Magnesium in PDB 5g0r: Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol
Enzymatic activity of Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol
All present enzymatic activity of Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol:
2.8.4.1;
Protein crystallography data
The structure of Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol, PDB code: 5g0r
was solved by
T.Wagner,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
38.80 /
1.25
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
82.200,
118.101,
122.640,
90.00,
92.03,
90.00
|
R / Rfree (%)
|
10.5 /
12.4
|
Other elements in 5g0r:
The structure of Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol also contains other interesting chemical elements:
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
18;
Binding sites:
The binding sites of Magnesium atom in the Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol
(pdb code 5g0r). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 18 binding sites of Magnesium where determined in the
Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol, PDB code: 5g0r:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 18 in 5g0r
Go back to
Magnesium Binding Sites List in 5g0r
Magnesium binding site 1 out
of 18 in the Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg551
b:33.0
occ:1.00
|
O
|
A:HOH2258
|
2.0
|
27.5
|
1.0
|
O
|
A:HOH2631
|
2.1
|
31.6
|
1.0
|
O
|
A:HOH2261
|
2.2
|
30.1
|
1.0
|
O
|
A:HOH2630
|
2.9
|
38.9
|
1.0
|
O
|
D:HOH2163
|
4.1
|
33.7
|
1.0
|
O
|
A:HOH2639
|
4.1
|
44.6
|
1.0
|
O
|
D:HOH2071
|
4.2
|
27.7
|
1.0
|
OE2
|
A:GLU134
|
4.3
|
25.4
|
1.0
|
OE1
|
A:GLU134
|
4.3
|
23.3
|
1.0
|
O
|
A:HOH2303
|
4.7
|
36.0
|
1.0
|
CD
|
A:GLU134
|
4.8
|
22.4
|
1.0
|
CG
|
D:PRO54
|
4.8
|
12.3
|
1.0
|
|
Magnesium binding site 2 out
of 18 in 5g0r
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Magnesium Binding Sites List in 5g0r
Magnesium binding site 2 out
of 18 in the Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg553
b:14.8
occ:0.46
|
O
|
A:HOH2632
|
1.9
|
33.0
|
1.0
|
O
|
A:HOH2634
|
2.0
|
29.7
|
1.0
|
O
|
A:HOH2633
|
2.0
|
36.8
|
1.0
|
O
|
A:HOH2579
|
2.1
|
22.2
|
1.0
|
O
|
A:HOH2576
|
2.1
|
26.6
|
1.0
|
O
|
A:HOH2589
|
2.1
|
27.9
|
1.0
|
O
|
A:HOH2575
|
4.1
|
17.6
|
1.0
|
O
|
A:HOH2299
|
4.4
|
38.3
|
1.0
|
OD2
|
A:ASP521
|
4.4
|
14.3
|
1.0
|
O
|
A:ASP516
|
4.5
|
12.9
|
1.0
|
O
|
A:HOH2586
|
4.6
|
18.4
|
1.0
|
O
|
A:HOH2588
|
4.6
|
34.4
|
1.0
|
OD1
|
A:ASP516
|
4.6
|
26.6
|
1.0
|
CG
|
A:ASP521
|
4.7
|
11.7
|
1.0
|
CB
|
A:ASP521
|
4.7
|
10.3
|
1.0
|
CB
|
A:ASP516
|
4.9
|
18.2
|
1.0
|
|
Magnesium binding site 3 out
of 18 in 5g0r
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Magnesium Binding Sites List in 5g0r
Magnesium binding site 3 out
of 18 in the Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg562
b:20.7
occ:1.00
|
O
|
A:HOH2136
|
2.2
|
19.8
|
1.0
|
O
|
A:HOH2635
|
2.3
|
28.3
|
1.0
|
O
|
D:HOH2257
|
2.3
|
16.7
|
1.0
|
O
|
D:HOH2283
|
2.4
|
16.3
|
1.0
|
O
|
A:HOH2138
|
2.5
|
17.2
|
1.0
|
O
|
D:HOH2294
|
4.0
|
39.1
|
1.0
|
O
|
D:HOH2259
|
4.2
|
12.8
|
1.0
|
O
|
A:GLY52
|
4.2
|
11.2
|
1.0
|
OD1
|
D:ASN517
|
4.3
|
10.2
|
1.0
|
O
|
D:HOH2510
|
4.5
|
33.2
|
1.0
|
O
|
D:ALA179
|
4.6
|
11.5
|
1.0
|
CA
|
D:ALA179
|
4.8
|
11.7
|
1.0
|
NZ
|
D:LYS164
|
4.8
|
9.6
|
1.0
|
O
|
D:PRO178
|
4.9
|
11.7
|
1.0
|
O
|
A:ARG51
|
4.9
|
10.4
|
1.0
|
C
|
A:GLY52
|
4.9
|
9.6
|
1.0
|
|
Magnesium binding site 4 out
of 18 in 5g0r
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Magnesium Binding Sites List in 5g0r
Magnesium binding site 4 out
of 18 in the Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg563
b:26.9
occ:1.00
|
O
|
A:LYS11
|
2.2
|
19.9
|
1.0
|
O
|
A:HOH2033
|
2.3
|
21.1
|
1.0
|
O
|
A:PHE14
|
2.3
|
19.1
|
1.0
|
O
|
A:HOH2034
|
2.4
|
30.5
|
1.0
|
O
|
A:HOH2046
|
2.4
|
28.3
|
1.0
|
O
|
A:HOH2035
|
2.5
|
35.2
|
1.0
|
C
|
A:LYS11
|
3.3
|
18.9
|
1.0
|
C
|
A:PHE14
|
3.4
|
19.2
|
1.0
|
CA
|
A:LYS11
|
3.8
|
18.0
|
1.0
|
CA
|
A:GLU15
|
3.8
|
24.6
|
1.0
|
O
|
A:GLU15
|
3.9
|
22.0
|
1.0
|
C
|
A:GLU15
|
4.0
|
21.4
|
1.0
|
N
|
A:GLU15
|
4.1
|
20.8
|
1.0
|
CB
|
A:LYS11
|
4.3
|
19.1
|
1.0
|
O
|
A:GLU16
|
4.4
|
19.6
|
1.0
|
N
|
A:LYS12
|
4.5
|
18.7
|
1.0
|
O
|
A:HOH2025
|
4.5
|
37.6
|
1.0
|
N
|
A:PHE14
|
4.5
|
17.8
|
1.0
|
CA
|
A:PHE14
|
4.6
|
18.2
|
1.0
|
O
|
A:HOH2022
|
4.6
|
28.2
|
1.0
|
CA
|
A:LYS12
|
4.9
|
20.5
|
1.0
|
N
|
A:GLU16
|
4.9
|
18.8
|
1.0
|
C
|
A:LYS12
|
4.9
|
18.6
|
1.0
|
O
|
A:LEU10
|
4.9
|
16.4
|
1.0
|
|
Magnesium binding site 5 out
of 18 in 5g0r
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Magnesium Binding Sites List in 5g0r
Magnesium binding site 5 out
of 18 in the Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1500
b:23.7
occ:0.50
|
O
|
A:HOH2636
|
2.0
|
31.9
|
1.0
|
O
|
B:HOH2290
|
2.1
|
25.2
|
1.0
|
O
|
A:HOH2637
|
2.3
|
48.0
|
1.0
|
O
|
B:HOH2322
|
2.5
|
32.3
|
1.0
|
O
|
A:HOH2638
|
2.6
|
38.4
|
1.0
|
O
|
B:HOH2323
|
2.7
|
38.5
|
1.0
|
O
|
B:HOH2291
|
4.1
|
24.6
|
1.0
|
CM
|
D:MHS257
|
4.2
|
13.4
|
1.0
|
OE1
|
B:GLU169
|
4.3
|
11.7
|
1.0
|
O
|
B:HOH2127
|
4.3
|
27.7
|
0.7
|
O
|
B:HOH2129
|
4.5
|
23.7
|
1.0
|
O
|
D:HOH2340
|
4.6
|
22.3
|
1.0
|
O
|
D:HOH2336
|
4.6
|
29.0
|
1.0
|
NZ
|
B:LYS184
|
4.6
|
9.7
|
1.0
|
O
|
B:HOH2321
|
4.7
|
19.3
|
1.0
|
|
Magnesium binding site 6 out
of 18 in 5g0r
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Magnesium Binding Sites List in 5g0r
Magnesium binding site 6 out
of 18 in the Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1501
b:24.1
occ:0.50
|
O
|
A:HOH2301
|
1.9
|
28.8
|
1.0
|
O
|
A:HOH2640
|
2.1
|
37.2
|
1.0
|
O
|
A:HOH2302
|
2.1
|
38.1
|
1.0
|
O
|
A:HOH2303
|
3.1
|
36.0
|
1.0
|
O
|
A:HOH2639
|
3.4
|
44.6
|
1.0
|
OD1
|
A:ASP177
|
3.9
|
20.6
|
1.0
|
OD2
|
A:ASP177
|
4.1
|
24.6
|
1.0
|
O
|
A:HOH2161
|
4.2
|
41.1
|
1.0
|
O
|
A:HOH2306
|
4.2
|
29.3
|
1.0
|
O
|
D:HOH2152
|
4.2
|
31.2
|
1.0
|
CG
|
A:ASP177
|
4.5
|
20.3
|
1.0
|
|
Magnesium binding site 7 out
of 18 in 5g0r
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Magnesium Binding Sites List in 5g0r
Magnesium binding site 7 out
of 18 in the Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg444
b:31.3
occ:1.00
|
O
|
B:HOH2510
|
2.0
|
46.3
|
1.0
|
O
|
B:HOH2369
|
2.1
|
27.3
|
1.0
|
O
|
B:HOH2368
|
2.1
|
23.8
|
1.0
|
O
|
B:HOH2509
|
2.1
|
40.2
|
1.0
|
O
|
B:HOH2511
|
2.2
|
38.4
|
1.0
|
O
|
B:HOH2375
|
4.0
|
38.6
|
1.0
|
ND2
|
B:ASN250
|
4.1
|
18.2
|
1.0
|
OD2
|
B:ASP254
|
4.1
|
17.5
|
1.0
|
OD1
|
B:ASP254
|
4.2
|
18.3
|
1.0
|
O
|
B:HOH2037
|
4.3
|
40.5
|
1.0
|
O
|
B:HOH2371
|
4.3
|
37.8
|
1.0
|
CG
|
B:ASP254
|
4.6
|
16.6
|
1.0
|
|
Magnesium binding site 8 out
of 18 in 5g0r
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Magnesium Binding Sites List in 5g0r
Magnesium binding site 8 out
of 18 in the Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg445
b:20.7
occ:0.22
|
OD1
|
B:ASP271
|
2.0
|
19.2
|
1.0
|
O
|
B:HOH2393
|
2.1
|
41.5
|
1.0
|
O
|
B:HOH2390
|
2.1
|
22.4
|
1.0
|
O
|
B:HOH2377
|
2.7
|
31.9
|
1.0
|
CG
|
B:ASP271
|
3.0
|
16.5
|
1.0
|
OD2
|
B:ASP271
|
3.4
|
17.2
|
1.0
|
O
|
B:HOH2378
|
3.5
|
38.5
|
1.0
|
O
|
B:HOH2196
|
4.1
|
37.7
|
1.0
|
CB
|
B:ASP271
|
4.3
|
14.9
|
1.0
|
OE1
|
B:GLU274
|
4.4
|
28.6
|
0.4
|
O
|
B:SER267
|
4.5
|
13.5
|
1.0
|
CA
|
B:ASP271
|
4.6
|
14.4
|
1.0
|
N
|
B:ASP271
|
4.6
|
14.6
|
1.0
|
O
|
B:HOH2184
|
4.7
|
39.1
|
1.0
|
OE2
|
B:GLU274
|
4.8
|
27.3
|
0.4
|
CB
|
B:ALA270
|
4.9
|
16.4
|
1.0
|
CD
|
B:GLU274
|
5.0
|
26.4
|
0.4
|
|
Magnesium binding site 9 out
of 18 in 5g0r
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Magnesium Binding Sites List in 5g0r
Magnesium binding site 9 out
of 18 in the Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg250
b:18.6
occ:1.00
|
O
|
C:HOH2158
|
2.1
|
20.9
|
1.0
|
O
|
C:HOH2053
|
2.1
|
16.7
|
1.0
|
OE2
|
C:GLU30
|
2.1
|
16.0
|
1.0
|
O
|
C:HOH2054
|
2.1
|
18.6
|
1.0
|
O
|
C:HOH2064
|
2.1
|
17.7
|
1.0
|
CD
|
C:GLU30
|
3.1
|
15.7
|
1.0
|
OE1
|
C:GLU30
|
3.4
|
16.9
|
1.0
|
NZ
|
C:LYS135
|
3.9
|
26.6
|
1.0
|
O
|
C:HOH2065
|
4.0
|
18.4
|
1.0
|
O
|
C:HOH2071
|
4.1
|
34.2
|
1.0
|
O
|
C:ILE31
|
4.2
|
16.9
|
1.0
|
O
|
C:HOH2056
|
4.2
|
25.6
|
1.0
|
OE2
|
C:GLU139
|
4.3
|
16.6
|
1.0
|
O
|
C:HOH2068
|
4.4
|
20.7
|
1.0
|
O
|
C:HOH2016
|
4.4
|
27.7
|
1.0
|
CG
|
C:GLU30
|
4.4
|
15.4
|
1.0
|
NZ
|
C:LYS27
|
4.5
|
17.7
|
1.0
|
CE
|
C:LYS135
|
4.9
|
25.1
|
1.0
|
|
Magnesium binding site 10 out
of 18 in 5g0r
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Magnesium Binding Sites List in 5g0r
Magnesium binding site 10 out
of 18 in the Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg251
b:11.6
occ:0.27
|
O
|
C:HOH2263
|
2.0
|
18.1
|
0.4
|
O
|
C:HOH2261
|
2.1
|
17.2
|
0.4
|
O
|
C:HOH2236
|
2.2
|
27.3
|
1.0
|
O
|
C:HOH2262
|
2.2
|
34.9
|
1.0
|
O
|
C:HOH2231
|
2.3
|
15.5
|
0.3
|
O
|
A:HOH2503
|
4.1
|
43.0
|
1.0
|
O
|
C:HOH2230
|
4.1
|
21.9
|
1.0
|
O
|
C:HOH2237
|
4.2
|
32.5
|
1.0
|
O
|
C:HOH2239
|
4.5
|
23.7
|
1.0
|
NE
|
C:ARG225
|
4.8
|
16.2
|
1.0
|
OD1
|
C:ASP226
|
4.8
|
19.2
|
1.0
|
CD
|
C:ARG225
|
4.9
|
16.2
|
1.0
|
|
Reference:
E.C.Duin,
T.Wagner,
S.Shima,
D.Prakash,
B.Cronin,
D.R.Yanez-Ruiz,
S.Duval,
R.Rumbeli,
R.T.Stemmler,
R.K.Thauer,
M.Kindermann.
Mode of Action Uncovered For the Specific Reduction of Methane Emissions From Ruminants By the Small Molecule 3-Nitrooxypropanol. Proc.Natl.Acad.Sci.Usa V. 113 6172 2016.
ISSN: ISSN 0027-8424
PubMed: 27140643
DOI: 10.1073/PNAS.1600298113
Page generated: Sun Sep 29 04:34:08 2024
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