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Zinc in PDB 2cim: Crystal Structure of Methanosarcina Barkeri Seryl-Trna Synthetase

Enzymatic activity of Crystal Structure of Methanosarcina Barkeri Seryl-Trna Synthetase

All present enzymatic activity of Crystal Structure of Methanosarcina Barkeri Seryl-Trna Synthetase:
6.1.1.11;

Protein crystallography data

The structure of Crystal Structure of Methanosarcina Barkeri Seryl-Trna Synthetase, PDB code: 2cim was solved by S.Bilokapic, T.Maier, D.Ahel, I.Gruic-Sovulj, D.Soll, I.Weygand-Durasevic, N.Ban, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.94 / 2.51
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 97.150, 97.150, 268.500, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 25.2

Other elements in 2cim:

The structure of Crystal Structure of Methanosarcina Barkeri Seryl-Trna Synthetase also contains other interesting chemical elements:

Platinum (Pt) 1 atom
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Methanosarcina Barkeri Seryl-Trna Synthetase (pdb code 2cim). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Methanosarcina Barkeri Seryl-Trna Synthetase, PDB code: 2cim:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2cim

Go back to Zinc Binding Sites List in 2cim
Zinc binding site 1 out of 2 in the Crystal Structure of Methanosarcina Barkeri Seryl-Trna Synthetase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Methanosarcina Barkeri Seryl-Trna Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1503

b:70.8
occ:1.00
OE2 A:GLU355 1.9 64.9 1.0
SG A:CYS306 2.6 68.5 1.0
SG A:CYS461 2.6 70.3 1.0
O A:HOH2070 2.7 43.5 1.0
CD A:GLU355 3.1 64.2 1.0
CB A:CYS461 3.1 64.6 1.0
O A:HOH2089 3.4 53.5 1.0
CB A:CYS306 3.4 65.2 1.0
OE1 A:GLU355 3.7 65.0 1.0
O A:ALA304 4.1 64.2 1.0
CG A:GLU355 4.2 62.0 1.0
O A:HOH2071 4.4 53.4 1.0
N A:CYS306 4.4 65.2 1.0
CA A:CYS306 4.5 65.6 1.0
CA A:CYS461 4.6 64.7 1.0
C A:CYS461 5.0 64.2 1.0
C A:ALA304 5.0 63.8 1.0

Zinc binding site 2 out of 2 in 2cim

Go back to Zinc Binding Sites List in 2cim
Zinc binding site 2 out of 2 in the Crystal Structure of Methanosarcina Barkeri Seryl-Trna Synthetase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Methanosarcina Barkeri Seryl-Trna Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1503

b:73.2
occ:1.00
OE2 B:GLU355 1.9 64.8 1.0
SG B:CYS461 2.4 70.2 1.0
SG B:CYS306 2.5 70.3 1.0
CB B:CYS461 3.0 66.4 1.0
CD B:GLU355 3.0 64.8 1.0
O B:HOH2098 3.3 47.4 1.0
CB B:CYS306 3.4 65.6 1.0
OE1 B:GLU355 3.6 65.0 1.0
O B:HOH2114 3.9 62.0 1.0
O B:HOH2079 4.1 56.5 1.0
O B:ALA304 4.1 64.2 1.0
CG B:GLU355 4.2 63.5 1.0
CA B:CYS461 4.4 66.4 1.0
N B:CYS306 4.5 64.7 1.0
CA B:CYS306 4.6 65.8 1.0
C B:CYS461 4.8 66.0 1.0
N B:SER462 4.8 65.7 1.0

Reference:

S.Bilokapic, T.Maier, D.Ahel, I.Gruic-Sovulj, D.Soll, I.Weygand-Durasevic, N.Ban. Structure of the Unusual Seryl-Trna Synthetase Reveals A Distinct Zinc-Dependent Mode of Substrate Recognition Embo J. V. 25 2498 2006.
ISSN: ISSN 0261-4189
PubMed: 16675947
DOI: 10.1038/SJ.EMBOJ.7601129
Page generated: Wed Dec 16 03:19:20 2020

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