Atomistry » Nickel » PDB 7fbw-7odg » 7nkg
Atomistry »
  Nickel »
    PDB 7fbw-7odg »
      7nkg »

Nickel in PDB 7nkg: Methyl-Coenzyme M Reductase From Methermicoccus Shengliensis at 1.6-A Resolution

Enzymatic activity of Methyl-Coenzyme M Reductase From Methermicoccus Shengliensis at 1.6-A Resolution

All present enzymatic activity of Methyl-Coenzyme M Reductase From Methermicoccus Shengliensis at 1.6-A Resolution:
2.8.4.1;

Protein crystallography data

The structure of Methyl-Coenzyme M Reductase From Methermicoccus Shengliensis at 1.6-A Resolution, PDB code: 7nkg was solved by M.Mueller, T.Wagner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.36 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 132.615, 148.177, 235.415, 90, 90, 90
R / Rfree (%) 17.3 / 19

Other elements in 7nkg:

The structure of Methyl-Coenzyme M Reductase From Methermicoccus Shengliensis at 1.6-A Resolution also contains other interesting chemical elements:

Potassium (K) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Methyl-Coenzyme M Reductase From Methermicoccus Shengliensis at 1.6-A Resolution (pdb code 7nkg). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Methyl-Coenzyme M Reductase From Methermicoccus Shengliensis at 1.6-A Resolution, PDB code: 7nkg:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 7nkg

Go back to Nickel Binding Sites List in 7nkg
Nickel binding site 1 out of 4 in the Methyl-Coenzyme M Reductase From Methermicoccus Shengliensis at 1.6-A Resolution


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 Methermicoccus Shengliensis at 1.6-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni606

b:17.1
occ:1.00
 NI A:F43606 0.0 17.1 1.0
NC A:F43606 2.1 17.1 1.0
ND A:F43606 2.1 16.0 1.0
NB A:F43606 2.1 16.6 1.0
NA A:F43606 2.1 16.1 1.0
OE1 A:GLN165 2.4 19.2 1.0
S1 D:COM601 2.5 21.5 1.0
C4B A:F43606 2.9 16.7 1.0
C1A A:F43606 3.0 15.3 1.0
C1C A:F43606 3.0 16.9 1.0
C1D A:F43606 3.1 16.5 1.0
C4C A:F43606 3.1 16.6 1.0
C4D A:F43606 3.1 15.8 1.0
C1B A:F43606 3.2 16.1 1.0
C1 D:COM601 3.2 22.6 1.0
C4A A:F43606 3.2 15.1 1.0
CHA A:F43606 3.2 15.4 1.0
CHC A:F43606 3.3 16.8 1.0
CHB A:F43606 3.4 15.7 1.0
CD A:GLN165 3.4 21.6 1.0
CHD A:F43606 3.5 16.6 1.0
NE2 A:GLN165 3.8 21.9 1.0
N5B A:F43606 3.8 16.1 1.0
C2 D:COM601 4.1 22.5 1.0
OH E:TYR364 4.2 18.4 1.0
OH D:TYR350 4.2 19.5 1.0
C3B A:F43606 4.3 16.3 1.0
C3A A:F43606 4.3 15.2 1.0
C2A A:F43606 4.3 15.3 1.0
C2C A:F43606 4.3 17.0 1.0
C3D A:F43606 4.4 16.2 1.0
C2D A:F43606 4.4 16.5 1.0
C3C A:F43606 4.4 16.9 1.0
C2B A:F43606 4.4 15.7 1.0
CAA A:F43606 4.6 14.7 1.0
CG A:GLN165 4.7 19.8 1.0
CAB A:F43606 4.8 16.8 1.0
C6B A:F43606 5.0 16.5 1.0
C7D A:F43606 5.0 16.7 1.0

Nickel binding site 2 out of 4 in 7nkg

Go back to Nickel Binding Sites List in 7nkg
Nickel binding site 2 out of 4 in the Methyl-Coenzyme M Reductase From Methermicoccus Shengliensis at 1.6-A Resolution


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 Methermicoccus Shengliensis at 1.6-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni602

b:16.4
occ:1.00
 NI D:F43602 0.0 16.4 1.0
ND D:F43602 2.1 15.7 1.0
NC D:F43602 2.1 16.1 1.0
NB D:F43602 2.1 16.5 1.0
NA D:F43602 2.1 15.7 1.0
OE1 D:GLN165 2.4 17.8 1.0
S1 A:COM603 2.5 20.7 1.0
C4B D:F43602 3.0 16.8 1.0
C1A D:F43602 3.0 15.8 1.0
C1C D:F43602 3.0 16.4 1.0
C1D D:F43602 3.1 15.5 1.0
C4D D:F43602 3.1 15.9 1.0
C4C D:F43602 3.1 14.9 1.0
C1B D:F43602 3.2 16.5 1.0
C1 A:COM603 3.2 20.9 1.0
C4A D:F43602 3.2 15.3 1.0
CHA D:F43602 3.2 16.1 1.0
CHC D:F43602 3.3 17.2 1.0
CHB D:F43602 3.4 16.0 1.0
CD D:GLN165 3.4 16.9 1.0
CHD D:F43602 3.5 15.2 1.0
NE2 D:GLN165 3.8 16.4 1.0
N5B D:F43602 3.9 16.9 1.0
C2 A:COM603 4.1 21.3 1.0
OH B:TYR364 4.2 18.0 1.0
OH A:TYR350 4.2 17.6 1.0
C3B D:F43602 4.3 16.3 1.0
C3A D:F43602 4.3 15.4 1.0
C2A D:F43602 4.3 15.6 1.0
C3D D:F43602 4.3 16.0 1.0
C2D D:F43602 4.3 15.1 1.0
C2C D:F43602 4.4 16.1 1.0
C3C D:F43602 4.4 15.5 1.0
C2B D:F43602 4.4 15.9 1.0
CAA D:F43602 4.6 15.1 1.0
CG D:GLN165 4.7 16.5 1.0
CAB D:F43602 4.8 15.8 1.0
C7D D:F43602 5.0 15.3 1.0
C6B D:F43602 5.0 17.2 1.0

Nickel binding site 3 out of 4 in 7nkg

Go back to Nickel Binding Sites List in 7nkg
Nickel binding site 3 out of 4 in the Methyl-Coenzyme M Reductase From Methermicoccus Shengliensis at 1.6-A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Methyl-Coenzyme M Reductase From Methermicoccus Shengliensis at 1.6-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ni605

b:39.2
occ:1.00
 NI G:F43605 0.0 39.2 1.0
NC G:F43605 2.0 40.3 1.0
NA G:F43605 2.0 38.4 1.0
ND G:F43605 2.0 39.2 1.0
NB G:F43605 2.1 39.3 1.0
OE1 G:GLN165 2.3 55.1 1.0
S1 J:COM601 2.6 43.3 1.0
C1A G:F43605 2.9 38.2 1.0
C4B G:F43605 3.0 40.1 1.0
C1C G:F43605 3.0 40.5 1.0
C4C G:F43605 3.0 40.5 1.0
C4D G:F43605 3.1 39.0 1.0
C1D G:F43605 3.1 39.2 1.0
C1B G:F43605 3.2 39.3 1.0
C4A G:F43605 3.2 38.2 1.0
CHA G:F43605 3.2 38.7 1.0
CHC G:F43605 3.3 40.2 1.0
C1 J:COM601 3.3 44.1 1.0
CHB G:F43605 3.3 38.8 1.0
CD G:GLN165 3.4 56.4 1.0
CHD G:F43605 3.4 39.9 1.0
NE2 G:GLN165 3.8 55.6 1.0
N5B G:F43605 3.8 39.9 1.0
C2 J:COM601 4.2 44.7 1.0
C3A G:F43605 4.2 38.3 1.0
OH K:TYR364 4.2 47.6 1.0
C2A G:F43605 4.2 37.6 1.0
OH J:TYR350 4.3 42.3 1.0
C3B G:F43605 4.3 40.6 1.0
C2C G:F43605 4.3 41.1 1.0
C3D G:F43605 4.3 39.0 1.0
C3C G:F43605 4.3 40.9 1.0
C2D G:F43605 4.3 39.3 1.0
C2B G:F43605 4.4 40.0 1.0
CAA G:F43605 4.5 39.5 1.0
CG G:GLN165 4.7 55.9 1.0
CAB G:F43605 4.8 41.8 1.0
C7D G:F43605 4.9 40.4 1.0
C6B G:F43605 4.9 39.9 1.0

Nickel binding site 4 out of 4 in 7nkg

Go back to Nickel Binding Sites List in 7nkg
Nickel binding site 4 out of 4 in the Methyl-Coenzyme M Reductase From Methermicoccus Shengliensis at 1.6-A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Methyl-Coenzyme M Reductase From Methermicoccus Shengliensis at 1.6-A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ni602

b:25.5
occ:1.00
 NI J:F43602 0.0 25.5 1.0
ND J:F43602 2.0 25.8 1.0
NB J:F43602 2.0 25.2 1.0
NC J:F43602 2.1 26.2 1.0
NA J:F43602 2.1 24.9 1.0
OE1 J:GLN165 2.4 30.9 1.0
S1 G:COM602 2.5 32.4 1.0
C4B J:F43602 2.9 25.8 1.0
C1A J:F43602 3.0 24.6 1.0
C1C J:F43602 3.0 26.4 1.0
C1D J:F43602 3.0 26.8 1.0
C4D J:F43602 3.1 25.6 1.0
C4C J:F43602 3.1 26.9 1.0
C1B J:F43602 3.2 25.0 1.0
CHA J:F43602 3.2 25.0 1.0
C1 G:COM602 3.2 33.0 1.0
C4A J:F43602 3.2 24.7 1.0
CHC J:F43602 3.3 26.1 1.0
CHB J:F43602 3.4 24.7 1.0
CD J:GLN165 3.4 31.0 1.0
CHD J:F43602 3.5 27.2 1.0
NE2 J:GLN165 3.8 32.4 1.0
N5B J:F43602 3.8 25.0 1.0
C2 G:COM602 4.2 33.6 1.0
C3B J:F43602 4.2 25.3 1.0
OH G:TYR350 4.3 32.5 1.0
OH H:TYR364 4.3 26.6 1.0
C3A J:F43602 4.3 24.2 1.0
C3D J:F43602 4.3 26.2 1.0
C2A J:F43602 4.3 23.9 1.0
C2D J:F43602 4.3 26.7 1.0
C2C J:F43602 4.3 27.0 1.0
C3C J:F43602 4.4 27.4 1.0
C2B J:F43602 4.4 25.0 1.0
CAA J:F43602 4.6 24.3 1.0
CG J:GLN165 4.7 28.9 1.0
CAB J:F43602 4.8 25.2 1.0
C7D J:F43602 4.9 27.4 1.0
C6B J:F43602 5.0 25.2 1.0

Reference:

J.M.Kurth, M.C.Muller, C.U.Welte, T.Wagner. Structural Insights Into the Methane-Generating Enzyme From A Methoxydotrophic Methanogen Reveal A Restrained Gallery of Post-Translational Modifications. Microorganisms V. 9 2021.
ISSN: ESSN 2076-2607
PubMed: 33919946
DOI: 10.3390/MICROORGANISMS9040837
Page generated: Thu Oct 10 09:17:59 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy