Nickel in PDB 7zkv: F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans

All present enzymatic activity of F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans:
1.2.7.4; 2.3.1.169;

The structure of F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans, PDB code: 7zkv 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)	42.38 / 2.07
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	142.64, 142.64, 291.31, 90, 90, 120
R / Rfree (%)	17.3 / 21.4

The structure of F231A Variant of the 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 F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans (pdb code 7zkv). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans, PDB code: 7zkv:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the F231A Variant of 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 F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni701 b:41.7 occ:0.41 NI A:RQM701 0.0 41.7 0.4 SG A:CYS546 2.1 43.7 0.5 O A:OH704 2.2 45.3 1.0 S4 A:RQM701 2.2 46.8 0.7 S1 A:RQM701 2.3 50.0 0.8 FE3 A:RQM701 2.7 31.8 0.5 FE2 A:RQM701 2.8 38.4 0.9 CB A:CYS546 3.3 41.1 0.5 CB A:CYS546 3.3 41.0 0.5 O A:OH705 3.4 43.4 1.0 FE1 A:RQM701 3.4 37.0 0.4 SG A:CYS546 3.5 48.5 0.5 S3 A:RQM701 3.5 48.0 0.8 FE4 A:RQM701 3.7 47.5 0.8 O A:HOH976 4.2 29.2 1.0 SG A:CYS316 4.3 37.8 1.0 SG A:CYS467 4.4 47.5 1.0 S2 A:RQM701 4.5 63.9 1.0 NZ A:LYS583 4.6 53.9 1.0 CA A:GLY466 4.7 38.5 1.0 CA A:CYS546 4.7 34.3 0.5 CA A:CYS546 4.7 34.4 0.5 NE2 A:HIS282 4.8 46.5 1.0 C A:GLY466 4.9 44.3 1.0 OG A:SER581 4.9 27.4 1.0 CE A:LYS583 4.9 47.1 1.0

Nickel binding site 2 out of 3 in the F231A Variant of 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 F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni801 b:29.6 occ:1.00 N B:CYS600 1.9 33.5 1.0 N B:GLY599 1.9 35.8 1.0 SG B:CYS598 2.2 30.8 1.0 SG B:CYS600 2.3 34.8 1.0 C B:GLY599 2.7 31.6 1.0 CA B:GLY599 2.8 30.3 1.0 NI B:NI803 2.8 35.7 1.0 CA B:CYS600 2.9 33.5 1.0 C B:CYS598 3.0 34.4 1.0 CB B:CYS600 3.0 36.2 1.0 CB B:CYS598 3.1 28.0 1.0 CA B:CYS598 3.4 29.6 1.0 C B:CYS600 3.7 31.8 1.0 N B:CYS598 3.7 27.6 1.0 N B:PHE601 3.7 22.4 1.0 O B:ACT804 3.8 34.8 1.0 CD1 B:LEU530 3.9 25.2 1.0 O B:GLY599 3.9 32.1 1.0 OXT B:ACT804 4.0 33.5 1.0 O B:CYS598 4.1 29.5 1.0 C B:ACT804 4.2 32.1 1.0 CD1 B:PHE232 4.7 31.5 1.0 O B:CYS600 4.7 26.8 1.0 C B:SER597 4.8 27.6 1.0 CE1 B:PHE232 4.9 33.7 1.0 CA B:PHE601 4.9 31.0 1.0 S3 B:SF4802 4.9 32.6 1.0

Nickel binding site 3 out of 3 in the F231A Variant of 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 F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni803 b:35.7 occ:1.00 O B:ACT804 2.0 34.8 1.0 OXT B:ACT804 2.3 33.5 1.0 SG B:CYS512 2.4 36.3 1.0 SG B:CYS598 2.4 30.8 1.0 SG B:CYS600 2.4 34.8 1.0 C B:ACT804 2.5 32.1 1.0 NI B:NI801 2.8 29.6 1.0 CB B:CYS512 3.2 29.0 1.0 CB B:CYS598 3.4 28.0 1.0 CB B:CYS600 3.4 36.2 1.0 FE1 B:SF4802 3.8 33.1 1.0 CH3 B:ACT804 4.0 30.6 1.0 N B:CYS600 4.1 33.5 1.0 N B:GLY599 4.3 35.8 1.0 S3 B:SF4802 4.3 32.6 1.0 CD1 B:ILE149 4.4 48.9 1.0 CA B:CYS600 4.4 33.5 1.0 CA B:CYS512 4.5 38.6 1.0 CG1 B:VAL152 4.5 39.5 1.0 CA B:CYS598 4.6 29.6 1.0 C B:CYS598 4.9 34.4 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