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Magnesium in PDB 6ond: Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced

Enzymatic activity of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced

All present enzymatic activity of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced:
1.2.7.4;

Protein crystallography data

The structure of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced, PDB code: 6ond was solved by E.C.Wittenborn, S.E.Cohen, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 93.27 / 1.72
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 (%) 14.9 / 17.6

Other elements in 6ond:

The structure of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced also contains other interesting chemical elements:

Iron (Fe) 40 atoms
Chlorine (Cl) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced (pdb code 6ond). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced, PDB code: 6ond:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 6ond

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Magnesium binding site 1 out of 7 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced


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 Produced Without Cooc, Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg704

b:23.5
occ:1.00
 O A:HOH1183 2.0 23.5 1.0
O A:HOH1158 2.1 26.6 1.0
O A:HOH1176 2.1 20.5 1.0
O A:HOH952 2.1 18.7 1.0
O A:SER541 4.2 16.5 1.0
NE2 A:GLN594 4.3 31.6 1.0
O A:HOH947 4.3 33.6 1.0
O A:HOH869 4.4 22.3 1.0
NE A:ARG624 4.4 28.1 1.0
O A:GLY598 4.4 14.5 1.0
CZ A:ARG624 4.6 24.6 1.0
CL A:CL707 4.6 28.9 1.0
O A:HOH816 4.6 25.9 1.0
NH2 A:ARG624 4.7 25.9 1.0
CD A:ARG624 4.9 19.0 1.0

Magnesium binding site 2 out of 7 in 6ond

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Magnesium binding site 2 out of 7 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced


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 Produced Without Cooc, Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg705

b:26.1
occ:1.00
 O A:HOH884 2.2 28.4 1.0
O A:HOH1016 2.2 22.3 1.0
O A:HOH1189 4.1 36.8 1.0
O A:ASP595 4.5 21.0 1.0
OD1 A:ASP595 4.7 31.9 1.0

Magnesium binding site 3 out of 7 in 6ond

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Magnesium binding site 3 out of 7 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced


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 Produced Without Cooc, Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg705

b:35.8
occ:1.00
 O A:HOH1250 1.9 39.1 1.0
O A:HOH1234 2.0 31.2 1.0
O B:HOH841 2.0 35.3 1.0
O A:HOH1273 2.1 33.1 1.0
O B:HOH964 2.2 32.7 1.0
O B:HOH1265 2.2 35.6 1.0
O A:HOH1107 4.2 43.3 1.0
OE2 B:GLU372 4.3 22.7 1.0
O B:HOH1136 4.3 31.0 1.0
O A:HOH906 4.4 42.7 1.0
OE1 B:GLU372 4.4 24.2 1.0
CB B:PRO361 4.6 20.8 1.0
CD B:GLU372 4.8 23.6 1.0
CA A:GLY184 4.9 19.3 1.0
O A:HOH1168 4.9 18.2 1.0

Magnesium binding site 4 out of 7 in 6ond

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Magnesium binding site 4 out of 7 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced


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 Produced Without Cooc, Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg705

b:36.8
occ:1.00
 O C:HOH1220 2.1 35.1 1.0
O C:HOH890 2.2 23.8 1.0
O C:HOH864 2.2 24.7 1.0
O C:HOH990 2.2 35.9 1.0
O C:HOH1163 2.3 39.5 1.0
O C:SER541 3.7 20.6 1.0
O C:HOH1174 4.1 27.0 1.0
OD1 C:ASP542 4.2 23.3 1.0
O C:HOH1169 4.3 31.3 1.0
OG C:SER541 4.3 20.2 1.0
CB C:SER541 4.5 20.9 1.0
O C:HOH1145 4.5 17.5 1.0
C C:SER541 4.6 18.1 1.0
O C:HOH1153 4.6 46.1 1.0
O C:GLY598 4.6 18.8 1.0
NE C:ARG624 4.7 25.7 1.0
CA C:GLY598 4.8 23.2 1.0
NE2 C:GLN594 4.9 41.9 1.0
CZ C:ARG624 4.9 23.7 1.0
NH2 C:ARG624 4.9 24.6 1.0

Magnesium binding site 5 out of 7 in 6ond

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Magnesium binding site 5 out of 7 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced


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 Produced Without Cooc, Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg706

b:40.8
occ:1.00
 O C:HOH1107 2.0 29.4 1.0
O C:HOH1255 2.2 41.8 1.0
O C:HOH918 2.2 37.7 1.0
O C:HOH920 2.2 22.1 1.0
O C:HOH1162 2.4 43.9 1.0
O C:HOH954 4.0 21.0 1.0
OE2 C:GLU109 4.2 26.9 1.0
OE1 C:GLU113 4.2 56.8 1.0
OE2 C:GLU106 4.4 32.8 0.5
CG C:GLU106 4.4 22.4 0.5
O C:HOH1152 4.7 22.5 1.0
O C:GLU106 4.7 16.5 0.5
O C:GLU106 4.7 16.9 0.5
CD C:GLU106 4.8 32.3 0.5
CB C:ALA110 4.8 18.1 1.0
CD C:GLU109 4.8 26.1 1.0

Magnesium binding site 6 out of 7 in 6ond

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Magnesium binding site 6 out of 7 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg707

b:44.2
occ:1.00
 O D:HOH1182 2.2 43.3 1.0
O C:HOH891 2.2 33.6 1.0
O C:HOH1229 2.5 40.7 1.0
O C:HOH872 2.6 40.1 1.0
O C:HOH1061 4.2 31.3 1.0
O C:HOH998 4.4 39.4 1.0
OE1 C:GLU372 4.5 25.4 1.0
OE2 C:GLU372 4.6 24.8 1.0
CB C:PRO361 4.6 24.3 1.0
O D:HOH961 4.6 42.7 1.0
O D:HOH984 4.7 40.9 1.0
O D:HOH1118 4.9 18.7 1.0
CA D:GLY184 4.9 21.7 1.0

Magnesium binding site 7 out of 7 in 6ond

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Magnesium binding site 7 out of 7 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg705

b:33.8
occ:1.00
 O D:HOH1158 2.1 32.0 1.0
O D:HOH885 2.2 24.0 1.0
O D:HOH1113 2.3 23.4 1.0
O D:SER541 4.1 21.5 1.0
O D:HOH849 4.1 24.3 1.0
O D:HOH816 4.1 27.5 1.0
NE D:ARG624 4.3 37.1 1.0
CZ D:ARG624 4.4 42.2 1.0
NH2 D:ARG624 4.6 36.5 1.0
O D:GLY598 4.6 19.2 1.0
O D:HOH1164 4.6 47.7 1.0
NE2 D:GLN594 4.6 31.9 1.0
CD D:ARG624 4.8 32.3 1.0
O D:HOH1100 4.8 20.8 1.0
NH1 D:ARG624 4.9 43.7 1.0

Reference:

E.C.Wittenborn, S.E.Cohen, M.Merrouch, C.Leger, V.Fourmond, S.Dementin, C.L.Drennan. Structural Insight Into Metallocofactor Maturation in Carbon Monoxide Dehydrogenase. J.Biol.Chem. V. 294 13017 2019.
ISSN: ESSN 1083-351X
PubMed: 31296570
DOI: 10.1074/JBC.RA119.009610
Page generated: Tue Oct 1 13:28:18 2024

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