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Zinc 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

Other elements in 1hbm:

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

Nickel (Ni) 2 atoms
Magnesium (Mg) 5 atoms
Chlorine (Cl) 2 atoms
Sodium (Na) 9 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Methyl-Coenzyme M Reductase Enzyme Product Complex (pdb code 1hbm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Methyl-Coenzyme M Reductase Enzyme Product Complex, PDB code: 1hbm:

Zinc binding site 1 out of 1 in 1hbm

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Methyl-Coenzyme M Reductase Enzyme Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1556

b:11.6
occ:0.50
O A:CYS218 2.7 10.7 1.0
O D:CYS218 2.7 8.7 1.0
O A:ARG216 2.8 9.7 1.0
O D:ARG216 2.8 10.3 1.0
O A:SER215 3.4 10.1 1.0
O D:SER215 3.4 9.8 1.0
NH2 D:ARG102 3.4 8.5 1.0
NH2 A:ARG102 3.5 8.8 1.0
C A:ARG216 3.6 9.6 1.0
C D:ARG216 3.6 10.4 1.0
O A:HOH2266 3.8 9.8 1.0
C A:CYS218 3.8 11.5 1.0
C D:CYS218 3.9 8.8 1.0
O D:HOH2275 3.9 8.4 1.0
CA D:ARG216 3.9 9.5 1.0
CA A:ARG216 3.9 8.7 1.0
CZ D:ARG102 4.0 9.7 1.0
NH1 D:ARG102 4.0 10.5 1.0
CZ A:ARG102 4.1 10.6 1.0
NH1 A:ARG102 4.1 10.0 1.0
N A:CYS218 4.4 8.6 1.0
N D:CYS218 4.4 6.8 1.0
C D:SER215 4.4 10.2 1.0
C A:SER215 4.4 9.7 1.0
C A:THR217 4.6 8.8 1.0
C D:THR217 4.6 7.1 1.0
N D:ASP219 4.6 9.0 1.0
CA D:ASP219 4.6 8.5 1.0
CA A:ASP219 4.6 11.1 1.0
N A:ASP219 4.6 10.4 1.0
N D:ARG216 4.6 9.6 1.0
N A:ARG216 4.7 9.4 1.0
N A:THR217 4.7 9.1 1.0
CA D:CYS218 4.7 7.7 1.0
N D:THR217 4.7 9.0 1.0
CA A:CYS218 4.7 8.4 1.0
O D:THR217 4.8 8.0 1.0
O A:THR217 4.8 8.5 1.0
NE D:ARG102 5.0 9.1 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: Wed Dec 16 02:51:06 2020

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