Nickel in PDB 1hbm: Methyl-Coenzyme M Reductase Enzyme Product Complex

The structure of Methyl-Coenzyme M Reductase Enzyme Product Complex, PDB code: 1hbm 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)	10.00 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.000, 118.300, 122.800, 90.00, 92.00, 90.00
R / Rfree (%)	16.4 / 19.3

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

Magnesium	(Mg)	5 atoms
Zinc	(Zn)	1 atom
Chlorine	(Cl)	2 atoms
Sodium	(Na)	9 atoms

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

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


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 Enzyme Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1550 b:14.6 occ:1.00 NI A:F431550 0.0 14.6 1.0 NB A:F431550 2.0 12.3 1.0 ND A:F431550 2.0 9.9 1.0 NC A:F431550 2.1 10.8 1.0 NA A:F431550 2.3 9.4 1.0 OS3 A:SHT1551 2.3 16.1 1.0 OE1 D:GLN147 2.3 15.5 1.0 C4B A:F431550 2.9 13.2 1.0 C1A A:F431550 2.9 9.2 1.0 C1C A:F431550 3.0 11.0 1.0 C4D A:F431550 3.0 10.3 1.0 C1D A:F431550 3.1 10.8 1.0 C4C A:F431550 3.2 11.2 1.0 C1B A:F431550 3.2 12.8 1.0 CHC A:F431550 3.2 10.8 1.0 CHA A:F431550 3.3 10.1 1.0 SG2 A:SHT1551 3.3 17.3 1.0 CD D:GLN147 3.3 14.7 1.0 C4A A:F431550 3.3 9.6 1.0 CHD A:F431550 3.6 9.9 1.0 CHB A:F431550 3.6 10.3 1.0 OS1 A:SHT1551 3.6 19.3 1.0 NE2 D:GLN147 3.6 13.9 1.0 OS2 A:SHT1551 3.9 19.8 1.0 N5B A:F431550 4.0 12.8 1.0 C3B A:F431550 4.3 12.1 1.0 C2C A:F431550 4.3 10.8 1.0 C3D A:F431550 4.4 10.5 1.0 OH A:TYR333 4.4 14.0 1.0 C3A A:F431550 4.4 10.3 1.0 C2A A:F431550 4.4 9.2 1.0 C2D A:F431550 4.4 9.7 1.0 C3C A:F431550 4.4 11.8 1.0 OH B:TYR367 4.5 11.2 1.0 C2B A:F431550 4.5 13.5 1.0 CG D:GLN147 4.6 13.9 1.0 CAA A:F431550 4.7 11.1 1.0 CD A:SHT1551 4.9 18.3 1.0 CAB A:F431550 4.9 12.9 1.0

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


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 Enzyme Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni1550 b:15.4 occ:1.00 NI D:F431550 0.0 15.4 1.0 ND D:F431550 2.1 12.4 1.0 NC D:F431550 2.1 10.9 1.0 NB D:F431550 2.2 13.5 1.0 NA D:F431550 2.2 11.5 1.0 OS3 D:SHT1551 2.3 15.5 1.0 OE1 A:GLN147 2.3 16.8 1.0 C1A D:F431550 2.9 12.2 1.0 C4B D:F431550 3.0 13.6 1.0 C1C D:F431550 3.0 11.7 1.0 C1D D:F431550 3.1 11.9 1.0 C4D D:F431550 3.1 12.3 1.0 C4C D:F431550 3.2 11.6 1.0 CHC D:F431550 3.3 12.2 1.0 C1B D:F431550 3.3 13.6 1.0 C4A D:F431550 3.3 12.0 1.0 CHA D:F431550 3.3 12.7 1.0 SG2 D:SHT1551 3.3 14.4 1.0 CD A:GLN147 3.3 16.0 1.0 CHD D:F431550 3.5 11.5 1.0 CHB D:F431550 3.5 11.7 1.0 OS2 D:SHT1551 3.6 17.1 1.0 NE2 A:GLN147 3.7 13.9 1.0 OS1 D:SHT1551 3.8 16.9 1.0 N5B D:F431550 4.0 13.7 1.0 OH D:TYR333 4.3 16.4 1.0 C2C D:F431550 4.3 11.2 1.0 C3A D:F431550 4.3 12.4 1.0 C3B D:F431550 4.4 13.8 1.0 C3D D:F431550 4.4 12.6 1.0 C2D D:F431550 4.4 13.1 1.0 C2A D:F431550 4.4 11.7 1.0 C3C D:F431550 4.4 11.2 1.0 OH E:TYR367 4.4 11.3 1.0 C2B D:F431550 4.6 14.3 1.0 CG A:GLN147 4.7 14.9 1.0 CAA D:F431550 4.7 12.1 1.0 CD D:SHT1551 4.9 15.7 1.0 CAB D:F431550 4.9 14.7 1.0 C7D D:F431550 5.0 12.1 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