Nickel in PDB 5g0r: 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;

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

The structure of Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol also contains other interesting chemical elements:

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

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

Nickel binding site 1 out of 2 in the Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni 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:Ni554 b:6.8 occ:1.00 NI A:F43554 0.0 6.8 1.0 NC A:F43554 2.0 7.8 1.0 ND A:F43554 2.1 6.5 1.0 NA A:F43554 2.1 6.6 1.0 NB A:F43554 2.1 6.8 1.0 OE1 A:GLN147 2.4 9.5 1.0 O D:HOH2395 2.5 4.3 1.0 C4B A:F43554 3.0 7.3 1.0 C1C A:F43554 3.0 7.1 1.0 C1A A:F43554 3.0 6.4 1.0 C1D A:F43554 3.1 6.9 1.0 C4D A:F43554 3.1 6.1 1.0 C4C A:F43554 3.1 7.0 1.0 C1B A:F43554 3.2 6.9 1.0 C4A A:F43554 3.2 6.2 1.0 CHA A:F43554 3.3 6.0 1.0 CHC A:F43554 3.3 8.1 1.0 CD A:GLN147 3.4 9.2 1.0 CHB A:F43554 3.4 6.9 1.0 CHD A:F43554 3.5 6.1 1.0 NE2 A:GLN147 3.7 9.5 1.0 N5B A:F43554 3.8 7.1 1.0 OH E:TYR367 4.1 7.5 1.0 C3A A:F43554 4.3 6.5 1.0 C3B A:F43554 4.3 7.7 1.0 OH D:TYR333 4.3 7.7 1.0 C2C A:F43554 4.3 7.5 1.0 C2A A:F43554 4.3 5.8 1.0 C3D A:F43554 4.4 6.3 1.0 C2D A:F43554 4.4 6.8 1.0 C3C A:F43554 4.4 7.7 1.0 C2B A:F43554 4.4 7.3 1.0 O D:HOH2218 4.6 22.9 1.0 CAA A:F43554 4.6 7.3 1.0 CG A:GLN147 4.7 8.7 1.0 CAB A:F43554 4.8 8.7 1.0 C6B A:F43554 4.9 8.5 1.0 C7D A:F43554 4.9 6.9 1.0

Nickel binding site 2 out of 2 in the Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni 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 D:Ni552 b:7.5 occ:1.00 NI D:F43552 0.0 7.5 1.0 ND D:F43552 2.0 7.1 1.0 NB D:F43552 2.1 7.9 1.0 NC D:F43552 2.1 7.5 1.0 NA D:F43552 2.1 7.3 1.0 OE1 D:GLN147 2.3 10.1 1.0 O A:HOH2457 2.6 5.2 1.0 C4B D:F43552 3.0 8.1 1.0 C1C D:F43552 3.0 8.1 1.0 C1A D:F43552 3.0 7.5 1.0 C4D D:F43552 3.1 7.0 1.0 C1D D:F43552 3.1 7.1 1.0 C4C D:F43552 3.1 7.6 1.0 C1B D:F43552 3.2 7.6 1.0 C4A D:F43552 3.3 7.3 1.0 CHA D:F43552 3.3 6.9 1.0 CD D:GLN147 3.3 9.9 1.0 CHC D:F43552 3.3 8.8 1.0 CHB D:F43552 3.4 6.7 1.0 CHD D:F43552 3.5 7.3 1.0 NE2 D:GLN147 3.6 10.7 1.0 N5B D:F43552 3.8 8.0 1.0 OH B:TYR367 4.1 8.4 1.0 C3B D:F43552 4.3 8.3 1.0 C3A D:F43552 4.3 7.4 1.0 OH A:TYR333 4.3 8.7 1.0 C3D D:F43552 4.3 6.9 1.0 C2D D:F43552 4.4 7.1 1.0 C2C D:F43552 4.4 8.0 1.0 C2A D:F43552 4.4 6.8 1.0 C3C D:F43552 4.4 8.3 1.0 C2B D:F43552 4.4 8.1 1.0 CAA D:F43552 4.6 7.7 1.0 CG D:GLN147 4.7 10.4 1.0 CAB D:F43552 4.8 9.0 1.0 C6B D:F43552 4.9 8.9 1.0 C7D D:F43552 5.0 7.7 1.0

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