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

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6b6x

Go back to Magnesium Binding Sites List in 6b6x
Magnesium binding site 1 out of 4 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 Magnesium with other atoms in the Mg 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:Mg704

b:42.5
occ:1.00
 O A:HOH919 2.1 25.3 1.0
O A:HOH1183 2.1 37.9 1.0
O A:HOH953 2.2 30.0 1.0
O A:HOH1090 2.4 44.9 1.0
O A:HOH895 2.4 47.5 1.0
OE2 A:GLU109 4.1 30.5 1.0
CG A:GLU106 4.2 21.6 0.5
OE1 A:GLU113 4.2 55.4 1.0
O A:HOH951 4.3 31.3 1.0
O B:HOH1257 4.4 58.8 1.0
O A:GLU106 4.6 16.7 0.5
OE1 A:GLU106 4.6 29.8 0.5
O A:HOH1117 4.7 24.2 1.0
O A:GLU106 4.7 17.9 0.5
CD A:GLU109 4.8 31.1 1.0
CD A:GLU106 4.8 31.3 0.5
CB A:ALA110 4.8 21.2 1.0
CG A:GLU109 5.0 18.8 1.0

Magnesium binding site 2 out of 4 in 6b6x

Go back to Magnesium Binding Sites List in 6b6x
Magnesium binding site 2 out of 4 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 Magnesium with other atoms in the Mg 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
A:Mg705

b:46.7
occ:1.00
 O B:HOH839 2.1 47.8 1.0
O B:HOH1212 2.2 42.7 1.0
O A:HOH815 2.2 43.7 1.0
O A:HOH1083 2.2 36.4 1.0
OE2 A:GLU372 4.2 31.1 1.0
O3 B:GOL707 4.2 51.3 1.0
O B:HOH877 4.3 27.4 1.0
O2 B:GOL707 4.3 56.7 1.0
OE1 A:GLU372 4.4 32.9 1.0
C2 B:GOL707 4.6 52.5 1.0
CB A:PRO361 4.7 28.6 1.0
CD A:GLU372 4.8 34.8 1.0
O B:HOH1163 4.8 18.8 1.0
CA B:GLY184 5.0 22.8 1.0

Magnesium binding site 3 out of 4 in 6b6x

Go back to Magnesium Binding Sites List in 6b6x
Magnesium binding site 3 out of 4 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 Magnesium with other atoms in the Mg 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:Mg709

b:40.2
occ:1.00
 O B:HOH1275 2.1 40.7 1.0
O B:HOH944 2.2 24.5 1.0
O B:HOH904 2.2 30.7 1.0
O B:HOH1203 2.2 41.0 1.0
O B:HOH864 2.2 35.9 1.0
O B:HOH1156 2.3 39.6 1.0
CG B:GLU106 4.1 20.7 0.5
OE1 B:GLU109 4.1 30.4 1.0
OE2 B:GLU106 4.2 29.9 0.5
O B:HOH957 4.3 25.2 1.0
OE1 B:GLU113 4.3 44.6 1.0
O B:GLU106 4.6 14.8 0.5
CD B:GLU106 4.6 29.1 0.5
O B:HOH1164 4.7 17.7 1.0
O B:GLU106 4.7 15.8 0.5
CD B:GLU109 4.8 28.4 1.0
CB B:ALA110 4.8 18.4 1.0
OE2 B:GLU113 4.9 44.3 1.0

Magnesium binding site 4 out of 4 in 6b6x

Go back to Magnesium Binding Sites List in 6b6x
Magnesium binding site 4 out of 4 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 Magnesium with other atoms in the Mg binding site number 4 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:Mg710

b:45.7
occ:1.00
 O A:HOH1175 2.2 33.4 1.0
O B:HOH827 2.2 38.9 1.0
O A:HOH1212 2.2 44.1 1.0
O B:HOH867 2.2 28.0 1.0
O A:HOH1098 3.9 36.4 1.0
O B:HOH1023 4.3 22.5 1.0
OE2 B:GLU372 4.3 22.0 1.0
O A:HOH1221 4.3 52.7 1.0
OE1 B:GLU372 4.3 23.8 1.0
O B:HOH1233 4.4 42.1 1.0
O A:HOH1017 4.5 45.5 1.0
CB B:PRO361 4.6 21.1 1.0
CA A:GLY184 4.7 16.9 1.0
O A:HOH1108 4.7 51.7 1.0
CD B:GLU372 4.8 22.9 1.0
O A:HOH1130 4.8 17.0 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: Mon Sep 30 19:37:09 2024

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