzymatic activity of Codh/Acs Complex of C. Hydrogenoformans:
1.2.7.4; 2.3.1.169;

The structure of Codh/Acs Complex of C. Hydrogenoformans, PDB code: 7zkj was solved by J.Ruickoldt, J.-H.Jeoung, Y.Basak, L.Domnik, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.35 / 2.04
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	141.586, 141.586, 290.124, 90, 90, 120
R / Rfree (%)	17.4 / 19.9

The structure of Codh/Acs Complex of C. Hydrogenoformans also contains other interesting chemical elements:

Sodium	(Na)	1 atom
Iron	(Fe)	14 atoms

The binding sites of Nickel atom in the Codh/Acs Complex of C. Hydrogenoformans (pdb code 7zkj). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Codh/Acs Complex of C. Hydrogenoformans, PDB code: 7zkj:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Codh/Acs Complex of C. Hydrogenoformans


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni701 b:51.6 occ:0.34 NI A:RQM701 0.0 51.6 0.3 O A:OH704 2.1 46.3 1.0 SG A:CYS546 2.2 48.6 0.6 S4 A:RQM701 2.2 40.6 0.6 S1 A:RQM701 2.3 50.7 0.8 FE3 A:RQM701 2.7 35.5 0.5 FE2 A:RQM701 2.9 49.5 0.8 FE1 A:RQM701 3.3 38.0 0.5 CB A:CYS546 3.4 44.1 0.4 SG A:CYS546 3.5 50.8 0.4 CB A:CYS546 3.5 44.2 0.6 O A:OH705 3.6 50.4 1.0 FE4 A:RQM701 3.7 46.5 0.8 S3 A:RQM701 3.8 43.5 0.7 S2 A:RQM701 4.4 53.8 0.9 O A:HOH995 4.5 33.4 1.0 SG A:CYS316 4.5 44.3 1.0 NZ A:LYS583 4.6 55.1 1.0 SG A:CYS467 4.6 40.5 1.0 OG A:SER581 4.6 32.9 1.0 NE2 A:HIS282 4.8 47.8 1.0 CE A:LYS583 4.8 48.4 1.0 CA A:CYS546 4.8 38.8 0.6 CA A:CYS546 4.8 38.9 0.4 CA A:GLY466 4.9 39.7 1.0 CB A:LYS583 5.0 33.8 1.0

Nickel binding site 2 out of 3 in the Codh/Acs Complex of C. Hydrogenoformans


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni801 b:33.6 occ:1.00 N B:CYS600 2.0 31.1 1.0 N B:GLY599 2.0 30.9 1.0 SG B:CYS598 2.2 34.4 1.0 SG B:CYS600 2.3 34.6 1.0 C B:GLY599 2.8 30.2 1.0 NI B:NI803 2.8 40.9 1.0 CA B:GLY599 2.9 27.8 1.0 CA B:CYS600 2.9 31.8 1.0 CB B:CYS600 3.0 34.5 1.0 C B:CYS598 3.1 34.0 1.0 CB B:CYS598 3.1 31.8 1.0 CA B:CYS598 3.4 37.3 1.0 C B:CYS600 3.7 33.8 1.0 N B:CYS598 3.7 32.1 1.0 N B:PHE601 3.7 31.2 1.0 CD1 B:LEU530 3.9 28.7 1.0 OXT B:ACT804 4.0 40.0 1.0 O B:GLY599 4.0 35.2 1.0 O B:ACT804 4.1 38.2 1.0 O B:CYS598 4.2 32.6 1.0 C B:ACT804 4.3 42.3 1.0 O B:CYS600 4.6 34.0 1.0 CD1 B:PHE232 4.7 34.5 1.0 CE1 B:PHE232 4.8 39.0 1.0 C B:SER597 4.8 30.0 1.0 S3 B:SF4802 4.9 36.2 1.0 CA B:PHE601 5.0 33.1 1.0 SG B:CYS512 5.0 36.1 1.0

Nickel binding site 3 out of 3 in the Codh/Acs Complex of C. Hydrogenoformans


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni803 b:40.9 occ:1.00 OXT B:ACT804 2.3 40.0 1.0 SG B:CYS512 2.4 36.1 1.0 SG B:CYS600 2.4 34.6 1.0 SG B:CYS598 2.4 34.4 1.0 O B:ACT804 2.4 38.2 1.0 C B:ACT804 2.6 42.3 1.0 NI B:NI801 2.8 33.6 1.0 CB B:CYS512 3.2 31.0 1.0 CB B:CYS598 3.3 31.8 1.0 CB B:CYS600 3.5 34.5 1.0 FE1 B:SF4802 3.8 36.4 1.0 N B:CYS600 4.2 31.1 1.0 CH3 B:ACT804 4.2 32.8 1.0 S3 B:SF4802 4.2 36.2 1.0 N B:GLY599 4.3 30.9 1.0 CD1 B:ILE149 4.4 46.9 1.0 CA B:CYS600 4.5 31.8 1.0 CG1 B:VAL152 4.5 37.9 1.0 CA B:CYS512 4.5 36.9 1.0 CA B:CYS598 4.6 37.3 1.0 C B:CYS598 4.9 34.0 1.0

J.Ruickoldt, Y.Basak, L.Domnik, J.H.Jeoung, H.Dobbek. On the Kinetics of CO2 Reduction By Ni, Fe-Co Dehydrogenases Acs Catal. 2022.
DOI: 10.1021/ACSCATAL.2C02221