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Nickel in PDB 1mro: Methyl-Coenzyme M Reductase

Protein crystallography data

The structure of Methyl-Coenzyme M Reductase, PDB code: 1mro was solved by U.Ermler, W.Grabarse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.16
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.720, 116.883, 122.582, 90.00, 92.02, 90.00
R / Rfree (%) 19.7 / 20.7

Other elements in 1mro:

The structure of Methyl-Coenzyme M Reductase also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Sodium (Na) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Methyl-Coenzyme M Reductase (pdb code 1mro). 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, PDB code: 1mro:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1mro

Go back to Nickel Binding Sites List in 1mro
Nickel binding site 1 out of 2 in the Methyl-Coenzyme M Reductase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni700

b:10.9
occ:1.00
NI A:F43700 0.0 10.9 1.0
NC A:F43700 2.0 11.6 1.0
ND A:F43700 2.0 11.6 1.0
NB A:F43700 2.1 11.3 1.0
NA A:F43700 2.2 11.4 1.0
OE1 A:GLN147 2.3 12.6 1.0
S1 D:COM9700 2.4 14.2 1.0
C1A A:F43700 2.9 11.4 1.0
C4B A:F43700 3.0 11.4 1.0
C1C A:F43700 3.0 11.5 1.0
C1D A:F43700 3.0 11.6 1.0
C4D A:F43700 3.1 11.5 1.0
C4C A:F43700 3.1 12.0 1.0
C1B A:F43700 3.2 11.8 1.0
C4A A:F43700 3.2 11.2 1.0
CD A:GLN147 3.3 12.6 1.0
CHA A:F43700 3.3 11.7 1.0
C1 D:COM9700 3.3 16.2 1.0
CHC A:F43700 3.4 11.5 1.0
CHD A:F43700 3.4 11.9 1.0
CHB A:F43700 3.5 11.1 1.0
NE2 A:GLN147 3.7 12.5 1.0
N5B A:F43700 3.9 12.0 1.0
C2 D:COM9700 4.1 16.7 1.0
OH E:TYR367 4.2 12.0 1.0
C3A A:F43700 4.3 12.1 1.0
C2C A:F43700 4.3 12.3 1.0
OH D:TYR333 4.3 11.9 1.0
C3D A:F43700 4.4 11.5 1.0
C3C A:F43700 4.4 12.4 1.0
C2D A:F43700 4.4 11.8 1.0
C2A A:F43700 4.4 11.9 1.0
C3B A:F43700 4.4 11.8 1.0
C2B A:F43700 4.6 11.8 1.0
CAA A:F43700 4.6 12.5 1.0
CG A:GLN147 4.7 12.5 1.0
C7D A:F43700 4.9 11.9 1.0
CAB A:F43700 5.0 12.6 1.0

Nickel binding site 2 out of 2 in 1mro

Go back to Nickel Binding Sites List in 1mro
Nickel binding site 2 out of 2 in the Methyl-Coenzyme M Reductase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni800

b:11.1
occ:1.00
NI D:F43800 0.0 11.1 1.0
ND D:F43800 1.9 11.5 1.0
NB D:F43800 2.0 11.6 1.0
NA D:F43800 2.1 11.4 1.0
NC D:F43800 2.1 11.5 1.0
OE1 D:GLN147 2.3 12.4 1.0
S1 A:COM9800 2.4 14.5 1.0
C4B D:F43800 2.9 11.1 1.0
C1A D:F43800 2.9 10.9 1.0
C1C D:F43800 3.0 11.1 1.0
C1D D:F43800 3.0 11.2 1.0
C4C D:F43800 3.1 11.4 1.0
C4D D:F43800 3.1 11.3 1.0
C4A D:F43800 3.2 11.2 1.0
C1B D:F43800 3.2 11.7 1.0
CD D:GLN147 3.3 12.5 1.0
CHA D:F43800 3.3 11.1 1.0
CHC D:F43800 3.3 11.3 1.0
C1 A:COM9800 3.4 15.4 1.0
CHB D:F43800 3.4 11.5 1.0
CHD D:F43800 3.5 11.4 1.0
NE2 D:GLN147 3.7 12.6 1.0
N5B D:F43800 3.9 11.7 1.0
C2 A:COM9800 4.1 15.6 1.0
OH B:TYR367 4.2 11.7 1.0
C3A D:F43800 4.3 12.0 1.0
C3B D:F43800 4.3 11.4 1.0
OH A:TYR333 4.3 11.5 1.0
C3C D:F43800 4.4 11.8 1.0
C2A D:F43800 4.4 12.0 1.0
C3D D:F43800 4.4 11.6 1.0
C2D D:F43800 4.4 11.1 1.0
C2C D:F43800 4.4 11.3 1.0
C2B D:F43800 4.5 12.0 1.0
CG D:GLN147 4.7 12.4 1.0
CAA D:F43800 4.7 13.2 1.0
CAB D:F43800 5.0 12.0 1.0
C6B D:F43800 5.0 12.5 1.0

Reference:

U.Ermler, W.Grabarse, S.Shima, M.Goubeaud, R.K.Thauer. Crystal Structure of Methyl-Coenzyme M Reductase: the Key Enzyme of Biological Methane Formation. Science V. 278 1457 1997.
ISSN: ISSN 0036-8075
PubMed: 9367957
DOI: 10.1126/SCIENCE.278.5342.1457
Page generated: Wed Dec 16 01:13:47 2020

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