Nickel in PDB 6vx0: Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Hour Air Exposure)

All present enzymatic activity of Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Hour Air Exposure):
1.2.7.4;

The structure of Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Hour Air Exposure), PDB code: 6vx0 was solved by E.C.Wittenborn, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	97.71 / 2.21
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.730, 112.000, 195.420, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 20.3

The structure of Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Hour Air Exposure) also contains other interesting chemical elements:

Iron

(Fe)

16 atoms

The binding sites of Nickel atom in the Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Hour Air Exposure) (pdb code 6vx0). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Hour Air Exposure), PDB code: 6vx0:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Hour Air Exposure)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Hour Air Exposure) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni702 b:61.2 occ:1.00 NI A:CUV702 0.0 61.2 1.0 NE2 A:HIS266 2.0 47.4 1.0 FE2 A:CUV702 2.3 55.0 1.0 NZ A:LYS556 2.5 40.2 1.0 SG A:CYS302 2.7 36.1 1.0 CD2 A:HIS266 2.7 43.2 1.0 SG A:CYS519 2.8 36.1 0.5 CE1 A:HIS266 3.1 39.7 1.0 FE1 A:CUV702 3.2 56.3 1.0 SG A:CYS519 3.4 37.9 0.5 S4 A:CUV702 3.6 58.1 1.0 CB A:CYS519 3.6 30.7 0.5 CB A:CYS519 3.6 30.7 0.5 CB A:CYS302 3.7 33.6 1.0 CE A:LYS556 4.0 39.8 1.0 CG A:HIS266 4.0 40.0 1.0 ND1 A:HIS266 4.1 37.9 1.0 S3 A:CUV702 4.5 54.3 1.0 SG A:CYS301 4.6 31.0 0.5 SG A:CYS340 4.7 42.0 1.0 FE3 A:CUV702 4.7 59.9 1.0 FE4 A:CUV702 4.7 51.9 1.0 N A:CYS519 4.8 27.9 0.5 CD A:LYS556 4.8 30.8 1.0 N A:CYS519 4.8 27.9 0.5 CA A:CYS519 4.8 29.2 0.5 CA A:CYS519 4.9 29.2 0.5 CA A:CYS302 5.0 33.6 1.0 OE1 A:GLN339 5.0 44.2 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Hour Air Exposure)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Hour Air Exposure) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni702 b:58.3 occ:1.00 NI B:CUV702 0.0 58.3 1.0 NE2 B:HIS266 2.0 40.4 1.0 FE2 B:CUV702 2.4 53.6 1.0 NZ B:LYS556 2.5 36.1 1.0 SG B:CYS519 2.7 32.6 0.5 CD2 B:HIS266 2.7 33.3 1.0 SG B:CYS302 2.8 30.6 1.0 CE1 B:HIS266 3.2 35.0 1.0 SG B:CYS519 3.3 42.4 0.5 CB B:CYS519 3.5 31.0 0.5 FE1 B:CUV702 3.5 56.4 1.0 CB B:CYS519 3.5 31.0 0.5 S4 B:CUV702 3.7 54.9 1.0 CB B:CYS302 3.9 29.6 1.0 O B:HOH1004 3.9 37.4 1.0 CG B:HIS266 3.9 30.3 1.0 CE B:LYS556 4.0 32.1 1.0 ND1 B:HIS266 4.1 28.0 1.0 S3 B:CUV702 4.5 53.1 1.0 SG B:CYS340 4.7 35.6 1.0 CA B:CYS519 4.7 29.9 0.5 SG B:CYS301 4.8 30.2 0.5 FE3 B:CUV702 4.8 53.9 1.0 CA B:CYS519 4.8 29.9 0.5 N B:CYS519 4.8 29.0 0.5 N B:CYS519 4.8 29.0 0.5 CD B:LYS556 4.8 31.9 1.0 FE4 B:CUV702 4.8 51.6 1.0 OE1 B:GLN339 4.8 39.6 1.0

E.C.Wittenborn, C.Guendon, M.Merrouch, M.Benvenuti, V.Fourmond, C.Leger, C.L.Drennan, S.Dementin. The Solvent-Exposed Fe-S D-Cluster Contributes to Oxygen-Resistance Indesulfovibrio Vulgarisni-Fe Carbon Monoxide Dehydrogenase. Acs Catalysis V. 10 7328 2020.
ISSN: ESSN 2155-5435
PubMed: 32655979
DOI: 10.1021/ACSCATAL.0C00934