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:
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
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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
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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
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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
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