Nickel in PDB 5a0y: Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution

All present enzymatic activity of Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution:
2.8.4.1;

The structure of Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution, PDB code: 5a0y was solved by T.Wagner, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.35 / 1.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.227, 118.300, 122.560, 90.00, 91.90, 90.00
R / Rfree (%)	11.1 / 12.9

The structure of Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution also contains other interesting chemical elements:

Magnesium	(Mg)	16 atoms
Potassium	(K)	1 atom
Chlorine	(Cl)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Nickel atom in the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution (pdb code 5a0y). 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 From Methanothermobacter Marburgensis at 1.1 A Resolution, PDB code: 5a0y:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 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 From Methanothermobacter Marburgensis at 1.1 A Resolution 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 7.0 1.0 ND A:F43554 2.1 6.4 1.0 NB A:F43554 2.1 6.8 1.0 NA A:F43554 2.1 6.8 1.0 OE1 A:GLN147 2.3 8.4 1.0 S1 D:COM555 2.4 9.0 1.0 C4B A:F43554 3.0 6.6 1.0 C1C A:F43554 3.0 6.9 1.0 C1A A:F43554 3.0 6.4 1.0 C4D A:F43554 3.1 6.5 1.0 C1D A:F43554 3.1 6.6 1.0 C4C A:F43554 3.1 6.9 1.0 C1B A:F43554 3.2 6.5 1.0 C4A A:F43554 3.3 6.2 1.0 C1 D:COM555 3.3 10.1 1.0 CHA A:F43554 3.3 6.3 1.0 CHC A:F43554 3.3 7.3 1.0 CD A:GLN147 3.3 8.0 1.0 CHB A:F43554 3.4 6.7 1.0 CHD A:F43554 3.5 6.9 1.0 NE2 A:GLN147 3.7 8.8 1.0 N5B A:F43554 3.9 6.9 1.0 C2 D:COM555 4.1 10.9 1.0 OH E:TYR367 4.1 9.2 1.0 C3B A:F43554 4.3 7.1 1.0 C3A A:F43554 4.3 6.5 1.0 C2C A:F43554 4.3 7.1 1.0 OH D:TYR333 4.4 8.1 1.0 C2A A:F43554 4.4 6.2 1.0 C3D A:F43554 4.4 6.2 1.0 C2D A:F43554 4.4 6.7 1.0 C3C A:F43554 4.4 7.4 1.0 C2B A:F43554 4.5 7.4 1.0 CAA A:F43554 4.7 6.5 1.0 CG A:GLN147 4.7 7.8 1.0 CAB A:F43554 4.9 7.4 1.0 C7D A:F43554 5.0 6.8 1.0 C6B A:F43554 5.0 7.4 1.0

Nickel binding site 2 out of 2 in the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 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 From Methanothermobacter Marburgensis at 1.1 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni552 b:7.7 occ:1.00 NI D:F43552 0.0 7.7 1.0 ND D:F43552 2.0 7.3 1.0 NC D:F43552 2.1 7.8 1.0 NB D:F43552 2.1 7.3 1.0 NA D:F43552 2.1 7.1 1.0 OE1 D:GLN147 2.3 9.4 1.0 S1 A:COM555 2.4 10.0 1.0 C4B D:F43552 3.0 7.7 1.0 C1A D:F43552 3.0 7.2 1.0 C1C D:F43552 3.0 7.7 1.0 C4D D:F43552 3.1 7.4 1.0 C1D D:F43552 3.1 7.3 1.0 C4C D:F43552 3.1 7.2 1.0 C1B D:F43552 3.2 7.7 1.0 C4A D:F43552 3.3 7.3 1.0 C1 A:COM555 3.3 11.6 1.0 CHA D:F43552 3.3 7.2 1.0 CD D:GLN147 3.3 9.7 1.0 CHC D:F43552 3.3 8.2 1.0 CHB D:F43552 3.4 7.4 1.0 CHD D:F43552 3.5 7.5 1.0 NE2 D:GLN147 3.7 10.6 1.0 N5B D:F43552 3.9 7.4 1.0 OH B:TYR367 4.1 9.7 1.0 C2 A:COM555 4.1 12.1 1.0 C3B D:F43552 4.3 8.1 1.0 C3A D:F43552 4.3 7.6 1.0 C2A D:F43552 4.3 7.3 1.0 OH A:TYR333 4.3 9.0 1.0 C2C D:F43552 4.4 7.7 1.0 C3D D:F43552 4.4 7.1 1.0 C2D D:F43552 4.4 7.7 1.0 C3C D:F43552 4.4 7.8 1.0 C2B D:F43552 4.5 7.8 1.0 CAA D:F43552 4.7 7.8 1.0 CG D:GLN147 4.7 9.4 1.0 CAB D:F43552 4.9 8.3 1.0 C7D D:F43552 5.0 7.7 1.0 C6B D:F43552 5.0 7.9 1.0

T.Wagner, J.Kahnt, U.Ermler, S.Shima. Didehydroaspartate Modification in Methyl-Coenzyme M Reductase Catalyzing Methane Formation. Angew.Chem.Int.Ed.Engl. V. 55 10630 2016.
ISSN: ISSN 1433-7851
PubMed: 27467699
DOI: 10.1002/ANIE.201603882