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Magnesium in PDB 6dc2: Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant

Enzymatic activity of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant

All present enzymatic activity of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant:
1.2.7.4;

Protein crystallography data

The structure of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant, PDB code: 6dc2 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) 93.27 / 1.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.790, 144.150, 123.690, 90.00, 98.50, 90.00
R / Rfree (%) 16.3 / 21.2

Other elements in 6dc2:

The structure of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant also contains other interesting chemical elements:

Iron (Fe) 40 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant (pdb code 6dc2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant, PDB code: 6dc2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6dc2

Go back to Magnesium Binding Sites List in 6dc2
Magnesium binding site 1 out of 5 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant


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 C301S Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg705

b:45.2
occ:1.00
 O B:HOH1113 2.4 46.1 1.0
O B:HOH1159 2.4 35.9 1.0
O B:HOH942 2.6 29.8 1.0
O A:HOH1038 4.1 36.7 1.0
CA A:GLY184 4.4 22.7 1.0
O B:HOH1058 4.6 38.9 1.0
O A:LEU183 4.7 19.6 1.0
N A:GLY184 4.8 20.8 1.0
OE1 B:GLU372 5.0 21.7 1.0

Magnesium binding site 2 out of 5 in 6dc2

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Magnesium binding site 2 out of 5 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant


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 C301S Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg706

b:41.0
occ:1.00
 O A:HOH997 2.1 23.8 1.0
O A:HOH1189 2.2 40.5 1.0
O A:HOH1138 2.3 40.3 1.0
O A:HOH1139 4.1 40.0 1.0
CG A:GLU106 4.1 29.5 0.5
O A:HOH975 4.2 29.6 1.0
O A:HOH1116 4.3 18.0 1.0
OE2 A:GLU106 4.3 38.4 0.5
OE2 A:GLU109 4.5 36.5 1.0
O A:GLU106 4.6 16.5 1.0
CB A:ALA110 4.6 19.3 1.0
CD A:GLU106 4.6 34.8 0.5
CA A:ALA110 5.0 22.6 1.0

Magnesium binding site 3 out of 5 in 6dc2

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Magnesium binding site 3 out of 5 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant


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 C301S Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg705

b:58.1
occ:1.00
 O B:HOH828 2.4 27.0 1.0
O B:HOH1150 2.4 31.7 1.0
O B:HOH1186 2.6 41.7 1.0
O B:HOH1069 2.8 43.8 1.0
CG B:GLU106 3.7 38.3 1.0
O B:GLU106 3.9 21.1 1.0
OE1 B:GLU109 4.1 27.7 1.0
O B:HOH1036 4.1 23.3 1.0
OE2 B:GLU106 4.2 53.6 1.0
CB B:ALA110 4.3 17.1 1.0
CD B:GLU106 4.4 50.0 1.0
OE1 B:GLU113 4.4 42.5 1.0
O B:HOH1028 4.4 22.6 1.0
N B:ALA110 4.6 17.6 1.0
CA B:ALA110 4.6 20.8 1.0
O B:HOH1037 4.7 52.2 1.0
C B:GLU106 4.8 21.0 1.0
CD B:GLU109 4.8 32.0 1.0
CB B:GLU106 4.9 18.0 1.0
CG B:GLU109 4.9 16.9 1.0
CA B:GLU106 5.0 16.9 1.0

Magnesium binding site 4 out of 5 in 6dc2

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Magnesium binding site 4 out of 5 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant


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 C301S Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg708

b:36.7
occ:1.00
 O C:HOH975 2.0 26.9 1.0
O C:HOH825 2.1 27.5 1.0
O C:HOH1191 2.2 42.3 1.0
O C:HOH1023 2.4 26.9 1.0
O C:HOH1097 2.4 41.3 1.0
O C:HOH1157 2.4 35.5 1.0
OE2 C:GLU109 4.1 32.1 1.0
O C:HOH909 4.2 24.2 1.0
OE1 C:GLU113 4.2 59.6 1.0
CG C:GLU106 4.3 37.0 1.0
CB C:ALA110 4.4 21.1 1.0
O C:HOH1106 4.5 19.9 1.0
O C:GLU106 4.5 17.3 1.0
CD C:GLU113 4.6 55.8 1.0
OE2 C:GLU113 4.7 55.8 1.0
CA C:ALA110 4.8 25.1 1.0
N C:ALA110 4.8 17.3 1.0
CD C:GLU109 4.8 34.1 1.0
OE1 C:GLU106 4.9 52.1 1.0
O C:HOH1112 4.9 48.2 1.0

Magnesium binding site 5 out of 5 in 6dc2

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Magnesium binding site 5 out of 5 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase C301S Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg704

b:64.2
occ:1.00
 O D:HOH1092 2.2 40.8 1.0
O D:HOH985 2.3 31.9 1.0
O D:HOH975 2.5 32.3 1.0
O D:HOH872 2.6 48.8 1.0
O D:HOH1055 2.8 45.4 1.0
OE1 D:GLU109 4.1 32.0 1.0
OE1 D:GLU113 4.3 56.2 1.0
O D:HOH1136 4.4 45.2 1.0
O D:HOH925 4.5 33.4 1.0
CG D:GLU106 4.6 30.3 0.5
CD D:GLU109 4.8 28.5 1.0
OE2 D:GLU106 4.8 34.5 0.5
O D:GLU106 5.0 21.6 0.5

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 23:06:00 2024

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