Atomistry » Nickel » PDB 4z8g-5bnc » 5a0y
Atomistry »
  Nickel »
    PDB 4z8g-5bnc »
      5a0y »

Nickel in PDB 5a0y: Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution

Enzymatic activity of Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution

All present enzymatic activity of Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution:
2.8.4.1;

Protein crystallography data

The structure of Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution, PDB code: 5a0y was solved by T.Wagner, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.35 / 1.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.227, 118.300, 122.560, 90.00, 91.90, 90.00
R / Rfree (%) 11.1 / 12.9

Other elements in 5a0y:

The structure of Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution also contains other interesting chemical elements:

Magnesium (Mg) 16 atoms
Potassium (K) 1 atom
Chlorine (Cl) 2 atoms
Sodium (Na) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution (pdb code 5a0y). 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 Methanothermobacter Marburgensis at 1.1 A Resolution, PDB code: 5a0y:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 5a0y

Go back to Nickel Binding Sites List in 5a0y
Nickel binding site 1 out of 2 in the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 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 Methanothermobacter Marburgensis at 1.1 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni554

b:6.8
occ:1.00
NI A:F43554 0.0 6.8 1.0
NC A:F43554 2.0 7.0 1.0
ND A:F43554 2.1 6.4 1.0
NB A:F43554 2.1 6.8 1.0
NA A:F43554 2.1 6.8 1.0
OE1 A:GLN147 2.3 8.4 1.0
S1 D:COM555 2.4 9.0 1.0
C4B A:F43554 3.0 6.6 1.0
C1C A:F43554 3.0 6.9 1.0
C1A A:F43554 3.0 6.4 1.0
C4D A:F43554 3.1 6.5 1.0
C1D A:F43554 3.1 6.6 1.0
C4C A:F43554 3.1 6.9 1.0
C1B A:F43554 3.2 6.5 1.0
C4A A:F43554 3.3 6.2 1.0
C1 D:COM555 3.3 10.1 1.0
CHA A:F43554 3.3 6.3 1.0
CHC A:F43554 3.3 7.3 1.0
CD A:GLN147 3.3 8.0 1.0
CHB A:F43554 3.4 6.7 1.0
CHD A:F43554 3.5 6.9 1.0
NE2 A:GLN147 3.7 8.8 1.0
N5B A:F43554 3.9 6.9 1.0
C2 D:COM555 4.1 10.9 1.0
OH E:TYR367 4.1 9.2 1.0
C3B A:F43554 4.3 7.1 1.0
C3A A:F43554 4.3 6.5 1.0
C2C A:F43554 4.3 7.1 1.0
OH D:TYR333 4.4 8.1 1.0
C2A A:F43554 4.4 6.2 1.0
C3D A:F43554 4.4 6.2 1.0
C2D A:F43554 4.4 6.7 1.0
C3C A:F43554 4.4 7.4 1.0
C2B A:F43554 4.5 7.4 1.0
CAA A:F43554 4.7 6.5 1.0
CG A:GLN147 4.7 7.8 1.0
CAB A:F43554 4.9 7.4 1.0
C7D A:F43554 5.0 6.8 1.0
C6B A:F43554 5.0 7.4 1.0

Nickel binding site 2 out of 2 in 5a0y

Go back to Nickel Binding Sites List in 5a0y
Nickel binding site 2 out of 2 in the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 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 Methanothermobacter Marburgensis at 1.1 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni552

b:7.7
occ:1.00
NI D:F43552 0.0 7.7 1.0
ND D:F43552 2.0 7.3 1.0
NC D:F43552 2.1 7.8 1.0
NB D:F43552 2.1 7.3 1.0
NA D:F43552 2.1 7.1 1.0
OE1 D:GLN147 2.3 9.4 1.0
S1 A:COM555 2.4 10.0 1.0
C4B D:F43552 3.0 7.7 1.0
C1A D:F43552 3.0 7.2 1.0
C1C D:F43552 3.0 7.7 1.0
C4D D:F43552 3.1 7.4 1.0
C1D D:F43552 3.1 7.3 1.0
C4C D:F43552 3.1 7.2 1.0
C1B D:F43552 3.2 7.7 1.0
C4A D:F43552 3.3 7.3 1.0
C1 A:COM555 3.3 11.6 1.0
CHA D:F43552 3.3 7.2 1.0
CD D:GLN147 3.3 9.7 1.0
CHC D:F43552 3.3 8.2 1.0
CHB D:F43552 3.4 7.4 1.0
CHD D:F43552 3.5 7.5 1.0
NE2 D:GLN147 3.7 10.6 1.0
N5B D:F43552 3.9 7.4 1.0
OH B:TYR367 4.1 9.7 1.0
C2 A:COM555 4.1 12.1 1.0
C3B D:F43552 4.3 8.1 1.0
C3A D:F43552 4.3 7.6 1.0
C2A D:F43552 4.3 7.3 1.0
OH A:TYR333 4.3 9.0 1.0
C2C D:F43552 4.4 7.7 1.0
C3D D:F43552 4.4 7.1 1.0
C2D D:F43552 4.4 7.7 1.0
C3C D:F43552 4.4 7.8 1.0
C2B D:F43552 4.5 7.8 1.0
CAA D:F43552 4.7 7.8 1.0
CG D:GLN147 4.7 9.4 1.0
CAB D:F43552 4.9 8.3 1.0
C7D D:F43552 5.0 7.7 1.0
C6B D:F43552 5.0 7.9 1.0

Reference:

T.Wagner, J.Kahnt, U.Ermler, S.Shima. Didehydroaspartate Modification in Methyl-Coenzyme M Reductase Catalyzing Methane Formation. Angew.Chem.Int.Ed.Engl. V. 55 10630 2016.
ISSN: ISSN 1433-7851
PubMed: 27467699
DOI: 10.1002/ANIE.201603882
Page generated: Wed Dec 16 01:39:04 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy