Atomistry » Magnesium » PDB 6oiw-6oqv » 6onc
Atomistry »
  Magnesium »
    PDB 6oiw-6oqv »
      6onc »

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

Go back to Magnesium Binding Sites List in 6onc
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

Go back to Magnesium Binding Sites List in 6onc
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

Go back to Magnesium Binding Sites List in 6onc
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

Go back to Magnesium Binding Sites List in 6onc
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

Go back to Magnesium Binding Sites List in 6onc
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

Go back to Magnesium Binding Sites List in 6onc
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

Go back to Magnesium Binding Sites List in 6onc
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

Go back to Magnesium Binding Sites List in 6onc
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: Tue Oct 1 13:27:57 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy