Atomistry » Nickel » PDB 4z8g-5bnc » 5a8w
Atomistry »
  Nickel »
    PDB 4z8g-5bnc »
      5a8w »

Nickel in PDB 5a8w: Methyl-Coenzyme M Reductase II From Methanothermobacter Wolfeii at 1. 8 A Resolution

Enzymatic activity of Methyl-Coenzyme M Reductase II From Methanothermobacter Wolfeii at 1. 8 A Resolution

All present enzymatic activity of Methyl-Coenzyme M Reductase II From Methanothermobacter Wolfeii at 1. 8 A Resolution:
2.8.4.1;

Protein crystallography data

The structure of Methyl-Coenzyme M Reductase II From Methanothermobacter Wolfeii at 1. 8 A Resolution, PDB code: 5a8w 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) 48.66 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 110.391, 102.185, 118.739, 89.20, 93.97, 90.98
R / Rfree (%) 16.5 / 20.1

Other elements in 5a8w:

The structure of Methyl-Coenzyme M Reductase II From Methanothermobacter Wolfeii at 1. 8 A Resolution also contains other interesting chemical elements:

Sodium (Na) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Methyl-Coenzyme M Reductase II From Methanothermobacter Wolfeii at 1. 8 A Resolution (pdb code 5a8w). 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 II From Methanothermobacter Wolfeii at 1. 8 A Resolution, PDB code: 5a8w:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 5a8w

Go back to Nickel Binding Sites List in 5a8w
Nickel binding site 1 out of 4 in the Methyl-Coenzyme M Reductase II From Methanothermobacter Wolfeii at 1. 8 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 II From Methanothermobacter Wolfeii at 1. 8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni1554

b:8.9
occ:1.00
 NI D:F431554 0.0 8.9 1.0
ND D:F431554 2.1 6.8 1.0
NC D:F431554 2.1 9.9 1.0
NB D:F431554 2.1 8.6 1.0
NA D:F431554 2.1 10.2 1.0
OE1 A:GLN151 2.3 14.4 1.0
S1 D:COM1555 2.6 13.7 0.6
C4B D:F431554 3.0 9.8 1.0
C1C D:F431554 3.0 8.2 1.0
C1A D:F431554 3.0 7.4 1.0
C4D D:F431554 3.0 6.6 1.0
C1D D:F431554 3.1 5.6 1.0
C4C D:F431554 3.1 1.7 1.0
C1B D:F431554 3.2 9.5 1.0
C4A D:F431554 3.2 3.9 1.0
C1 D:COM1555 3.3 11.2 0.6
CD A:GLN151 3.3 13.1 1.0
CHC D:F431554 3.3 10.3 1.0
CHA D:F431554 3.3 7.0 1.0
CHB D:F431554 3.5 5.0 1.0
CHD D:F431554 3.5 6.8 1.0
NE2 A:GLN151 3.7 12.1 1.0
N5B D:F431554 3.7 9.3 1.0
OH E:TYR367 4.1 12.5 1.0
C3A D:F431554 4.2 9.4 1.0
OH D:TYR336 4.2 14.3 1.0
C3B D:F431554 4.3 11.6 1.0
C3D D:F431554 4.3 7.8 1.0
C2D D:F431554 4.3 5.4 1.0
C2 D:COM1555 4.3 8.0 0.6
C2A D:F431554 4.3 6.6 1.0
C2C D:F431554 4.4 10.0 1.0
C3C D:F431554 4.4 6.7 1.0
C2B D:F431554 4.4 9.2 1.0
CAA D:F431554 4.5 10.1 1.0
CG A:GLN151 4.6 14.2 1.0
C6B D:F431554 4.9 12.9 1.0
CAB D:F431554 4.9 8.8 1.0

Nickel binding site 2 out of 4 in 5a8w

Go back to Nickel Binding Sites List in 5a8w
Nickel binding site 2 out of 4 in the Methyl-Coenzyme M Reductase II From Methanothermobacter Wolfeii at 1. 8 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 II From Methanothermobacter Wolfeii at 1. 8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni1556

b:11.8
occ:1.00
 NI D:F431556 0.0 11.8 1.0
ND D:F431556 2.0 6.8 1.0
NB D:F431556 2.0 11.4 1.0
NC D:F431556 2.1 11.5 1.0
NA D:F431556 2.1 9.2 1.0
OE1 D:GLN151 2.3 15.9 1.0
S1 A:COM1553 2.6 9.9 0.6
C4B D:F431556 2.9 8.8 1.0
C1C D:F431556 3.0 9.4 1.0
C1A D:F431556 3.0 10.7 1.0
C1D D:F431556 3.0 8.3 1.0
C4D D:F431556 3.1 9.1 1.0
C4C D:F431556 3.1 3.6 1.0
C1B D:F431556 3.2 9.2 1.0
C1 A:COM1553 3.2 14.9 0.6
C4A D:F431556 3.3 4.3 1.0
CHA D:F431556 3.3 8.3 1.0
CHC D:F431556 3.3 9.0 1.0
CD D:GLN151 3.4 15.3 1.0
CHB D:F431556 3.4 6.5 1.0
CHD D:F431556 3.5 7.5 1.0
NE2 D:GLN151 3.8 16.8 1.0
N5B D:F431556 3.8 10.9 1.0
OH B:TYR367 4.1 13.3 1.0
OH A:TYR336 4.2 15.3 1.0
C3B D:F431556 4.2 14.2 1.0
C2 A:COM1553 4.3 13.9 0.6
C3D D:F431556 4.3 9.6 1.0
C3A D:F431556 4.3 7.9 1.0
C2D D:F431556 4.3 9.5 1.0
C2C D:F431556 4.3 7.3 1.0
C2A D:F431556 4.4 7.9 1.0
C3C D:F431556 4.4 7.5 1.0
C2B D:F431556 4.4 12.0 1.0
CAA D:F431556 4.6 9.7 1.0
CG D:GLN151 4.7 13.8 1.0
CAB D:F431556 4.8 14.9 1.0
C6B D:F431556 4.9 16.4 1.0
C7D D:F431556 5.0 7.6 1.0

Nickel binding site 3 out of 4 in 5a8w

Go back to Nickel Binding Sites List in 5a8w
Nickel binding site 3 out of 4 in the Methyl-Coenzyme M Reductase II From Methanothermobacter Wolfeii at 1. 8 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 II From Methanothermobacter Wolfeii at 1. 8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ni1554

b:9.4
occ:1.00
 NI G:F431554 0.0 9.4 1.0
NC G:F431554 2.0 11.6 1.0
ND G:F431554 2.0 10.9 1.0
NB G:F431554 2.1 10.8 1.0
NA G:F431554 2.1 6.1 1.0
OE1 J:GLN151 2.3 17.2 1.0
S1 G:COM1553 2.6 7.2 0.6
C4B G:F431554 2.9 9.4 1.0
C1A G:F431554 3.0 8.7 1.0
C1C G:F431554 3.0 7.4 1.0
C4D G:F431554 3.0 7.5 1.0
C1D G:F431554 3.1 11.6 1.0
C4C G:F431554 3.1 5.6 1.0
C1B G:F431554 3.2 10.4 1.0
C4A G:F431554 3.2 4.3 1.0
CD J:GLN151 3.3 19.0 1.0
CHA G:F431554 3.3 6.7 1.0
CHC G:F431554 3.3 10.8 1.0
C1 G:COM1553 3.4 9.2 0.6
CHB G:F431554 3.4 6.3 1.0
CHD G:F431554 3.5 9.4 1.0
NE2 J:GLN151 3.6 11.4 1.0
N5B G:F431554 3.8 13.2 1.0
OH H:TYR367 4.1 14.5 1.0
OH G:TYR336 4.2 15.8 1.0
C3A G:F431554 4.2 9.5 1.0
C3B G:F431554 4.2 7.2 1.0
C2 G:COM1553 4.3 10.1 0.6
C3D G:F431554 4.3 6.8 1.0
C2A G:F431554 4.3 7.9 1.0
C2C G:F431554 4.3 9.3 1.0
C2D G:F431554 4.3 12.0 1.0
C3C G:F431554 4.4 8.6 1.0
C2B G:F431554 4.4 10.7 1.0
CAA G:F431554 4.5 11.2 1.0
CG J:GLN151 4.6 17.8 1.0
CAB G:F431554 4.9 10.2 1.0
C6B G:F431554 4.9 15.7 1.0
C7D G:F431554 5.0 9.2 1.0

Nickel binding site 4 out of 4 in 5a8w

Go back to Nickel Binding Sites List in 5a8w
Nickel binding site 4 out of 4 in the Methyl-Coenzyme M Reductase II From Methanothermobacter Wolfeii at 1. 8 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 II From Methanothermobacter Wolfeii at 1. 8 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ni1554

b:10.9
occ:1.00
 NI J:F431554 0.0 10.9 1.0
ND J:F431554 2.1 8.6 1.0
NB J:F431554 2.1 12.1 1.0
NC J:F431554 2.1 10.3 1.0
NA J:F431554 2.1 11.3 1.0
OE1 G:GLN151 2.3 16.5 1.0
S1 J:COM1555 2.6 11.5 0.7
C4B J:F431554 2.9 9.8 1.0
C1A J:F431554 3.0 7.2 1.0
C1C J:F431554 3.0 7.0 1.0
C4D J:F431554 3.1 10.4 1.0
C1D J:F431554 3.1 10.4 1.0
C4C J:F431554 3.2 4.1 1.0
C1B J:F431554 3.2 8.4 1.0
C4A J:F431554 3.3 3.9 1.0
CHA J:F431554 3.3 7.6 1.0
CD G:GLN151 3.3 18.2 1.0
CHC J:F431554 3.3 8.6 1.0
CHB J:F431554 3.5 4.8 1.0
CHD J:F431554 3.5 9.1 1.0
NE2 G:GLN151 3.8 15.4 1.0
N5B J:F431554 3.8 9.8 1.0
C1 J:COM1555 3.9 10.4 0.7
OH K:TYR367 4.1 13.6 1.0
C2 J:COM1555 4.1 13.4 0.7
C3B J:F431554 4.3 12.8 1.0
C3A J:F431554 4.3 8.4 1.0
OH J:TYR336 4.3 12.8 1.0
C3D J:F431554 4.3 10.1 1.0
C2D J:F431554 4.3 11.7 1.0
C2A J:F431554 4.4 9.3 1.0
C2C J:F431554 4.4 11.2 1.0
C2B J:F431554 4.4 11.8 1.0
C3C J:F431554 4.4 11.7 1.0
CAA J:F431554 4.6 10.9 1.0
CG G:GLN151 4.6 17.7 1.0
CAB J:F431554 4.8 12.1 1.0
C6B J:F431554 4.9 12.6 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: Thu Oct 10 06:13:46 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy