Nickel in PDB 7zkk: A216H Variant of the Codh/Acs Complex of C. Hydrogenoformans

All present enzymatic activity of A216H Variant of the Codh/Acs Complex of C. Hydrogenoformans:
1.2.7.4; 2.3.1.169;

The structure of A216H Variant of the Codh/Acs Complex of C. Hydrogenoformans, PDB code: 7zkk 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)	45.12 / 1.97
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	142.63, 142.63, 291.34, 90, 90, 120
R / Rfree (%)	15.8 / 19.2

The structure of A216H Variant of the Codh/Acs Complex of C. Hydrogenoformans also contains other interesting chemical elements:

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

The binding sites of Nickel atom in the A216H Variant of the Codh/Acs Complex of C. Hydrogenoformans (pdb code 7zkk). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the A216H Variant of the Codh/Acs Complex of C. Hydrogenoformans, PDB code: 7zkk:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the A216H 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 A216H Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni701 b:62.1 occ:0.35 NI A:RQM701 0.0 62.1 0.3 SG A:CYS546 2.1 55.5 0.7 O A:OH704 2.2 55.5 1.0 S4 A:RQM701 2.3 43.8 0.7 S1 A:RQM701 2.3 41.9 0.8 FE3 A:RQM701 2.7 37.9 0.6 FE2 A:RQM701 2.8 53.9 0.9 O A:OH705 3.4 56.8 1.0 FE1 A:RQM701 3.4 38.0 0.6 CB A:CYS546 3.4 44.4 0.3 CB A:CYS546 3.5 43.9 0.7 S3 A:RQM701 3.7 46.8 0.8 FE4 A:RQM701 3.8 42.1 0.9 SG A:CYS546 3.9 51.0 0.3 O A:HOH1002 4.3 26.4 1.0 SG A:CYS316 4.3 41.6 1.0 S2 A:RQM701 4.5 53.1 0.9 NZ A:LYS583 4.5 50.5 1.0 SG A:CYS467 4.6 35.5 1.0 CA A:GLY466 4.7 32.8 1.0 CA A:CYS546 4.7 36.2 0.3 CA A:CYS546 4.8 36.0 0.7 OG A:SER581 4.8 34.5 1.0 C A:GLY466 4.8 36.6 1.0 NE2 A:HIS282 4.8 51.1 1.0

Nickel binding site 2 out of 3 in the A216H 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 A216H Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni801 b:27.2 occ:1.00 N B:CYS600 1.9 27.6 1.0 N B:GLY599 2.0 30.2 1.0 SG B:CYS598 2.2 29.5 1.0 SG B:CYS600 2.3 29.6 1.0 C B:GLY599 2.8 24.7 1.0 NI B:NI803 2.8 34.3 1.0 CA B:GLY599 2.8 23.5 1.0 CA B:CYS600 2.9 28.5 1.0 CB B:CYS600 3.0 27.7 1.0 CB B:CYS598 3.1 27.2 1.0 C B:CYS598 3.1 30.1 1.0 CA B:CYS598 3.4 25.8 1.0 C B:CYS600 3.6 26.6 1.0 N B:CYS598 3.7 26.6 1.0 N B:PHE601 3.7 20.8 1.0 O B:ACT804 3.8 37.1 1.0 CD1 B:LEU530 3.9 26.3 1.0 OXT B:ACT804 3.9 32.6 1.0 O B:GLY599 3.9 28.6 1.0 O B:CYS598 4.2 29.9 1.0 C B:ACT804 4.2 33.2 1.0 O B:CYS600 4.6 23.7 1.0 CD1 B:PHE232 4.7 33.2 1.0 S3 B:SF4802 4.8 28.4 1.0 C B:SER597 4.9 26.7 1.0 CE1 B:PHE232 4.9 34.5 1.0 CA B:PHE601 4.9 25.6 1.0 CD2 B:PHE601 4.9 28.0 1.0

Nickel binding site 3 out of 3 in the A216H 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 A216H Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni803 b:34.3 occ:1.00 OXT B:ACT804 2.1 32.6 1.0 O B:ACT804 2.1 37.1 1.0 SG B:CYS512 2.4 29.4 1.0 SG B:CYS598 2.5 29.5 1.0 SG B:CYS600 2.5 29.6 1.0 C B:ACT804 2.5 33.2 1.0 NI B:NI801 2.8 27.2 1.0 CB B:CYS512 3.2 25.7 1.0 CB B:CYS598 3.4 27.2 1.0 CB B:CYS600 3.4 27.7 1.0 FE1 B:SF4802 3.8 28.9 1.0 CH3 B:ACT804 4.0 31.5 1.0 N B:CYS600 4.0 27.6 1.0 N B:GLY599 4.3 30.2 1.0 S3 B:SF4802 4.3 28.4 1.0 CD1 B:ILE149 4.4 54.7 1.0 CA B:CYS600 4.4 28.5 1.0 CA B:CYS512 4.5 29.5 1.0 CG1 B:VAL152 4.5 30.0 1.0 CA B:CYS598 4.6 25.8 1.0 C B:CYS598 4.9 30.1 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 Catalysis 2022.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.2C02221