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Zinc in PDB 3m2r: Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues

Enzymatic activity of Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues

All present enzymatic activity of Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues:
2.8.4.1;

Protein crystallography data

The structure of Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues, PDB code: 3m2r was solved by P.E.Cedervall, M.Dey, S.W.Ragsdale, C.M.Wilmot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.49 / 1.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.016, 118.260, 122.387, 90.00, 91.84, 90.00
R / Rfree (%) 14.3 / 16.6

Other elements in 3m2r:

The structure of Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Magnesium (Mg) 9 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues (pdb code 3m2r). 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 Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues, PDB code: 3m2r:

Zinc binding site 1 out of 1 in 3m2r

Go back to Zinc Binding Sites List in 3m2r
Zinc binding site 1 out of 1 in the Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn558

b:10.2
occ:0.60
 O D:CYS218 2.7 6.5 1.0
O A:CYS218 2.8 6.2 1.0
O A:ARG216 2.8 6.3 1.0
O D:ARG216 2.8 7.1 1.0
O D:SER215 3.3 6.4 1.0
O A:SER215 3.3 6.8 1.0
NH1 D:ARG102 3.4 7.2 1.0
NH1 A:ARG102 3.5 6.2 1.0
C D:ARG216 3.6 6.5 1.0
C A:ARG216 3.6 5.5 1.0
O D:HOH573 3.7 7.0 1.0
O A:HOH597 3.8 6.7 1.0
C A:CYS218 3.8 5.6 1.0
C D:CYS218 3.8 5.5 1.0
CA D:ARG216 3.8 5.6 1.0
CA A:ARG216 3.9 6.0 1.0
CZ D:ARG102 3.9 6.7 1.0
CZ A:ARG102 4.0 6.0 1.0
NH2 A:ARG102 4.0 6.5 1.0
NH2 D:ARG102 4.0 6.6 1.0
N A:CYS218 4.3 5.7 1.0
N D:CYS218 4.4 5.4 1.0
C D:SER215 4.4 6.7 1.0
C A:SER215 4.4 5.9 1.0
C D:THR217 4.5 6.3 1.0
C A:THR217 4.6 5.8 1.0
CA A:ASP219 4.6 6.0 1.0
N D:ASP219 4.6 5.5 1.0
N D:ARG216 4.6 6.2 1.0
CA D:ASP219 4.6 6.0 1.0
N A:ASP219 4.6 5.6 1.0
N A:ARG216 4.6 6.2 1.0
N D:THR217 4.7 5.9 1.0
N A:THR217 4.7 6.2 1.0
CA A:CYS218 4.7 6.2 1.0
CA D:CYS218 4.7 5.5 1.0
O A:THR217 4.8 6.2 1.0
O D:THR217 4.8 6.8 1.0
NE D:ARG102 4.9 6.2 1.0
NE A:ARG102 4.9 6.4 1.0

Reference:

P.E.Cedervall, M.Dey, A.R.Pearson, S.W.Ragsdale, C.M.Wilmot. Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues. Biochemistry V. 49 7683 2010.
ISSN: ISSN 0006-2960
PubMed: 20707311
DOI: 10.1021/BI100458D
Page generated: Sat Oct 26 09:03:21 2024

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