Nickel in PDB 1e6v: Methyl-Coenzyme M Reductase From Methanopyrus Kandleri

The structure of Methyl-Coenzyme M Reductase From Methanopyrus Kandleri, PDB code: 1e6v was solved by W.Grabarse, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.519, 115.740, 268.510, 90.00, 90.00, 90.00
R / Rfree (%)	23.9 / 27.8

The binding sites of Nickel atom in the Methyl-Coenzyme M Reductase From Methanopyrus Kandleri (pdb code 1e6v). 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 Methanopyrus Kandleri, PDB code: 1e6v:
Jump to Nickel binding site number: 1; 2;

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


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 Methanopyrus Kandleri within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1553 b:26.2 occ:1.00 NI A:F431553 0.0 26.2 1.0 ND A:F431553 2.0 26.1 1.0 NC A:F431553 2.1 26.1 1.0 OE1 A:GLN150 2.1 19.0 1.0 NB A:F431553 2.1 26.0 1.0 NA A:F431553 2.1 26.1 1.0 S1 A:COM1555 2.5 17.3 1.0 C1A A:F431553 2.9 26.2 1.0 C4B A:F431553 2.9 25.9 1.0 C1C A:F431553 3.0 26.1 1.0 CD A:GLN150 3.0 18.6 1.0 C1D A:F431553 3.1 26.0 1.0 C4D A:F431553 3.1 26.2 1.0 C4C A:F431553 3.1 26.1 1.0 C1B A:F431553 3.2 25.9 1.0 C4A A:F431553 3.3 26.0 1.0 CHA A:F431553 3.3 26.1 1.0 CHC A:F431553 3.3 26.0 1.0 C1 A:COM1555 3.4 17.0 1.0 CHB A:F431553 3.4 25.9 1.0 NE2 A:GLN150 3.4 18.9 1.0 CHD A:F431553 3.5 26.0 1.0 N5B A:F431553 3.9 25.7 1.0 C2 A:COM1555 4.2 17.0 1.0 C3A A:F431553 4.3 25.9 1.0 C3B A:F431553 4.3 25.6 1.0 C3D A:F431553 4.3 26.1 1.0 C2C A:F431553 4.4 26.3 1.0 OH D:TYR336 4.4 16.2 1.0 C2A A:F431553 4.4 26.1 1.0 C2D A:F431553 4.4 25.9 1.0 CG A:GLN150 4.4 18.4 1.0 C3C A:F431553 4.4 26.2 1.0 OH E:TYR368 4.4 25.4 1.0 CAA A:F431553 4.6 25.8 1.0 C2B A:F431553 4.6 25.8 1.0 CAB A:F431553 5.0 25.4 1.0

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


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 Methanopyrus Kandleri within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni1553 b:26.2 occ:1.00 NI D:F431553 0.0 26.2 1.0 ND D:F431553 2.0 26.1 1.0 NC D:F431553 2.1 26.1 1.0 OE1 D:GLN150 2.1 19.0 1.0 NB D:F431553 2.1 26.0 1.0 NA D:F431553 2.1 26.1 1.0 S1 D:COM1555 2.5 17.3 1.0 C1A D:F431553 2.9 26.2 1.0 C4B D:F431553 2.9 25.9 1.0 C1C D:F431553 3.0 26.1 1.0 CD D:GLN150 3.0 18.6 1.0 C1D D:F431553 3.1 26.0 1.0 C4D D:F431553 3.1 26.2 1.0 C4C D:F431553 3.1 26.1 1.0 C1B D:F431553 3.2 25.9 1.0 C4A D:F431553 3.3 26.0 1.0 CHA D:F431553 3.3 26.1 1.0 CHC D:F431553 3.3 26.0 1.0 C1 D:COM1555 3.4 17.0 1.0 CHB D:F431553 3.4 25.9 1.0 NE2 D:GLN150 3.4 18.9 1.0 CHD D:F431553 3.5 26.0 1.0 N5B D:F431553 3.9 25.7 1.0 C2 D:COM1555 4.2 17.0 1.0 C3A D:F431553 4.3 25.9 1.0 C3D D:F431553 4.3 26.1 1.0 C3B D:F431553 4.3 25.6 1.0 C2C D:F431553 4.4 26.3 1.0 C2A D:F431553 4.4 26.1 1.0 OH A:TYR336 4.4 16.2 1.0 C2D D:F431553 4.4 25.9 1.0 CG D:GLN150 4.4 18.4 1.0 C3C D:F431553 4.4 26.2 1.0 OH B:TYR368 4.4 25.4 1.0 CAA D:F431553 4.6 25.8 1.0 C2B D:F431553 4.6 25.8 1.0 CAB D:F431553 5.0 25.4 1.0

W.Grabarse, F.Mahlert, S.Shima, R.K.Thauer, U.Ermler. Comparison of Three Methyl-Coenzyme M Reductases From Phylogenetically Distant Organisms: Unusual Amino Acid Modification, Conservation and Adaptation J.Mol.Biol. V. 303 329 2000.
ISSN: ISSN 0022-2836
PubMed: 11023796
DOI: 10.1006/JMBI.2000.4136