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Nickel in PDB 6b6v: Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, As-Isolated (Protein Batch 1), Canonical C-Cluster

Enzymatic activity of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, As-Isolated (Protein Batch 1), Canonical C-Cluster

All present enzymatic activity of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, As-Isolated (Protein Batch 1), Canonical C-Cluster:
1.2.7.4;

Protein crystallography data

The structure of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, As-Isolated (Protein Batch 1), Canonical C-Cluster, PDB code: 6b6v 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) 97.13 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.650, 111.960, 195.290, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 20.6

Other elements in 6b6v:

The structure of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, As-Isolated (Protein Batch 1), Canonical C-Cluster also contains other interesting chemical elements:

Iron (Fe) 18 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, As-Isolated (Protein Batch 1), Canonical C-Cluster (pdb code 6b6v). 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 Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, As-Isolated (Protein Batch 1), Canonical C-Cluster, PDB code: 6b6v:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 6b6v

Go back to Nickel Binding Sites List in 6b6v
Nickel binding site 1 out of 2 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, As-Isolated (Protein Batch 1), Canonical C-Cluster


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 Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, As-Isolated (Protein Batch 1), Canonical C-Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni702

b:41.4
occ:0.50
 NI A:XCC702 0.0 41.4 0.5
SG A:CYS519 2.2 45.3 1.0
S1 A:XCC702 2.2 41.2 1.0
S4 A:XCC702 2.3 40.1 1.0
FE2 A:XCC702 2.6 53.9 1.0
FE3 A:XCC702 2.7 40.5 1.0
FE4 A:XCC702 3.3 38.9 1.0
FE1 A:XCC702 3.3 39.3 1.0
S3 A:XCC702 3.3 38.1 1.0
CB A:CYS519 3.6 32.4 1.0
SG A:CYS302 4.0 51.4 1.0
S2 A:XCC702 4.3 34.4 1.0
NE2 A:HIS266 4.4 49.8 1.0
O A:HOH884 4.5 36.3 1.0
SG A:CYS448 4.5 38.0 1.0
CA A:GLY477 4.8 21.3 1.0
CA A:CYS519 4.8 33.1 1.0

Nickel binding site 2 out of 2 in 6b6v

Go back to Nickel Binding Sites List in 6b6v
Nickel binding site 2 out of 2 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, As-Isolated (Protein Batch 1), Canonical C-Cluster


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 Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, As-Isolated (Protein Batch 1), Canonical C-Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni703

b:43.1
occ:0.50
 NI B:XCC703 0.0 43.1 0.5
SG B:CYS519 2.2 40.4 1.0
S1 B:XCC703 2.2 37.9 1.0
S4 B:XCC703 2.3 36.4 1.0
FE2 B:XCC703 2.6 50.4 1.0
FE3 B:XCC703 2.7 37.7 1.0
FE1 B:XCC703 3.4 35.3 1.0
FE4 B:XCC703 3.4 37.2 1.0
CB B:CYS519 3.6 37.4 1.0
S3 B:XCC703 3.7 39.6 1.0
SG B:CYS302 4.2 42.0 1.0
S2 B:XCC703 4.4 35.8 1.0
NE2 B:HIS266 4.4 38.0 1.0
O B:HOH893 4.4 31.4 1.0
SG B:CYS448 4.5 29.8 1.0
NZ B:LYS556 4.8 31.8 1.0
CA B:CYS519 4.8 28.7 1.0
CA B:GLY477 4.9 23.5 1.0
C B:GLY447 4.9 35.8 1.0
CA B:GLY447 5.0 36.7 1.0
OG B:SER554 5.0 37.0 1.0

Reference:

E.C.Wittenborn, M.Merrouch, C.Ueda, L.Fradale, C.Leger, V.Fourmond, M.E.Pandelia, S.Dementin, C.L.Drennan. Redox-Dependent Rearrangements of the Nifes Cluster of Carbon Monoxide Dehydrogenase. Elife V. 7 2018.
ISSN: ESSN 2050-084X
PubMed: 30277213
DOI: 10.7554/ELIFE.39451
Page generated: Thu Oct 10 08:18:27 2024

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