Nickel in PDB 5n1q: Methyl-Coenzyme M Reductase III From Methanothermococcus Thermolithotrophicus at 1.9 A Resolution

All present enzymatic activity of Methyl-Coenzyme M Reductase III From Methanothermococcus Thermolithotrophicus at 1.9 A Resolution:
2.8.4.1;

The structure of Methyl-Coenzyme M Reductase III From Methanothermococcus Thermolithotrophicus at 1.9 A Resolution, PDB code: 5n1q was solved by T.Wagner, C.E.Wegner, U.Ermler, S.Shima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.63 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	111.811, 77.224, 145.458, 90.00, 107.01, 90.00
R / Rfree (%)	16.9 / 19

The structure of Methyl-Coenzyme M Reductase III From Methanothermococcus Thermolithotrophicus at 1.9 A Resolution also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Potassium	(K)	1 atom

The binding sites of Nickel atom in the Methyl-Coenzyme M Reductase III From Methanothermococcus Thermolithotrophicus at 1.9 A Resolution (pdb code 5n1q). 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 III From Methanothermococcus Thermolithotrophicus at 1.9 A Resolution, PDB code: 5n1q:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Methyl-Coenzyme M Reductase III From Methanothermococcus Thermolithotrophicus at 1.9 A Resolution


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 III From Methanothermococcus Thermolithotrophicus at 1.9 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni602 b:27.9 occ:1.00 NI A:F43602 0.0 27.9 1.0 ND A:F43602 2.0 24.3 1.0 NC A:F43602 2.1 26.9 1.0 NB A:F43602 2.1 29.5 1.0 NA A:F43602 2.1 24.1 1.0 OE1 A:GLN151 2.1 25.1 1.0 S1 A:COM604 2.6 29.9 0.8 C4B A:F43602 3.0 30.1 1.0 C1A A:F43602 3.0 23.4 1.0 C1C A:F43602 3.0 28.1 1.0 C1D A:F43602 3.0 24.8 1.0 C4D A:F43602 3.1 23.4 1.0 C4C A:F43602 3.1 26.2 1.0 C1B A:F43602 3.2 27.3 1.0 C4A A:F43602 3.2 25.9 1.0 CD A:GLN151 3.2 36.7 1.0 CHA A:F43602 3.2 24.7 1.0 CHC A:F43602 3.3 30.2 1.0 CHB A:F43602 3.4 25.9 1.0 C1 A:COM604 3.4 28.4 0.8 CHD A:F43602 3.5 24.8 1.0 NE2 A:GLN151 3.7 32.7 1.0 N5B A:F43602 3.8 27.9 1.0 C2 A:COM604 4.2 28.0 0.8 OH E:TYR367 4.2 35.5 1.0 C3B A:F43602 4.3 29.9 1.0 C3A A:F43602 4.3 25.4 1.0 C3D A:F43602 4.3 24.0 1.0 C2D A:F43602 4.3 25.4 1.0 C2A A:F43602 4.3 24.1 1.0 OH D:TYR336 4.4 30.2 1.0 C2C A:F43602 4.4 27.4 1.0 C3C A:F43602 4.4 27.6 1.0 C2B A:F43602 4.4 28.7 1.0 CG A:GLN151 4.5 28.2 1.0 CAA A:F43602 4.7 27.3 1.0 CAB A:F43602 4.8 30.5 1.0 C6B A:F43602 4.9 29.3 1.0 C7D A:F43602 4.9 25.0 1.0

Nickel binding site 2 out of 2 in the Methyl-Coenzyme M Reductase III From Methanothermococcus Thermolithotrophicus at 1.9 A Resolution


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 III From Methanothermococcus Thermolithotrophicus at 1.9 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni602 b:23.6 occ:1.00 NI D:F43602 0.0 23.6 1.0 ND D:F43602 2.0 23.8 1.0 NC D:F43602 2.1 23.8 1.0 NB D:F43602 2.1 23.8 1.0 NA D:F43602 2.1 21.8 1.0 OE1 D:GLN151 2.2 27.4 1.0 S1 D:COM601 2.5 26.1 0.8 C4B D:F43602 3.0 23.9 1.0 C1A D:F43602 3.0 21.6 1.0 C1C D:F43602 3.0 25.0 1.0 C1D D:F43602 3.0 25.2 1.0 C4D D:F43602 3.1 23.2 1.0 C4C D:F43602 3.1 23.5 1.0 C1B D:F43602 3.2 23.6 1.0 CD D:GLN151 3.2 29.3 1.0 C4A D:F43602 3.2 22.1 1.0 CHA D:F43602 3.2 21.7 1.0 CHC D:F43602 3.3 23.7 1.0 CHB D:F43602 3.4 20.0 1.0 CHD D:F43602 3.5 23.9 1.0 C1 D:COM601 3.5 24.6 0.8 NE2 D:GLN151 3.6 20.3 1.0 N5B D:F43602 3.8 22.4 1.0 C2 D:COM601 4.2 24.4 0.8 C3B D:F43602 4.3 24.9 1.0 C3A D:F43602 4.3 21.7 1.0 OH B:TYR367 4.3 38.4 1.0 C2D D:F43602 4.3 25.1 1.0 C3D D:F43602 4.3 22.5 1.0 OH A:TYR336 4.3 27.6 1.0 C2A D:F43602 4.3 22.7 1.0 C2C D:F43602 4.4 23.2 1.0 C3C D:F43602 4.4 22.6 1.0 C2B D:F43602 4.4 25.4 1.0 CG D:GLN151 4.5 28.4 1.0 CAA D:F43602 4.7 22.9 1.0 CAB D:F43602 4.8 26.5 1.0 C6B D:F43602 4.9 26.2 1.0 C7D D:F43602 4.9 24.8 1.0

T.Wagner, C.E.Wegner, J.Kahnt, U.Ermler, S.Shima. Phylogenetic and Structural Comparisons of the Three Types of Methyl Coenzyme M Reductase From Methanococcales and Methanobacteriales. J.Bacteriol. V. 199 2017.
ISSN: ESSN 1098-5530
PubMed: 28559298
DOI: 10.1128/JB.00197-17