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Nickel in PDB 6b6w: Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, As-Isolated (Protein Batch 2), Oxidized C-Cluster

Enzymatic activity of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, As-Isolated (Protein Batch 2), Oxidized C-Cluster

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

Protein crystallography data

The structure of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, As-Isolated (Protein Batch 2), Oxidized C-Cluster, PDB code: 6b6w 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) 64.90 / 1.72
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.430, 155.230, 66.570, 90.00, 102.85, 90.00
R / Rfree (%) 15.1 / 17.6

Other elements in 6b6w:

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

Magnesium (Mg) 4 atoms
Iron (Fe) 26 atoms
Chlorine (Cl) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, As-Isolated (Protein Batch 2), Oxidized C-Cluster (pdb code 6b6w). 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 2), Oxidized C-Cluster, PDB code: 6b6w:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 6b6w

Go back to Nickel Binding Sites List in 6b6w
Nickel binding site 1 out of 2 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, As-Isolated (Protein Batch 2), Oxidized 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 2), Oxidized C-Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni705

b:21.1
occ:0.70
NI A:CUV705 0.0 21.1 0.7
FE2 A:XCC704 1.2 23.4 0.2
NE2 A:HIS266 1.9 21.9 0.2
NE2 A:HIS266 2.2 22.5 0.8
NZ A:LYS556 2.3 32.2 1.0
SG A:CYS519 2.5 22.8 0.7
SG A:CYS302 2.6 19.6 0.8
SG A:CYS302 2.7 17.2 0.2
CD2 A:HIS266 2.7 18.6 0.2
CD2 A:HIS266 2.8 17.7 0.8
FE2 A:CUV705 3.0 28.5 0.8
CE1 A:HIS266 3.1 20.1 0.2
CE A:LYS556 3.2 31.1 1.0
SG A:CYS519 3.2 24.6 0.3
FE1 A:CUV705 3.4 23.8 0.8
CB A:CYS519 3.4 17.9 0.7
CB A:CYS519 3.4 17.7 0.3
CE1 A:HIS266 3.4 22.5 0.8
S3 A:XCC704 3.5 33.0 0.2
S4 A:XCC704 3.5 16.3 0.2
FE1 A:XCC704 3.7 29.6 0.2
CB A:CYS302 3.7 18.6 0.2
CB A:CYS302 3.8 19.0 0.8
S4 A:CUV705 3.8 24.9 0.8
CG A:HIS266 3.9 19.6 0.2
ND1 A:HIS266 4.1 20.5 0.2
CG A:HIS266 4.1 17.8 0.8
ND1 A:HIS266 4.3 21.0 0.8
SG A:CYS340 4.5 22.5 0.2
CD A:LYS556 4.6 27.5 1.0
SG A:CYS340 4.6 21.5 0.8
CA A:CYS519 4.6 14.6 0.7
CA A:CYS519 4.6 15.2 0.3
N A:CYS519 4.6 14.8 0.7
N A:CYS519 4.6 14.9 0.3
SG A:CYS301 4.7 28.4 1.0
S1 A:XCC704 4.7 13.5 0.2
FE4 A:XCC704 4.8 27.1 0.2
OE1 A:GLN339 4.9 18.5 0.5
FE3 A:XCC704 4.9 22.1 0.2
S3 A:CUV705 5.0 25.5 0.8
FE3 A:CUV705 5.0 23.2 0.8
CA A:CYS302 5.0 14.8 0.8
O A:HOH824 5.0 30.5 1.0

Nickel binding site 2 out of 2 in 6b6w

Go back to Nickel Binding Sites List in 6b6w
Nickel binding site 2 out of 2 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase, As-Isolated (Protein Batch 2), Oxidized 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 2), Oxidized C-Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni712

b:18.6
occ:0.70
NI B:CUV712 0.0 18.6 0.7
FE2 B:XCC711 1.3 17.9 0.2
NE2 B:HIS266 1.8 17.4 0.2
NE2 B:HIS266 2.2 19.9 0.8
NZ B:LYS556 2.3 23.0 1.0
SG B:CYS519 2.4 18.7 0.8
SG B:CYS302 2.6 21.1 0.8
CD2 B:HIS266 2.7 17.5 0.2
CD2 B:HIS266 2.8 17.6 0.8
SG B:CYS302 2.9 7.9 0.2
CE1 B:HIS266 3.0 17.3 0.2
FE2 B:CUV712 3.1 22.8 0.8
CE B:LYS556 3.2 27.4 1.0
FE1 B:CUV712 3.3 21.9 0.8
SG B:CYS519 3.4 18.9 0.2
CE1 B:HIS266 3.4 18.4 0.8
CB B:CYS519 3.5 14.1 0.8
CB B:CYS519 3.5 14.5 0.2
S4 B:XCC711 3.5 15.6 0.2
S3 B:XCC711 3.6 30.0 0.2
CB B:CYS302 3.8 14.2 0.8
CB B:CYS302 3.8 16.2 0.2
FE1 B:XCC711 3.8 23.1 0.2
S4 B:CUV712 3.8 21.9 0.8
CG B:HIS266 3.9 17.4 0.2
ND1 B:HIS266 4.0 16.4 0.2
CG B:HIS266 4.1 17.1 0.8
ND1 B:HIS266 4.3 14.7 0.8
SG B:CYS340 4.5 17.8 0.8
CD B:LYS556 4.6 22.9 1.0
SG B:CYS340 4.6 19.6 0.2
SG B:CYS301 4.7 23.4 1.0
CA B:CYS519 4.7 12.7 0.8
N B:CYS519 4.7 13.2 0.8
N B:CYS519 4.7 13.8 0.2
CA B:CYS519 4.7 13.4 0.2
O B:HOH841 4.8 29.3 1.0
S1 B:XCC711 4.8 14.5 0.2
OE1 B:GLN339 4.8 21.4 0.5
FE4 B:XCC711 4.9 31.1 0.2
NE2 B:HIS97 5.0 15.4 1.0
CA B:CYS302 5.0 12.2 0.8

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: Wed Dec 16 01:50:24 2020

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