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Nickel in PDB 1e6y: Methyl-Coenzyme M Reductase From Methanosarcina Barkeri

Enzymatic activity of Methyl-Coenzyme M Reductase From Methanosarcina Barkeri

All present enzymatic activity of Methyl-Coenzyme M Reductase From Methanosarcina Barkeri:
2.8.4.1;

Protein crystallography data

The structure of Methyl-Coenzyme M Reductase From Methanosarcina Barkeri, PDB code: 1e6y was solved by W.Grabarse, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 113.678, 153.099, 153.288, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 17.9

Nickel Binding Sites:

The binding sites of Nickel atom in the Methyl-Coenzyme M Reductase From Methanosarcina Barkeri (pdb code 1e6y). 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 Methanosarcina Barkeri, PDB code: 1e6y:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1e6y

Go back to Nickel Binding Sites List in 1e6y
Nickel binding site 1 out of 2 in the Methyl-Coenzyme M Reductase From Methanosarcina Barkeri


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 Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni2570

b:9.1
occ:1.00
NI A:F432570 0.0 9.1 1.0
ND A:F432570 2.0 9.2 1.0
NC A:F432570 2.1 9.9 1.0
NB A:F432570 2.1 9.8 1.0
NA A:F432570 2.1 9.6 1.0
OE1 A:GLN1161 2.3 10.1 1.0
S1 D:COM5572 2.5 17.3 1.0
C1A A:F432570 2.9 9.2 1.0
C4B A:F432570 2.9 10.4 1.0
C1C A:F432570 3.0 10.2 1.0
C1D A:F432570 3.0 9.8 1.0
C4C A:F432570 3.1 10.3 1.0
C4D A:F432570 3.2 8.7 1.0
C1B A:F432570 3.2 10.1 1.0
C4A A:F432570 3.2 8.4 1.0
CD A:GLN1161 3.3 10.2 1.0
CHC A:F432570 3.3 10.4 1.0
CHA A:F432570 3.4 8.5 1.0
CHB A:F432570 3.4 9.1 1.0
CHD A:F432570 3.5 10.6 1.0
C1 D:COM5572 3.5 16.0 1.0
NE2 A:GLN1161 3.6 9.3 1.0
N5B A:F432570 4.0 9.9 1.0
C2 D:COM5572 4.2 17.7 1.0
OH D:TYR4346 4.3 12.4 1.0
C3A A:F432570 4.3 8.9 1.0
OH E:TYR5365 4.3 10.7 1.0
C3B A:F432570 4.3 10.8 1.0
C2C A:F432570 4.4 10.0 1.0
C3C A:F432570 4.4 10.1 1.0
C2A A:F432570 4.4 9.1 1.0
C2D A:F432570 4.4 9.5 1.0
C3D A:F432570 4.4 9.0 1.0
CAA A:F432570 4.5 8.8 1.0
C2B A:F432570 4.6 10.6 1.0
CG A:GLN1161 4.6 9.4 1.0

Nickel binding site 2 out of 2 in 1e6y

Go back to Nickel Binding Sites List in 1e6y
Nickel binding site 2 out of 2 in the Methyl-Coenzyme M Reductase From Methanosarcina Barkeri


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 Methanosarcina Barkeri within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni5570

b:10.2
occ:1.00
NI D:F435570 0.0 10.2 1.0
ND D:F435570 2.0 9.0 1.0
NC D:F435570 2.1 9.4 1.0
NB D:F435570 2.1 9.3 1.0
NA D:F435570 2.2 9.4 1.0
OE1 D:GLN4161 2.2 11.8 1.0
S1 A:COM2572 2.5 16.9 1.0
C1A D:F435570 2.9 9.0 1.0
C4B D:F435570 2.9 9.6 1.0
C1C D:F435570 3.0 9.5 1.0
C1D D:F435570 3.0 10.0 1.0
C4C D:F435570 3.1 10.0 1.0
C4D D:F435570 3.1 9.1 1.0
C1B D:F435570 3.2 10.0 1.0
C4A D:F435570 3.3 8.8 1.0
CD D:GLN4161 3.3 11.6 1.0
CHC D:F435570 3.3 9.8 1.0
CHA D:F435570 3.4 8.3 1.0
CHB D:F435570 3.4 9.7 1.0
C1 A:COM2572 3.4 15.9 1.0
CHD D:F435570 3.5 10.1 1.0
NE2 D:GLN4161 3.7 10.8 1.0
N5B D:F435570 3.9 10.0 1.0
C2 A:COM2572 4.1 17.9 1.0
OH B:TYR2365 4.3 9.8 1.0
C3A D:F435570 4.3 9.1 1.0
OH A:TYR1346 4.3 12.7 1.0
C2C D:F435570 4.3 9.2 1.0
C3B D:F435570 4.3 10.1 1.0
C3D D:F435570 4.4 9.3 1.0
C2D D:F435570 4.4 8.9 1.0
C3C D:F435570 4.4 9.8 1.0
C2A D:F435570 4.4 8.9 1.0
CAA D:F435570 4.5 8.6 1.0
C2B D:F435570 4.6 10.4 1.0
CG D:GLN4161 4.6 10.3 1.0
C7D D:F435570 5.0 10.9 1.0

Reference:

W.Grabarse, F.Mahlert, S.Shima, R.K.Thauer, U.Ermler. Comparison of Three Methyl-Coenzyme M Reductases From Phylogenetically Distant Organisms: Unusual Amino Acid Modification, Conservation and Adaptation J.Mol.Biol. V. 303 329 2000.
ISSN: ISSN 0022-2836
PubMed: 11023796
DOI: 10.1006/JMBI.2000.4136
Page generated: Wed Dec 16 01:11:32 2020

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