Nickel in PDB 1hbn: Methyl-Coenzyme M Reductase

The structure of Methyl-Coenzyme M Reductase, PDB code: 1hbn was solved by U.Ermler, W.Grabarse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.16
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.720, 116.883, 122.582, 90.00, 92.02, 90.00
R / Rfree (%)	12.4 / 19

The structure of Methyl-Coenzyme M Reductase also contains other interesting chemical elements:

Magnesium	(Mg)	18 atoms
Zinc	(Zn)	1 atom
Chlorine	(Cl)	2 atoms
Sodium	(Na)	10 atoms

The binding sites of Nickel atom in the Methyl-Coenzyme M Reductase (pdb code 1hbn). 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, PDB code: 1hbn:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Methyl-Coenzyme M Reductase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1550 b:10.3 occ:1.00 NI A:F431550 0.0 10.3 1.0 ND A:F431550 2.0 10.5 1.0 NB A:F431550 2.1 10.6 1.0 NC A:F431550 2.1 10.3 1.0 NA A:F431550 2.1 9.3 1.0 OE1 D:GLN147 2.3 11.4 1.0 S1 A:COM1552 2.4 12.0 1.0 C1A A:F431550 3.0 10.0 1.0 C4B A:F431550 3.0 10.4 1.0 C1C A:F431550 3.1 10.6 1.0 C1D A:F431550 3.1 9.8 1.0 C4D A:F431550 3.1 10.3 1.0 C1B A:F431550 3.2 11.1 1.0 C4C A:F431550 3.2 10.1 1.0 C4A A:F431550 3.2 9.7 1.0 C1 A:COM1552 3.3 13.8 1.0 CD D:GLN147 3.3 11.3 1.0 CHA A:F431550 3.3 10.7 1.0 CHC A:F431550 3.4 10.5 1.0 CHB A:F431550 3.4 11.1 1.0 CHD A:F431550 3.5 10.4 1.0 NE2 D:GLN147 3.7 12.0 1.0 N5B A:F431550 3.9 11.5 1.0 C2 A:COM1552 4.1 14.2 1.0 OH B:TYR367 4.2 12.3 1.0 C3A A:F431550 4.3 10.7 1.0 C3B A:F431550 4.3 10.4 1.0 OH A:TYR333 4.4 12.6 1.0 C2C A:F431550 4.4 10.6 1.0 C3D A:F431550 4.4 10.1 1.0 C2A A:F431550 4.4 10.0 1.0 C2D A:F431550 4.4 10.2 1.0 C3C A:F431550 4.4 10.8 1.0 C2B A:F431550 4.5 11.3 1.0 CAA A:F431550 4.6 11.6 1.0 CG D:GLN147 4.6 12.3 1.0 CAB A:F431550 4.9 11.8 1.0

Nickel binding site 2 out of 2 in the Methyl-Coenzyme M Reductase


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni1550 b:10.7 occ:1.00 NI D:F431550 0.0 10.7 1.0 NC D:F431550 2.0 11.1 1.0 ND D:F431550 2.0 9.8 1.0 NB D:F431550 2.1 10.2 1.0 NA D:F431550 2.2 10.2 1.0 OE1 A:GLN147 2.3 12.4 1.0 S1 D:COM1552 2.4 12.4 1.0 C4B D:F431550 3.0 10.9 1.0 C1A D:F431550 3.0 10.8 1.0 C1C D:F431550 3.0 11.1 1.0 C1D D:F431550 3.1 10.4 1.0 C4D D:F431550 3.1 10.4 1.0 C4C D:F431550 3.1 11.0 1.0 C1B D:F431550 3.2 10.6 1.0 C4A D:F431550 3.2 10.4 1.0 C1 D:COM1552 3.3 14.6 1.0 CHA D:F431550 3.3 10.8 1.0 CHC D:F431550 3.4 11.2 1.0 CD A:GLN147 3.4 11.9 1.0 CHD D:F431550 3.4 10.6 1.0 CHB D:F431550 3.5 11.1 1.0 NE2 A:GLN147 3.7 12.5 1.0 N5B D:F431550 3.9 11.8 1.0 C2 D:COM1552 4.1 15.2 1.0 OH E:TYR367 4.2 12.9 1.0 OH D:TYR333 4.3 13.0 1.0 C2C D:F431550 4.3 11.0 1.0 C3B D:F431550 4.3 11.6 1.0 C3A D:F431550 4.3 11.1 1.0 C3D D:F431550 4.3 10.8 1.0 C2D D:F431550 4.4 10.6 1.0 C3C D:F431550 4.4 11.5 1.0 C2A D:F431550 4.4 10.1 1.0 C2B D:F431550 4.5 11.3 1.0 CAA D:F431550 4.6 11.9 1.0 CG A:GLN147 4.7 11.7 1.0 CAB D:F431550 4.9 12.1 1.0 C7D D:F431550 4.9 11.3 1.0

W.Grabarse, F.Mahlert, E.C.Duin, M.Goubeaud, S.Shima, R.K.Thauer, V.Lamzin, U.Ermler. On the Mechanism of Biological Methane Formation: Structural Evidence For Conformational Changes in Methyl-Coenzyme M Reductase Upon Substrate Binding J.Mol.Biol. V. 309 315 2001.
ISSN: ISSN 0022-2836
PubMed: 11491299
DOI: 10.1006/JMBI.2001.4647