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Chlorine 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
Magnesium (Mg) 18 atoms
Potassium (K) 1 atom
Sodium (Na) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol, PDB code: 5g0r:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 5g0r

Go back to Chlorine Binding Sites List in 5g0r
Chlorine binding site 1 out of 3 in the Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl1551

b:18.7
occ:1.00
 O D:HOH2243 3.1 11.9 1.0
N A:GLY61 3.2 11.9 1.0
O A:HOH2156 3.4 28.6 1.0
CE1 D:HIS131 3.6 16.8 1.0
CA A:ILE60 4.0 12.5 1.0
C A:ILE60 4.1 12.3 1.0
NE2 D:HIS131 4.1 16.1 1.0
CA A:GLY61 4.1 11.6 1.0
O A:ASP59 4.3 14.9 1.0
O D:HOH2244 4.3 16.6 1.0
CD1 A:ILE60 4.4 17.0 1.0
CG2 A:ILE60 4.4 13.9 1.0
CB A:ILE60 4.7 13.8 1.0
ND1 D:HIS131 4.7 16.1 1.0
OG1 D:THR135 4.7 10.7 1.0
OG D:SER237 4.8 12.0 1.0
O A:GLY61 4.9 13.4 1.0

Chlorine binding site 2 out of 3 in 5g0r

Go back to Chlorine Binding Sites List in 5g0r
Chlorine binding site 2 out of 3 in the Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
B:Cl1444

b:16.2
occ:1.00
 O B:HOH2428 3.1 16.0 1.0
O B:HOH2361 3.1 13.3 1.0
O B:HOH2173 3.1 19.4 1.0
NH1 B:ARG235 3.3 12.3 1.0
CD1 C:LEU248 3.5 50.4 1.0
CB B:ALA300 3.7 12.2 1.0
CD B:ARG235 3.8 12.6 1.0
O B:HOH2360 3.9 25.9 1.0
CB B:ARG235 3.9 11.6 1.0
CG B:ARG235 4.1 11.7 1.0
CZ B:ARG235 4.3 11.8 1.0
NE B:ARG235 4.5 12.6 1.0
O B:HOH2358 4.7 11.9 1.0
O B:ALA232 4.7 12.0 1.0
O B:HOH2010 4.8 33.7 1.0
OD1 B:ASP298 4.8 14.8 1.0
CG C:LEU248 4.8 46.3 1.0
O C:HOH2259 4.9 36.9 1.0
N B:MET236 4.9 11.0 1.0

Chlorine binding site 3 out of 3 in 5g0r

Go back to Chlorine Binding Sites List in 5g0r
Chlorine binding site 3 out of 3 in the Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
E:Cl1444

b:20.1
occ:1.00
 O E:HOH2139 3.1 22.1 1.0
O E:HOH2348 3.1 19.5 1.0
O E:HOH2286 3.2 16.5 1.0
NH1 E:ARG235 3.3 16.7 1.0
CD2 F:LEU248 3.6 39.8 1.0
CB E:ALA300 3.7 14.5 1.0
CD E:ARG235 3.8 16.6 1.0
CB E:ARG235 3.9 14.8 1.0
O E:HOH2287 4.0 28.1 1.0
CG E:ARG235 4.1 15.8 1.0
CZ E:ARG235 4.3 17.1 1.0
CG F:LEU248 4.5 38.8 1.0
NE E:ARG235 4.5 16.9 1.0
O E:HOH2285 4.7 15.7 1.0
O E:ALA232 4.8 15.5 1.0
OD1 E:ASP298 4.8 18.2 1.0
N E:MET236 4.9 13.6 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: Sat Dec 12 11:46:16 2020

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