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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

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