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Magnesium 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:

Nickel (Ni) 2 atoms
Iron (Fe) 26 atoms
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 6b6w

Go back to Magnesium Binding Sites List in 6b6w
Magnesium binding site 1 out of 4 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 Magnesium with other atoms in the Mg 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:Mg702

b:48.9
occ:1.00
 O A:HOH811 2.1 32.3 1.0
O B:HOH1239 2.2 31.1 1.0
O B:HOH1304 2.3 45.1 1.0
O A:HOH1085 2.3 31.9 1.0
O3 B:GOL706 3.8 45.5 0.5
O B:HOH1033 3.9 37.3 1.0
C3 B:GOL706 3.9 45.3 0.5
O2 B:GOL706 4.0 44.0 0.5
OE2 A:GLU372 4.1 23.8 1.0
O2 B:GOL706 4.2 45.3 0.5
O3 B:GOL706 4.2 45.6 0.5
O B:HOH1061 4.3 24.2 1.0
C2 B:GOL706 4.4 44.8 0.5
O B:HOH1192 4.4 46.0 1.0
OE1 A:GLU372 4.4 25.9 1.0
O B:HOH1181 4.4 20.5 1.0
CB A:PRO361 4.5 22.0 1.0
CD A:GLU372 4.7 26.1 1.0
CA B:GLY184 4.9 20.1 1.0

Magnesium binding site 2 out of 4 in 6b6w

Go back to Magnesium Binding Sites List in 6b6w
Magnesium binding site 2 out of 4 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 Magnesium with other atoms in the Mg 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
A:Mg703

b:50.0
occ:1.00
 O A:HOH984 2.3 21.2 1.0
O A:HOH829 2.5 22.2 1.0
CG A:GLU106 4.1 15.2 0.5
OE2 A:GLU109 4.1 24.8 1.0
OE2 A:GLU106 4.2 24.4 0.5
OE1 A:GLU113 4.3 47.8 1.0
O A:HOH1009 4.4 25.1 1.0
CD A:GLU106 4.6 25.7 0.5
O A:HOH1120 4.6 23.0 1.0
O A:GLU106 4.7 12.9 0.5
O A:GLU106 4.8 12.9 0.5
CD A:GLU109 4.9 24.5 1.0

Magnesium binding site 3 out of 4 in 6b6w

Go back to Magnesium Binding Sites List in 6b6w
Magnesium binding site 3 out of 4 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 Magnesium with other atoms in the Mg binding site number 3 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:Mg709

b:35.7
occ:1.00
 O B:HOH832 2.1 31.6 1.0
O B:HOH845 2.2 26.3 1.0
O A:HOH1269 2.2 43.0 1.0
O A:HOH1241 2.2 30.0 1.0
OE2 B:GLU372 4.2 18.9 1.0
O A:HOH1308 4.2 44.4 1.0
OE1 B:GLU372 4.2 18.6 1.0
O B:HOH1016 4.3 19.6 1.0
O B:HOH1161 4.4 35.9 1.0
O A:HOH1128 4.4 42.3 1.0
O B:HOH1330 4.5 37.2 1.0
CB B:PRO361 4.5 16.2 1.0
CD B:GLU372 4.7 18.7 1.0
O A:HOH1189 4.8 17.8 1.0
CA A:GLY184 4.8 13.6 1.0
O A:HOH1171 5.0 39.2 1.0

Magnesium binding site 4 out of 4 in 6b6w

Go back to Magnesium Binding Sites List in 6b6w
Magnesium binding site 4 out of 4 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 Magnesium with other atoms in the Mg binding site number 4 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:Mg710

b:36.9
occ:1.00
 O B:HOH1034 2.1 21.0 1.0
O B:HOH1257 2.1 42.8 1.0
O B:HOH1384 2.1 32.5 1.0
O B:HOH815 2.3 32.1 1.0
O B:HOH894 2.4 23.8 1.0
O B:HOH1220 2.5 38.9 1.0
CG B:GLU106 4.1 13.5 0.5
OE1 B:GLU109 4.1 24.0 1.0
OE2 B:GLU106 4.1 21.5 0.5
O B:HOH1045 4.2 21.6 1.0
O B:HOH1047 4.3 56.5 1.0
OE1 B:GLU113 4.4 40.1 1.0
CD B:GLU106 4.6 23.9 0.5
O B:HOH1214 4.6 17.6 1.0
O B:GLU106 4.7 12.9 0.5
O B:GLU106 4.8 12.6 0.5
CD B:GLU109 4.8 19.7 1.0
CB B:ALA110 4.9 16.8 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 19:36:57 2024

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