Nickel in PDB 5a8k: Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 A Resolution

All present enzymatic activity of Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 A Resolution:
2.8.4.1;

The structure of Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 A Resolution, PDB code: 5a8k 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)	48.47 / 1.41
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	84.140, 150.540, 187.090, 90.00, 90.00, 90.00
R / Rfree (%)	11.4 / 14

The structure of Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 A Resolution also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Potassium	(K)	5 atoms
Calcium	(Ca)	12 atoms

The binding sites of Nickel atom in the Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 A Resolution (pdb code 5a8k). 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 Wolfeii at 1.4 A Resolution, PDB code: 5a8k:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 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 Wolfeii at 1.4 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1550 b:6.5 occ:1.00 NI A:F431550 0.0 6.5 1.0 ND A:F431550 2.1 5.1 1.0 NB A:F431550 2.1 5.9 1.0 NC A:F431550 2.1 6.6 1.0 NA A:F431550 2.1 5.9 1.0 OE1 D:GLN147 2.4 10.2 1.0 S1 A:COM556 2.5 9.8 0.7 C4B A:F431550 3.0 6.6 1.0 C1A A:F431550 3.0 5.3 1.0 C1C A:F431550 3.0 6.3 1.0 C1D A:F431550 3.1 5.8 1.0 C4D A:F431550 3.1 5.8 1.0 C4C A:F431550 3.1 6.2 1.0 C1B A:F431550 3.2 6.0 1.0 C4A A:F431550 3.2 5.9 1.0 CHA A:F431550 3.3 5.5 1.0 CD D:GLN147 3.3 9.5 1.0 CHC A:F431550 3.4 6.0 1.0 C1 A:COM556 3.4 13.6 0.7 CHB A:F431550 3.4 6.8 1.0 CHD A:F431550 3.5 6.2 1.0 NE2 D:GLN147 3.7 9.4 1.0 N5B A:F431550 3.8 7.1 1.0 C2 A:COM556 4.1 15.9 0.7 OH B:TYR367 4.2 8.1 1.0 C3B A:F431550 4.3 6.8 1.0 OH A:TYR333 4.3 9.7 1.0 C3A A:F431550 4.3 5.4 1.0 C3D A:F431550 4.3 5.5 1.0 C2C A:F431550 4.3 6.6 1.0 C2D A:F431550 4.3 5.6 1.0 C2A A:F431550 4.4 5.3 1.0 C3C A:F431550 4.4 7.0 1.0 C2B A:F431550 4.4 6.6 1.0 CAA A:F431550 4.6 6.7 1.0 CG D:GLN147 4.7 8.1 1.0 CAB A:F431550 4.8 7.1 1.0 C6B A:F431550 4.9 8.2 1.0 C7D A:F431550 5.0 7.0 1.0

Nickel binding site 2 out of 2 in the Methyl-Coenzyme M Reductase From Methanothermobacter Wolfeii at 1.4 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 Wolfeii at 1.4 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni1550 b:6.3 occ:1.00 NI D:F431550 0.0 6.3 1.0 NC D:F431550 2.0 6.0 1.0 NB D:F431550 2.1 6.0 1.0 ND D:F431550 2.1 6.1 1.0 NA D:F431550 2.1 5.6 1.0 OE1 A:GLN147 2.4 9.8 1.0 S1 D:COM555 2.5 8.6 0.7 C4B D:F431550 2.9 6.1 1.0 C1C D:F431550 3.0 5.8 1.0 C1A D:F431550 3.0 5.7 1.0 C4D D:F431550 3.1 5.7 1.0 C4C D:F431550 3.1 6.7 1.0 C1D D:F431550 3.1 5.5 1.0 C1B D:F431550 3.2 5.7 1.0 C4A D:F431550 3.2 6.2 1.0 C1 D:COM555 3.3 13.4 0.7 CHA D:F431550 3.3 5.0 1.0 CHC D:F431550 3.3 6.1 1.0 CD A:GLN147 3.4 8.3 1.0 CHB D:F431550 3.4 6.2 1.0 CHD D:F431550 3.5 6.1 1.0 NE2 A:GLN147 3.7 9.7 1.0 N5B D:F431550 3.8 6.2 1.0 C2 D:COM555 4.1 14.5 0.7 OH E:TYR367 4.2 8.2 1.0 C3B D:F431550 4.3 6.4 1.0 OH D:TYR333 4.3 8.4 1.0 C3A D:F431550 4.3 6.2 1.0 C3D D:F431550 4.3 5.7 1.0 C2C D:F431550 4.3 6.0 1.0 C2D D:F431550 4.4 5.2 1.0 C2A D:F431550 4.4 5.9 1.0 C3C D:F431550 4.4 6.4 1.0 C2B D:F431550 4.4 6.3 1.0 CAA D:F431550 4.7 6.8 1.0 CG A:GLN147 4.7 7.3 1.0 CAB D:F431550 4.8 7.2 1.0 C6B D:F431550 4.9 8.5 1.0 C7D D:F431550 4.9 6.6 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