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Nickel in PDB 6vwy: Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic)

Enzymatic activity of Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic)

All present enzymatic activity of Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic):
1.2.7.4;

Protein crystallography data

The structure of Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic), PDB code: 6vwy 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) 73.68 / 1.83
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.560, 147.360, 66.050, 90.00, 110.78, 90.00
R / Rfree (%) 14.7 / 17.8

Other elements in 6vwy:

The structure of Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic) also contains other interesting chemical elements:

Iron (Fe) 28 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic) (pdb code 6vwy). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic), PDB code: 6vwy:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 6vwy

Go back to Nickel Binding Sites List in 6vwy
Nickel binding site 1 out of 4 in the Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic)


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 C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni703

b:42.7
occ:0.20
 NI A:XCC703 0.0 42.7 0.2
SG A:CYS519 2.2 28.0 0.5
S1 A:XCC703 2.3 23.1 0.8
S4 A:CUV704 2.3 26.5 0.2
FE2 A:XCC703 2.4 50.2 0.8
S4 A:XCC703 2.4 26.2 0.8
S1 A:CUV704 2.4 25.9 0.2
FE3 A:CUV704 2.5 16.8 0.2
FE3 A:XCC703 2.5 29.2 0.8
FE1 A:CUV704 2.6 24.1 0.2
NI A:CUV704 2.8 16.5 0.2
FE1 A:XCC703 2.9 30.1 0.8
FE4 A:XCC703 3.0 36.0 0.8
S3 A:XCC703 3.0 48.9 0.8
FE2 A:CUV704 3.1 17.0 0.2
FE4 A:CUV704 3.1 17.2 0.2
CB A:CYS519 3.6 25.3 0.5
S2 A:CUV704 3.6 28.5 0.2
CB A:CYS519 3.7 25.6 0.5
SG A:CYS302 3.8 29.2 0.5
S3 A:CUV704 3.8 17.4 0.2
SG A:CYS302 3.9 30.2 0.5
S2 A:XCC703 3.9 25.4 0.8
NZ A:LYS556 4.1 27.0 0.5
SG A:CYS519 4.3 30.9 0.5
NE2 A:HIS266 4.3 22.8 0.5
SG A:CYS448 4.6 25.8 0.5
NE2 A:HIS266 4.6 26.6 0.5
CE1 A:HIS266 4.7 25.6 0.5
SG A:CYS448 4.8 21.7 0.5
CA A:GLY477 4.8 24.4 1.0
NZ A:LYS556 4.8 25.6 0.5
CA A:CYS519 4.8 24.3 0.5
SG A:CYS340 4.8 23.1 0.5
O A:HOH901 4.8 22.1 1.0
CA A:CYS519 4.8 24.4 0.5
CE A:LYS556 4.9 23.1 0.5
SG A:CYS340 4.9 24.3 0.5

Nickel binding site 2 out of 4 in 6vwy

Go back to Nickel Binding Sites List in 6vwy
Nickel binding site 2 out of 4 in the Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic)


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 C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni704

b:16.5
occ:0.20
 NI A:CUV704 0.0 16.5 0.2
FE2 A:XCC703 1.2 50.2 0.8
NE2 A:HIS266 1.6 22.8 0.5
NE2 A:HIS266 2.2 26.6 0.5
CE1 A:HIS266 2.4 25.6 0.5
CD2 A:HIS266 2.6 23.9 0.5
SG A:CYS302 2.7 30.2 0.5
NZ A:LYS556 2.7 27.0 0.5
CD2 A:HIS266 2.8 20.9 0.5
NI A:XCC703 2.8 42.7 0.2
SG A:CYS519 2.8 30.9 0.5
FE2 A:CUV704 2.9 17.0 0.2
SG A:CYS302 2.9 29.2 0.5
NZ A:LYS556 3.0 25.6 0.5
SG A:CYS519 3.2 28.0 0.5
CE A:LYS556 3.3 23.1 0.5
FE1 A:CUV704 3.3 24.1 0.2
S3 A:XCC703 3.4 48.9 0.8
CB A:CYS519 3.4 25.6 0.5
CB A:CYS519 3.4 25.3 0.5
CE1 A:HIS266 3.5 24.9 0.5
ND1 A:HIS266 3.5 23.5 0.5
FE1 A:XCC703 3.6 30.1 0.8
S4 A:XCC703 3.7 26.2 0.8
CB A:CYS302 3.7 27.5 0.5
CG A:HIS266 3.8 23.8 0.5
S4 A:CUV704 3.8 26.5 0.2
CB A:CYS302 3.9 27.2 0.5
CG A:HIS266 3.9 24.5 0.5
O A:HOH912 4.1 37.1 1.0
CE A:LYS556 4.2 22.4 0.5
ND1 A:HIS266 4.3 24.6 0.5
SG A:CYS340 4.5 23.1 0.5
SG A:CYS301 4.6 18.4 0.3
SG A:CYS340 4.6 24.3 0.5
CA A:CYS519 4.6 24.3 0.5
CA A:CYS519 4.6 24.4 0.5
CD A:LYS556 4.7 25.3 0.5
N A:CYS519 4.7 21.8 0.5
N A:CYS519 4.7 21.9 0.5
O A:HOH971 4.7 34.2 1.0
OE1 A:GLN339 4.7 36.7 1.0
CD A:LYS556 4.8 25.4 0.5
S3 A:CUV704 4.9 17.4 0.2
FE3 A:CUV704 4.9 16.8 0.2
FE4 A:XCC703 4.9 36.0 0.8
FE3 A:XCC703 4.9 29.2 0.8
S1 A:XCC703 4.9 23.1 0.8
NE2 A:HIS97 5.0 25.6 1.0

Nickel binding site 3 out of 4 in 6vwy

Go back to Nickel Binding Sites List in 6vwy
Nickel binding site 3 out of 4 in the Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni702

b:36.8
occ:0.20
 NI B:XCC702 0.0 36.8 0.2
S1 B:XCC702 2.2 23.4 0.8
SG B:CYS519 2.3 28.5 0.5
S4 B:CUV703 2.4 28.8 0.2
S4 B:XCC702 2.4 28.2 0.8
FE2 B:XCC702 2.5 50.6 0.8
S1 B:CUV703 2.5 29.5 0.2
FE3 B:CUV703 2.5 26.3 0.2
FE1 B:CUV703 2.6 31.4 0.2
FE3 B:XCC702 2.6 25.5 0.8
NI B:CUV703 2.7 19.9 0.2
FE1 B:XCC702 2.8 30.8 0.8
S3 B:XCC702 2.8 33.8 0.8
FE4 B:XCC702 2.9 31.5 0.8
FE2 B:CUV703 3.0 27.2 0.2
FE4 B:CUV703 3.1 23.4 0.2
S2 B:CUV703 3.6 30.6 0.2
SG B:CYS302 3.6 31.1 0.5
CB B:CYS519 3.7 26.3 0.5
CB B:CYS519 3.7 26.2 0.5
SG B:CYS302 3.7 30.5 0.5
S3 B:CUV703 3.7 18.7 0.2
S2 B:XCC702 3.9 24.3 0.8
NZ B:LYS556 4.2 24.6 0.5
SG B:CYS519 4.3 33.6 0.5
NE2 B:HIS266 4.5 22.3 0.5
NE2 B:HIS266 4.6 24.1 0.5
SG B:CYS448 4.7 25.8 0.5
CA B:GLY477 4.7 28.2 1.0
O B:HOH948 4.8 26.2 1.0
CA B:CYS519 4.8 22.4 0.5
SG B:CYS340 4.9 25.1 0.5
CA B:CYS519 4.9 22.4 0.5
SG B:CYS448 4.9 26.3 0.5
SG B:CYS340 4.9 24.0 0.5
N B:CYS478 4.9 27.7 0.5
SG B:CYS478 4.9 20.9 0.5
CE B:LYS556 5.0 21.0 0.5
N B:CYS478 5.0 27.6 0.5
NZ B:LYS556 5.0 21.9 0.5

Nickel binding site 4 out of 4 in 6vwy

Go back to Nickel Binding Sites List in 6vwy
Nickel binding site 4 out of 4 in the Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of C45G/T50C D. Vulgaris Carbon Monoxide Dehydrogenase (Anaerobic) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni703

b:19.9
occ:0.20
 NI B:CUV703 0.0 19.9 0.2
FE2 B:XCC702 1.0 50.6 0.8
NE2 B:HIS266 1.8 22.3 0.5
NE2 B:HIS266 2.2 24.1 0.5
CE1 B:HIS266 2.6 24.4 0.5
CD2 B:HIS266 2.7 22.4 0.5
NI B:XCC702 2.7 36.8 0.2
SG B:CYS302 2.8 31.1 0.5
SG B:CYS302 2.8 30.5 0.5
SG B:CYS519 2.8 33.6 0.5
NZ B:LYS556 2.9 21.9 0.5
CD2 B:HIS266 3.0 21.3 0.5
FE2 B:CUV703 3.0 27.2 0.2
NZ B:LYS556 3.0 24.6 0.5
S3 B:XCC702 3.2 33.8 0.8
CE B:LYS556 3.3 21.0 0.5
FE1 B:CUV703 3.3 31.4 0.2
SG B:CYS519 3.4 28.5 0.5
CB B:CYS519 3.4 26.2 0.5
CE1 B:HIS266 3.4 21.0 0.5
CB B:CYS519 3.5 26.3 0.5
FE1 B:XCC702 3.5 30.8 0.8
S4 B:XCC702 3.6 28.2 0.8
CB B:CYS302 3.7 26.2 0.5
CB B:CYS302 3.8 27.2 0.5
S4 B:CUV703 3.8 28.8 0.2
ND1 B:HIS266 3.8 22.6 0.5
CG B:HIS266 4.0 22.7 0.5
CG B:HIS266 4.0 24.1 0.5
O B:HOH914 4.1 32.1 1.0
ND1 B:HIS266 4.3 19.6 0.5
CE B:LYS556 4.3 19.7 0.5
SG B:CYS340 4.4 24.0 0.5
SG B:CYS301 4.5 18.2 0.3
SG B:CYS340 4.6 25.1 0.5
CA B:CYS519 4.7 22.4 0.5
N B:CYS519 4.7 19.9 0.5
N B:CYS519 4.7 20.0 0.5
CA B:CYS519 4.7 22.4 0.5
CD B:LYS556 4.8 25.9 0.5
CD B:LYS556 4.8 25.6 0.5
FE4 B:XCC702 4.8 31.5 0.8
O B:HOH868 4.9 31.9 1.0
FE3 B:XCC702 4.9 25.5 0.8
OE1 B:GLN339 4.9 36.5 1.0
S1 B:XCC702 4.9 23.4 0.8
S3 B:CUV703 4.9 18.7 0.2
FE3 B:CUV703 4.9 26.3 0.2
CA B:CYS302 5.0 25.4 0.5

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 08:55:34 2024

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