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Chlorine 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:

Nickel (Ni) 2 atoms
Magnesium (Mg) 4 atoms
Iron (Fe) 18 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 3 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6b6x

Go back to Chlorine Binding Sites List in 6b6x
Chlorine binding site 1 out of 3 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 Chlorine with other atoms in the Cl 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:Cl706

b:31.9
occ:1.00
 N A:LYS65 3.2 42.7 1.0
CB A:ARG64 3.7 31.9 1.0
CA A:ARG64 3.8 30.1 1.0
O A:HOH934 3.9 33.6 1.0
N A:ASP66 3.9 36.0 1.0
C A:ARG64 3.9 41.3 1.0
CB A:LYS65 4.0 53.1 1.0
CG A:LYS65 4.0 61.6 1.0
CA A:LYS65 4.0 41.6 1.0
CG A:ARG64 4.1 30.6 1.0
OD1 A:ASP66 4.2 30.0 1.0
CG A:ASP66 4.4 38.1 1.0
C A:LYS65 4.5 39.2 1.0
NE A:ARG64 4.5 25.8 1.0
OD2 A:ASP66 4.8 34.8 1.0
CB A:ASP66 4.8 34.4 1.0
CD A:ARG64 4.9 31.0 1.0

Chlorine binding site 2 out of 3 in 6b6x

Go back to Chlorine Binding Sites List in 6b6x
Chlorine binding site 2 out of 3 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 Chlorine with other atoms in the Cl 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:Cl711

b:43.8
occ:1.00
 O B:HOH1154 2.8 46.1 1.0
N B:ASN164 3.1 18.0 1.0
NH1 B:ARG163 3.5 39.9 1.0
N B:ALA165 3.6 18.1 1.0
NE B:ARG163 3.7 34.8 1.0
O B:ALA165 3.8 18.8 1.0
CZ B:ARG163 3.8 40.0 1.0
CA B:ASN164 3.9 20.0 1.0
CA B:ARG163 3.9 17.2 1.0
CB B:ASN164 3.9 27.0 1.0
C B:ARG163 4.0 21.8 1.0
CB B:ARG163 4.0 16.1 1.0
C B:ASN164 4.2 19.3 1.0
O B:HOH881 4.3 27.4 1.0
O B:HOH1172 4.4 43.6 1.0
CA B:ALA165 4.6 16.2 1.0
ND2 B:ASN164 4.6 37.3 1.0
C B:ALA165 4.6 17.3 1.0
CG B:ASN164 4.6 34.1 1.0
CD B:ARG163 4.7 29.1 1.0
NH2 B:ARG163 4.8 38.4 1.0
CG B:ARG163 4.9 24.9 1.0
CB B:ALA165 5.0 20.5 1.0

Chlorine binding site 3 out of 3 in 6b6x

Go back to Chlorine Binding Sites List in 6b6x
Chlorine binding site 3 out of 3 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl712

b:40.8
occ:1.00
 NE B:ARG621 3.0 35.4 1.0
NH1 B:ARG621 3.1 21.8 1.0
NE2 B:GLN594 3.2 41.4 1.0
O B:HOH811 3.3 26.8 1.0
CZ B:ARG621 3.5 26.4 1.0
ND1 B:HIS617 3.7 39.9 1.0
O B:GLY598 3.8 24.9 1.0
CG B:PRO570 3.8 24.2 1.0
OE1 B:GLN594 3.8 46.2 1.0
O B:HOH932 3.8 35.1 1.0
CD B:GLN594 3.9 36.8 1.0
CD B:ARG621 4.2 36.2 1.0
CE1 B:HIS617 4.3 36.2 1.0
CG B:HIS617 4.4 37.8 1.0
CB B:HIS617 4.6 28.6 1.0
CB B:PRO570 4.7 20.8 1.0
C B:GLY598 4.8 22.1 1.0
CD B:PRO570 4.8 23.0 1.0
CA B:ALA599 4.8 26.1 1.0
NH2 B:ARG621 4.8 23.4 1.0
CG B:ARG621 4.9 28.9 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: Fri Jul 26 22:33:32 2024

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