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Nickel in PDB 1hbm: Methyl-Coenzyme M Reductase Enzyme Product Complex

Protein crystallography data

The structure of Methyl-Coenzyme M Reductase Enzyme Product Complex, PDB code: 1hbm 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) 10.00 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.000, 118.300, 122.800, 90.00, 92.00, 90.00
R / Rfree (%) 16.4 / 19.3

Nickel Binding Sites:

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

Nickel binding site 1 out of 2 in 1hbm

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


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 Enzyme Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1550

b:14.6
occ:1.00
NI A:F431550 0.0 14.6 1.0
NB A:F431550 2.0 12.3 1.0
ND A:F431550 2.0 9.9 1.0
NC A:F431550 2.1 10.8 1.0
NA A:F431550 2.3 9.4 1.0
OS3 A:SHT1551 2.3 16.1 1.0
OE1 D:GLN147 2.3 15.5 1.0
C4B A:F431550 2.9 13.2 1.0
C1A A:F431550 2.9 9.2 1.0
C1C A:F431550 3.0 11.0 1.0
C4D A:F431550 3.0 10.3 1.0
C1D A:F431550 3.1 10.8 1.0
C4C A:F431550 3.2 11.2 1.0
C1B A:F431550 3.2 12.8 1.0
CHC A:F431550 3.2 10.8 1.0
CHA A:F431550 3.3 10.1 1.0
SG2 A:SHT1551 3.3 17.3 1.0
CD D:GLN147 3.3 14.7 1.0
C4A A:F431550 3.3 9.6 1.0
CHD A:F431550 3.6 9.9 1.0
CHB A:F431550 3.6 10.3 1.0
OS1 A:SHT1551 3.6 19.3 1.0
NE2 D:GLN147 3.6 13.9 1.0
OS2 A:SHT1551 3.9 19.8 1.0
N5B A:F431550 4.0 12.8 1.0
C3B A:F431550 4.3 12.1 1.0
C2C A:F431550 4.3 10.8 1.0
C3D A:F431550 4.4 10.5 1.0
OH A:TYR333 4.4 14.0 1.0
C3A A:F431550 4.4 10.3 1.0
C2A A:F431550 4.4 9.2 1.0
C2D A:F431550 4.4 9.7 1.0
C3C A:F431550 4.4 11.8 1.0
OH B:TYR367 4.5 11.2 1.0
C2B A:F431550 4.5 13.5 1.0
CG D:GLN147 4.6 13.9 1.0
CAA A:F431550 4.7 11.1 1.0
CD A:SHT1551 4.9 18.3 1.0
CAB A:F431550 4.9 12.9 1.0

Nickel binding site 2 out of 2 in 1hbm

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


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 Enzyme Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni1550

b:15.4
occ:1.00
NI D:F431550 0.0 15.4 1.0
ND D:F431550 2.1 12.4 1.0
NC D:F431550 2.1 10.9 1.0
NB D:F431550 2.2 13.5 1.0
NA D:F431550 2.2 11.5 1.0
OS3 D:SHT1551 2.3 15.5 1.0
OE1 A:GLN147 2.3 16.8 1.0
C1A D:F431550 2.9 12.2 1.0
C4B D:F431550 3.0 13.6 1.0
C1C D:F431550 3.0 11.7 1.0
C1D D:F431550 3.1 11.9 1.0
C4D D:F431550 3.1 12.3 1.0
C4C D:F431550 3.2 11.6 1.0
CHC D:F431550 3.3 12.2 1.0
C1B D:F431550 3.3 13.6 1.0
C4A D:F431550 3.3 12.0 1.0
CHA D:F431550 3.3 12.7 1.0
SG2 D:SHT1551 3.3 14.4 1.0
CD A:GLN147 3.3 16.0 1.0
CHD D:F431550 3.5 11.5 1.0
CHB D:F431550 3.5 11.7 1.0
OS2 D:SHT1551 3.6 17.1 1.0
NE2 A:GLN147 3.7 13.9 1.0
OS1 D:SHT1551 3.8 16.9 1.0
N5B D:F431550 4.0 13.7 1.0
OH D:TYR333 4.3 16.4 1.0
C2C D:F431550 4.3 11.2 1.0
C3A D:F431550 4.3 12.4 1.0
C3B D:F431550 4.4 13.8 1.0
C3D D:F431550 4.4 12.6 1.0
C2D D:F431550 4.4 13.1 1.0
C2A D:F431550 4.4 11.7 1.0
C3C D:F431550 4.4 11.2 1.0
OH E:TYR367 4.4 11.3 1.0
C2B D:F431550 4.6 14.3 1.0
CG A:GLN147 4.7 14.9 1.0
CAA D:F431550 4.7 12.1 1.0
CD D:SHT1551 4.9 15.7 1.0
CAB D:F431550 4.9 14.7 1.0
C7D D:F431550 5.0 12.1 1.0

Reference:

W.Grabarse, F.Mahlert, E.C.Duin, M.Goubeaud, S.Shima, R.K.Thauer, V.Lamzin, U.Ermler. On the Mechanism of Biological Methane Formation: Structural Evidence For Conformational Changes in Methyl-Coenzyme M Reductase Upon Substrate Binding J.Mol.Biol. V. 309 315 2001.
ISSN: ISSN 0022-2836
PubMed: 11491299
DOI: 10.1006/JMBI.2001.4647
Page generated: Fri Sep 25 07:54:23 2020
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