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

Protein crystallography data

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

Nickel Binding Sites:

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 1e6v

Go back to Nickel Binding Sites List in 1e6v
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 1e6v

Go back to Nickel Binding Sites List in 1e6v
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

Reference:

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
Page generated: Fri Sep 25 07:51:13 2020
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