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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

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