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Nickel in PDB 6b6x: Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster

Enzymatic activity of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster

All present enzymatic activity of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster:
1.2.7.4;

Protein crystallography data

The structure of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster, PDB code: 6b6x 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) 64.87 / 1.84
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.650, 154.870, 66.490, 90.00, 102.67, 90.00
R / Rfree (%) 14.4 / 17.1

Other elements in 6b6x:

The structure of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Iron (Fe) 18 atoms
Chlorine (Cl) 3 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster (pdb code 6b6x). 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, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster, PDB code: 6b6x:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 6b6x

Go back to Nickel Binding Sites List in 6b6x
Nickel binding site 1 out of 2 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), 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, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni702

b:27.9
occ:0.50
 NI A:XCC702 0.0 27.9 0.5
SG A:CYS519 2.2 21.8 0.6
S1 A:XCC702 2.3 27.2 1.0
S4 A:XCC702 2.3 26.0 1.0
FE3 A:XCC702 2.7 26.7 1.0
O A:HOH884 2.9 37.5 1.0
FE2 A:XCC702 3.0 39.0 1.0
FE1 A:XCC702 3.4 30.3 1.0
CB A:CYS519 3.4 21.9 0.6
CB A:CYS519 3.4 22.4 0.4
FE4 A:XCC702 3.5 26.1 1.0
S3 A:XCC702 3.8 28.7 1.0
SG A:CYS519 4.1 37.0 0.4
SG A:CYS302 4.3 26.5 1.0
S2 A:XCC702 4.4 27.7 1.0
SG A:CYS448 4.5 23.5 1.0
O A:HOH927 4.6 23.3 1.0
CA A:CYS519 4.7 20.5 0.4
CA A:CYS519 4.7 20.6 0.6
CA A:GLY447 4.7 33.0 1.0
OG A:SER554 4.8 20.0 1.0
NZ A:LYS556 4.8 30.7 1.0
NE2 A:HIS266 4.9 32.3 1.0

Nickel binding site 2 out of 2 in 6b6x

Go back to Nickel Binding Sites List in 6b6x
Nickel binding site 2 out of 2 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, Dithionite-Reduced (Protein Batch 2), 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, Dithionite-Reduced (Protein Batch 2), Canonical C- Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni703

b:25.5
occ:0.50
 NI B:XCC703 0.0 25.5 0.5
SG B:CYS519 2.1 19.3 0.6
S4 B:XCC703 2.3 25.7 1.0
S1 B:XCC703 2.3 26.0 1.0
FE3 B:XCC703 2.7 23.5 1.0
O B:HOH820 2.9 36.0 1.0
FE2 B:XCC703 3.1 34.9 1.0
CB B:CYS519 3.3 17.1 0.6
CB B:CYS519 3.3 17.2 0.4
FE1 B:XCC703 3.5 26.7 1.0
FE4 B:XCC703 3.7 24.7 1.0
S3 B:XCC703 3.9 27.6 1.0
SG B:CYS519 3.9 27.3 0.4
O B:HOH1056 4.4 23.0 1.0
SG B:CYS302 4.4 23.6 1.0
SG B:CYS448 4.5 22.0 1.0
S2 B:XCC703 4.5 24.6 1.0
NZ B:LYS556 4.7 31.2 1.0
CA B:CYS519 4.7 17.9 0.4
CA B:CYS519 4.7 17.9 0.6
CA B:GLY447 4.7 27.4 1.0
OG B:SER554 4.8 18.4 1.0
NE2 B:HIS266 4.9 24.4 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 08:18:46 2024

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