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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:

Nickel (Ni) 2 atoms
Potassium (K) 1 atom
Chlorine (Cl) 3 atoms
Sodium (Na) 3 atoms

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

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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 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 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 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 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 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 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 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 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 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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