Nickel in PDB 6vx1: Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure)

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

The structure of Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day Air Exposure), PDB code: 6vx1 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)	73.45 / 2.78
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.610, 112.120, 194.430, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 21.4

The structure of Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day 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 Day Air Exposure) (pdb code 6vx1). 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 Day Air Exposure), PDB code: 6vx1:
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 Day 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 Day Air Exposure) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni702 b:76.8 occ:1.00 NI A:CUV702 0.0 76.8 1.0 NE2 A:HIS266 2.0 62.6 1.0 SG A:CYS302 2.3 58.7 1.0 FE2 A:CUV702 2.4 77.2 1.0 CD2 A:HIS266 2.7 58.5 1.0 SG A:CYS519 2.8 40.1 0.5 NZ A:LYS556 2.9 53.6 1.0 CE1 A:HIS266 3.1 57.4 1.0 SG A:CYS519 3.3 48.9 0.5 CB A:CYS519 3.3 41.4 0.5 CB A:CYS519 3.3 41.4 0.5 CB A:CYS302 3.5 49.5 1.0 FE1 A:CUV702 3.5 82.4 1.0 CG A:HIS266 3.9 51.9 1.0 S4 A:CUV702 4.0 67.5 1.0 CE A:LYS556 4.0 47.1 1.0 ND1 A:HIS266 4.1 56.9 1.0 SG A:CYS301 4.4 50.3 0.5 S3 A:CUV702 4.5 63.2 1.0 N A:CYS519 4.5 38.2 0.5 N A:CYS519 4.5 38.1 0.5 CA A:CYS519 4.6 37.1 0.5 CA A:CYS519 4.6 37.1 0.5 CA A:CYS302 4.7 48.2 1.0 FE3 A:CUV702 4.8 90.2 1.0 N A:CYS302 4.8 49.7 1.0 S1 A:CUV702 4.9 73.8 1.0 SG A:CYS340 4.9 63.5 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (2 Day 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 Day Air Exposure) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni702 b:78.2 occ:1.00 NI B:CUV702 0.0 78.2 1.0 NE2 B:HIS266 2.0 56.5 1.0 SG B:CYS302 2.3 48.3 1.0 CD2 B:HIS266 2.5 55.0 1.0 FE2 B:CUV702 2.6 78.7 1.0 NZ B:LYS556 2.6 53.8 1.0 SG B:CYS519 2.7 42.2 0.5 CE1 B:HIS266 3.2 57.1 1.0 CB B:CYS519 3.2 40.6 0.5 CB B:CYS519 3.2 40.6 0.5 CB B:CYS302 3.4 47.4 1.0 FE1 B:CUV702 3.5 76.9 1.0 SG B:CYS519 3.6 52.5 0.5 CG B:HIS266 3.7 50.8 1.0 CE B:LYS556 3.9 47.7 1.0 S4 B:CUV702 4.0 75.3 1.0 ND1 B:HIS266 4.0 53.6 1.0 N B:CYS519 4.4 40.9 0.5 N B:CYS519 4.4 41.0 0.5 CA B:CYS519 4.4 38.6 0.5 CA B:CYS519 4.4 38.7 0.5 S3 B:CUV702 4.5 68.7 1.0 CA B:CYS302 4.6 47.7 1.0 SG B:CYS301 4.6 44.7 0.5 N B:CYS302 4.8 50.9 1.0 FE3 B:CUV702 4.9 87.4 1.0 CD B:LYS556 5.0 45.4 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