Magnesium in PDB 6onc: Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, As-Isolated

Enzymatic activity of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, As-Isolated

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

Protein crystallography data

The structure of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, As-Isolated, PDB code: 6onc 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 / 1.50
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 (%) 15.4 / 17.8

Other elements in 6onc:

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

Iron (Fe) 40 atoms
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, As-Isolated (pdb code 6onc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, As-Isolated, PDB code: 6onc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6onc

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Magnesium binding site 1 out of 8 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, As-Isolated


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, As-Isolated within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg705

b:26.3
occ:1.00
O A:HOH1074 2.0 19.9 1.0
O A:HOH969 2.0 23.7 1.0
O A:HOH1292 2.1 28.7 1.0
O A:HOH865 2.2 23.0 1.0
O A:HOH1415 2.3 29.0 1.0
O A:HOH827 2.5 30.1 1.0
CG A:GLU106 4.1 16.1 0.5
OE2 A:GLU109 4.1 21.5 1.0
OE1 A:GLU113 4.2 25.3 1.0
OE2 A:GLU106 4.2 16.2 0.5
O A:HOH1353 4.2 38.2 1.0
O A:HOH1011 4.3 19.4 1.0
OE2 A:GLU113 4.6 27.2 1.0
O A:GLU106 4.6 15.1 0.5
O A:GLU106 4.6 14.8 0.5
O A:HOH1088 4.6 42.3 1.0
CD A:GLU106 4.6 20.6 0.5
CD A:GLU113 4.7 24.0 1.0
O A:HOH1241 4.7 16.2 1.0
CD A:GLU109 4.8 20.2 1.0
CB A:ALA110 4.8 15.8 1.0
O A:HOH1014 4.9 47.0 1.0

Magnesium binding site 2 out of 8 in 6onc

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Magnesium binding site 2 out of 8 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, As-Isolated


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, As-Isolated within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg705

b:30.6
occ:1.00
O B:HOH994 2.1 20.2 1.0
O B:HOH1205 2.1 31.0 1.0
O B:HOH1028 2.1 27.9 1.0
O B:HOH1483 2.2 31.6 1.0
O B:HOH1022 2.2 24.6 1.0
O B:HOH1309 2.2 31.5 1.0
OE1 B:GLU109 4.0 20.9 1.0
O B:HOH1420 4.2 47.5 1.0
O B:HOH1018 4.2 22.3 1.0
OE1 B:GLU113 4.2 33.9 1.0
CG B:GLU106 4.3 20.3 1.0
OE2 B:GLU106 4.3 33.4 1.0
O B:HOH1375 4.4 48.8 1.0
O B:HOH1178 4.5 49.8 1.0
O B:HOH1270 4.7 20.4 1.0
O B:GLU106 4.7 17.6 1.0
CD B:GLU109 4.7 20.1 1.0
CD B:GLU106 4.7 33.1 1.0
OE2 B:GLU113 4.8 38.9 1.0
CD B:GLU113 4.9 35.1 1.0
CB B:ALA110 4.9 15.7 1.0

Magnesium binding site 3 out of 8 in 6onc

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Magnesium binding site 3 out of 8 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, As-Isolated


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, As-Isolated within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg706

b:42.0
occ:1.00
O B:HOH822 2.1 32.7 1.0
O A:HOH1309 2.2 35.8 1.0
O B:HOH968 2.3 26.6 1.0
O A:HOH1028 4.0 34.0 1.0
O A:HOH1130 4.1 40.5 1.0
O A:HOH1397 4.2 46.7 1.0
OE2 B:GLU372 4.3 21.2 1.0
O B:HOH1236 4.3 28.5 1.0
OE1 B:GLU372 4.4 21.0 1.0
O A:HOH1098 4.5 35.8 1.0
CB B:PRO361 4.6 20.4 1.0
O B:HOH1177 4.6 36.6 1.0
O A:HOH1240 4.7 16.6 1.0
O B:HOH1381 4.7 31.4 1.0
CA A:GLY184 4.8 19.5 1.0
CD B:GLU372 4.8 17.3 1.0
O A:HOH1245 4.9 37.9 1.0

Magnesium binding site 4 out of 8 in 6onc

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Magnesium binding site 4 out of 8 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, As-Isolated


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, As-Isolated within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg705

b:28.7
occ:1.00
O C:HOH1119 2.1 21.2 1.0
O C:HOH1308 2.2 30.9 1.0
O C:HOH1126 2.2 31.6 1.0
O C:HOH1023 2.2 21.3 1.0
O C:HOH1463 2.2 29.5 1.0
O C:HOH1042 2.3 26.1 1.0
OE2 C:GLU109 4.1 22.7 1.0
O C:HOH1399 4.1 46.8 1.0
O C:HOH1021 4.2 20.9 1.0
OE1 C:GLU113 4.2 32.8 1.0
O C:HOH1121 4.2 42.9 1.0
O C:HOH1412 4.3 46.1 1.0
CG C:GLU106 4.3 18.7 1.0
OE2 C:GLU106 4.5 29.4 1.0
O C:HOH1253 4.6 17.9 1.0
OE2 C:GLU113 4.7 31.8 1.0
O C:GLU106 4.7 15.8 1.0
CD C:GLU106 4.8 28.0 1.0
O C:HOH1077 4.8 37.0 1.0
CD C:GLU109 4.8 20.4 1.0
CB C:ALA110 4.8 16.5 1.0
CD C:GLU113 4.8 33.1 1.0

Magnesium binding site 5 out of 8 in 6onc

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Magnesium binding site 5 out of 8 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, As-Isolated


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, As-Isolated within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg706

b:34.8
occ:1.00
O D:HOH1344 2.0 32.8 1.0
O D:HOH1313 2.2 44.9 1.0
O C:HOH1046 2.2 27.5 1.0
O C:HOH877 2.3 28.6 1.0
O C:HOH1414 2.5 44.3 1.0
O D:HOH1175 3.7 30.7 1.0
O D:HOH1212 4.1 26.6 1.0
O C:HOH1203 4.2 27.9 1.0
OE2 C:GLU372 4.4 19.6 1.0
O C:HOH1183 4.4 31.2 1.0
CB C:PRO361 4.5 19.3 1.0
OE1 C:GLU372 4.5 18.0 1.0
O D:HOH1048 4.5 37.7 1.0
O D:HOH1110 4.6 42.1 1.0
O D:HOH1230 4.6 16.5 1.0
CD C:GLU372 4.9 14.8 1.0
CA D:GLY184 4.9 17.4 1.0

Magnesium binding site 6 out of 8 in 6onc

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Magnesium binding site 6 out of 8 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, As-Isolated


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, As-Isolated within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg706

b:34.0
occ:1.00
O D:HOH1012 2.0 23.9 1.0
O D:HOH1416 2.1 37.1 1.0
O D:HOH856 2.1 35.8 1.0
O D:HOH892 2.2 25.7 1.0
O D:HOH1254 2.2 37.7 1.0
O D:HOH1148 2.5 51.8 1.0
OE1 D:GLU109 4.1 26.4 1.0
O D:HOH1367 4.1 49.8 1.0
O C:HOH1431 4.1 52.6 1.0
CG D:GLU106 4.1 16.5 0.5
O D:HOH1076 4.2 22.8 1.0
OE1 D:GLU113 4.2 37.3 1.0
OE2 D:GLU106 4.3 22.8 0.5
O D:GLU106 4.6 17.1 0.5
O D:GLU106 4.6 17.0 0.5
CD D:GLU106 4.7 22.2 0.5
CD D:GLU109 4.7 22.8 1.0
OE2 D:GLU113 4.7 37.8 1.0
O D:HOH1241 4.7 21.5 1.0
CB D:ALA110 4.8 19.1 1.0
CD D:GLU113 4.8 35.3 1.0
O D:HOH921 4.9 45.8 1.0

Magnesium binding site 7 out of 8 in 6onc

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Magnesium binding site 7 out of 8 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, As-Isolated


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, As-Isolated within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg707

b:34.4
occ:1.00
OE1 D:GLN406 2.1 34.9 1.0
O D:HOH1192 2.1 37.9 1.0
O D:HOH1077 2.1 30.3 1.0
O D:HOH838 2.4 34.3 1.0
O D:HOH1385 2.5 45.4 1.0
CD D:GLN406 3.0 36.5 1.0
NE2 D:GLN406 3.4 30.5 1.0
O D:HOH1160 3.8 42.7 1.0
O D:SER405 4.3 29.1 0.5
O D:HOH837 4.3 34.6 1.0
O D:HOH1031 4.3 44.8 1.0
CG D:GLN406 4.3 30.3 1.0
CA D:GLN406 4.6 22.6 1.0
O D:SER405 4.7 29.6 0.5
CB D:GLN406 4.8 26.1 1.0
CD D:PRO407 4.8 20.8 1.0

Magnesium binding site 8 out of 8 in 6onc

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Magnesium binding site 8 out of 8 in the Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, As-Isolated


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Desulfovibrio Vulgaris Carbon Monoxide Dehydrogenase Produced Without Cooc, As-Isolated within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg708

b:43.2
occ:1.00
O C:HOH1338 2.0 37.9 1.0
O D:HOH900 2.1 38.6 1.0
O D:HOH816 2.5 34.6 1.0
O D:HOH1402 2.7 40.4 1.0
O C:HOH1272 2.9 35.3 1.0
O C:HOH1154 3.2 36.5 1.0
O D:HOH1137 4.0 29.5 1.0
O C:HOH926 4.2 29.2 1.0
CB D:PRO361 4.2 24.4 1.0
O C:HOH1264 4.3 17.4 1.0
OE2 D:GLU372 4.4 22.4 1.0
OE1 D:GLU372 4.5 21.4 1.0
O C:HOH1058 4.6 36.5 1.0
CA C:GLY184 4.7 17.3 1.0
O C:HOH1210 4.7 34.5 1.0
O D:HOH1348 4.9 30.1 1.0
CD D:GLU372 4.9 20.4 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: Mon Dec 14 23:44:05 2020

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