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Nickel in PDB 6vwz: Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (20 Minute Air Exposure)

Enzymatic activity of Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (20 Minute Air Exposure)

All present enzymatic activity of Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (20 Minute Air Exposure):
1.2.7.4;

Protein crystallography data

The structure of Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (20 Minute Air Exposure), PDB code: 6vwz 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) 73.63 / 2.49
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 (%) 18.1 / 21.1

Other elements in 6vwz:

The structure of Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (20 Minute Air Exposure) also contains other interesting chemical elements:

Iron (Fe) 20 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (20 Minute Air Exposure) (pdb code 6vwz). 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 (20 Minute Air Exposure), PDB code: 6vwz:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 6vwz

Go back to Nickel Binding Sites List in 6vwz
Nickel binding site 1 out of 2 in the Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (20 Minute 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 (20 Minute Air Exposure) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni702

b:51.5
occ:1.00
 NI A:CUV702 0.0 51.5 1.0
NE2 A:HIS266 2.0 42.4 1.0
FE2 A:CUV702 2.2 47.0 1.0
SG A:CYS302 2.3 34.1 1.0
CD2 A:HIS266 2.7 36.4 1.0
SG A:CYS519 2.8 44.2 1.0
NZ A:LYS556 2.8 34.3 1.0
CE1 A:HIS266 3.2 35.7 1.0
CB A:CYS519 3.5 24.6 1.0
CB A:CYS302 3.5 30.5 1.0
FE1 A:CUV702 3.6 50.7 1.0
S4 A:CUV702 3.9 53.1 1.0
CG A:HIS266 3.9 34.2 1.0
ND1 A:HIS266 4.1 37.4 1.0
CE A:LYS556 4.2 32.9 1.0
S3 A:CUV702 4.2 52.2 1.0
SG A:CYS301 4.3 34.7 0.5
N A:CYS519 4.6 25.1 1.0
CA A:CYS519 4.7 26.4 1.0
CA A:CYS302 4.7 30.0 1.0
N A:CYS302 4.8 29.0 1.0
SG A:CYS340 4.8 36.6 1.0
FE3 A:CUV702 4.9 58.3 1.0
S1 A:CUV702 4.9 51.8 1.0
FE4 A:CUV702 4.9 52.6 1.0

Nickel binding site 2 out of 2 in 6vwz

Go back to Nickel Binding Sites List in 6vwz
Nickel binding site 2 out of 2 in the Crystal Structure of Air-Exposed C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (20 Minute 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 (20 Minute Air Exposure) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni703

b:55.5
occ:1.00
 NI B:CUV703 0.0 55.5 1.0
NE2 B:HIS266 2.0 36.9 1.0
FE2 B:CUV703 2.3 54.0 1.0
SG B:CYS302 2.3 32.1 1.0
CD2 B:HIS266 2.6 29.5 1.0
SG B:CYS519 2.8 37.3 0.5
NZ B:LYS556 3.0 36.0 1.0
SG B:CYS519 3.1 35.7 0.5
CE1 B:HIS266 3.2 32.8 1.0
CB B:CYS519 3.4 26.6 0.5
CB B:CYS519 3.4 26.8 0.5
CB B:CYS302 3.5 29.8 1.0
S4 B:CUV703 3.6 54.0 1.0
CG B:HIS266 3.9 32.7 1.0
FE1 B:CUV703 3.9 49.3 1.0
ND1 B:HIS266 4.1 31.9 1.0
S3 B:CUV703 4.2 52.2 1.0
CE B:LYS556 4.3 32.2 1.0
SG B:CYS301 4.4 33.1 0.5
N B:CYS519 4.5 26.8 0.5
N B:CYS519 4.5 26.8 0.5
CA B:CYS519 4.6 25.0 0.5
CA B:CYS519 4.6 25.1 0.5
CA B:CYS302 4.7 30.2 1.0
FE3 B:CUV703 4.7 55.0 1.0
S1 B:CUV703 4.7 55.5 1.0
N B:CYS302 4.8 29.1 1.0
FE4 B:CUV703 4.8 54.3 1.0
SG B:CYS340 4.8 33.9 1.0

Reference:

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
Page generated: Thu Oct 10 08:57:00 2024

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