Atomistry » Magnesium » PDB 5fux-5gg7 » 5g0r
Atomistry »
  Magnesium »
    PDB 5fux-5gg7 »
      5g0r »

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

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

Go back to 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

Go back to 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

Go back to 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

Go back to 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

Go back to 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

Go back to 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

Go back to 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

Go back to 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

Go back to 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: Mon Dec 14 20:20:11 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy