Atomistry » Nickel » PDB 1a5n-1fwb » 1e6v
Atomistry »
  Nickel »
    PDB 1a5n-1fwb »
      1e6v »

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: Wed Dec 16 01:11:31 2020

Last articles

Zn in 7L3L
Zn in 7KSO
Zn in 7KSR
Zn in 7KTP
Zn in 7LMM
Zn in 7LMK
Zn in 7LLZ
Zn in 7LLF
Zn in 7L0N
Zn in 7LBR
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy