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Nickel in PDB 5a8r: Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 A Resolution

Enzymatic activity of Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 A Resolution

All present enzymatic activity of Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 A Resolution:
2.8.4.1;

Protein crystallography data

The structure of Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 A Resolution, PDB code: 5a8r 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) 55.36 / 2.15
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 216.660, 246.610, 103.650, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 19.6

Other elements in 5a8r:

The structure of Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 A Resolution also contains other interesting chemical elements:

Potassium (K) 7 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 A Resolution (pdb code 5a8r). 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 Marburgensis at 2.15 A Resolution, PDB code: 5a8r:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 5a8r

Go back to Nickel Binding Sites List in 5a8r
Nickel binding site 1 out of 4 in the Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 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 Marburgensis at 2.15 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni603

b:13.2
occ:1.00
 NI A:F43603 0.0 13.2 1.0
NC A:F43603 2.0 12.3 1.0
ND A:F43603 2.0 7.4 1.0
NB A:F43603 2.1 7.2 1.0
NA A:F43603 2.1 14.8 1.0
OE1 A:GLN150 2.4 15.2 1.0
S1 D:COM601 2.8 25.4 1.0
C1A A:F43603 2.9 15.6 1.0
C4B A:F43603 2.9 8.6 1.0
C1C A:F43603 3.0 13.8 1.0
C1D A:F43603 3.0 12.9 1.0
C4C A:F43603 3.0 13.3 1.0
C4D A:F43603 3.1 13.4 1.0
C1B A:F43603 3.1 12.0 1.0
C4A A:F43603 3.2 12.6 1.0
CHA A:F43603 3.2 8.5 1.0
CD A:GLN150 3.3 13.8 1.0
C1 D:COM601 3.3 25.9 1.0
CHC A:F43603 3.3 13.2 1.0
CHB A:F43603 3.4 7.7 1.0
CHD A:F43603 3.4 8.1 1.0
NE2 A:GLN150 3.5 9.2 1.0
N5B A:F43603 3.7 19.3 1.0
OH E:TYR367 4.2 20.1 1.0
C3B A:F43603 4.3 13.1 1.0
C3A A:F43603 4.3 11.2 1.0
C2 D:COM601 4.3 28.3 1.0
C2A A:F43603 4.3 16.4 1.0
OH D:TYR335 4.3 11.8 1.0
C2C A:F43603 4.3 15.6 1.0
C2D A:F43603 4.3 13.1 1.0
C3D A:F43603 4.3 9.6 1.0
C3C A:F43603 4.3 12.4 1.0
C2B A:F43603 4.4 18.0 1.0
CAA A:F43603 4.6 14.4 1.0
CG A:GLN150 4.7 12.2 1.0
CAB A:F43603 4.8 15.2 1.0
C6B A:F43603 4.9 20.2 1.0
C7D A:F43603 4.9 15.5 1.0

Nickel binding site 2 out of 4 in 5a8r

Go back to Nickel Binding Sites List in 5a8r
Nickel binding site 2 out of 4 in the Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 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 Marburgensis at 2.15 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni603

b:15.6
occ:1.00
 NI D:F43603 0.0 15.6 1.0
ND D:F43603 2.0 6.4 1.0
NC D:F43603 2.0 13.0 1.0
NB D:F43603 2.1 19.2 1.0
NA D:F43603 2.1 16.4 1.0
OE1 D:GLN150 2.4 16.1 1.0
S1 A:COM601 2.8 25.5 1.0
C1A D:F43603 2.9 12.2 1.0
C4B D:F43603 3.0 16.9 1.0
C1C D:F43603 3.0 16.8 1.0
C1D D:F43603 3.0 14.6 1.0
C4C D:F43603 3.0 15.1 1.0
C4D D:F43603 3.1 11.1 1.0
C1B D:F43603 3.1 15.8 1.0
C4A D:F43603 3.2 16.8 1.0
CHA D:F43603 3.3 1.9 1.0
CHC D:F43603 3.3 14.9 1.0
CD D:GLN150 3.3 17.9 1.0
C1 A:COM601 3.3 19.5 1.0
CHB D:F43603 3.4 7.2 1.0
CHD D:F43603 3.4 12.2 1.0
NE2 D:GLN150 3.6 14.2 1.0
N5B D:F43603 3.7 21.9 1.0
C2 A:COM601 4.2 25.6 1.0
OH A:TYR335 4.2 13.7 1.0
C3A D:F43603 4.2 18.9 1.0
C3B D:F43603 4.3 12.1 1.0
C2A D:F43603 4.3 12.4 1.0
OH B:TYR367 4.3 19.8 1.0
C3D D:F43603 4.3 7.0 1.0
C2D D:F43603 4.3 11.9 1.0
C2C D:F43603 4.3 14.0 1.0
C3C D:F43603 4.3 12.7 1.0
C2B D:F43603 4.4 20.9 1.0
CAA D:F43603 4.6 17.2 1.0
CG D:GLN150 4.7 21.0 1.0
CAB D:F43603 4.9 6.5 1.0
C6B D:F43603 4.9 24.0 1.0
C7D D:F43603 4.9 15.8 1.0

Nickel binding site 3 out of 4 in 5a8r

Go back to Nickel Binding Sites List in 5a8r
Nickel binding site 3 out of 4 in the Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 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 Marburgensis at 2.15 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ni603

b:22.6
occ:1.00
 NI G:F43603 0.0 22.6 1.0
ND G:F43603 2.0 16.5 1.0
NC G:F43603 2.0 19.8 1.0
NB G:F43603 2.0 20.0 1.0
NA G:F43603 2.1 14.7 1.0
OE1 J:GLN150 2.4 23.3 1.0
S1 G:COM601 2.9 34.6 1.0
C4B G:F43603 2.9 26.3 1.0
C1A G:F43603 2.9 12.7 1.0
C1C G:F43603 3.0 24.1 1.0
C1D G:F43603 3.0 21.7 1.0
C4C G:F43603 3.0 23.1 1.0
C4D G:F43603 3.1 20.0 1.0
C1B G:F43603 3.1 20.2 1.0
C4A G:F43603 3.2 16.9 1.0
CHA G:F43603 3.2 13.5 1.0
CD J:GLN150 3.3 23.3 1.0
CHC G:F43603 3.3 23.0 1.0
C1 G:COM601 3.3 29.4 1.0
CHB G:F43603 3.4 19.1 1.0
CHD G:F43603 3.4 19.6 1.0
NE2 J:GLN150 3.4 18.7 1.0
N5B G:F43603 3.7 27.0 1.0
C3B G:F43603 4.2 24.8 1.0
C3A G:F43603 4.2 15.1 1.0
C2A G:F43603 4.3 14.4 1.0
C2 G:COM601 4.3 31.9 1.0
C3D G:F43603 4.3 21.3 1.0
C2D G:F43603 4.3 21.6 1.0
C2C G:F43603 4.3 20.6 1.0
OH G:TYR335 4.3 16.3 1.0
C3C G:F43603 4.3 24.0 1.0
OH H:TYR367 4.3 27.0 1.0
C2B G:F43603 4.4 23.6 1.0
CAA G:F43603 4.7 16.1 1.0
CG J:GLN150 4.7 23.6 1.0
CAB G:F43603 4.8 22.9 1.0
C7D G:F43603 4.9 23.5 1.0
C6B G:F43603 4.9 30.6 1.0

Nickel binding site 4 out of 4 in 5a8r

Go back to Nickel Binding Sites List in 5a8r
Nickel binding site 4 out of 4 in the Methyl-Coenzyme M Reductase II From Methanothermobacter Marburgensis at 2.15 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 Marburgensis at 2.15 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ni603

b:13.2
occ:1.00
 NI J:F43603 0.0 13.2 1.0
ND J:F43603 2.0 3.2 1.0
NC J:F43603 2.0 11.8 1.0
NB J:F43603 2.0 10.8 1.0
NA J:F43603 2.1 10.3 1.0
OE1 G:GLN150 2.4 11.6 1.0
S1 J:COM601 2.9 29.4 1.0
C1A J:F43603 2.9 3.9 1.0
C4B J:F43603 2.9 18.6 1.0
C1C J:F43603 3.0 16.0 1.0
C1D J:F43603 3.0 11.3 1.0
C4D J:F43603 3.0 9.0 1.0
C4C J:F43603 3.0 11.4 1.0
C1B J:F43603 3.1 13.9 1.0
C4A J:F43603 3.2 13.3 1.0
CHA J:F43603 3.2 16.6 1.0
CHC J:F43603 3.3 11.6 1.0
CD G:GLN150 3.3 23.1 1.0
C1 J:COM601 3.3 18.0 1.0
CHB J:F43603 3.4 10.8 1.0
CHD J:F43603 3.4 10.0 1.0
NE2 G:GLN150 3.6 11.7 1.0
N5B J:F43603 3.8 13.2 1.0
C2 J:COM601 4.1 25.6 1.0
C3A J:F43603 4.2 7.8 1.0
C3B J:F43603 4.3 14.6 1.0
OH J:TYR335 4.3 15.3 1.0
C2A J:F43603 4.3 5.9 1.0
C3D J:F43603 4.3 6.3 1.0
C2D J:F43603 4.3 9.1 1.0
C2C J:F43603 4.3 10.1 1.0
C3C J:F43603 4.3 18.2 1.0
OH K:TYR367 4.3 28.5 1.0
C2B J:F43603 4.4 19.9 1.0
CAA J:F43603 4.6 16.0 1.0
CG G:GLN150 4.7 13.3 1.0
CAB J:F43603 4.8 14.0 1.0
C7D J:F43603 4.9 13.4 1.0
C6B J:F43603 4.9 21.5 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 06:13:24 2024

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