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Zinc in PDB 4gri: Crystal Structure of A Glutamyl-Trna Synthetase Glurs From Borrelia Burgdorferi Bound to Glutamic Acid and Zinc

Enzymatic activity of Crystal Structure of A Glutamyl-Trna Synthetase Glurs From Borrelia Burgdorferi Bound to Glutamic Acid and Zinc

All present enzymatic activity of Crystal Structure of A Glutamyl-Trna Synthetase Glurs From Borrelia Burgdorferi Bound to Glutamic Acid and Zinc:
6.1.1.17;

Protein crystallography data

The structure of Crystal Structure of A Glutamyl-Trna Synthetase Glurs From Borrelia Burgdorferi Bound to Glutamic Acid and Zinc, PDB code: 4gri was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.17 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.460, 110.310, 197.880, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 28.5

Other elements in 4gri:

The structure of Crystal Structure of A Glutamyl-Trna Synthetase Glurs From Borrelia Burgdorferi Bound to Glutamic Acid and Zinc also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Glutamyl-Trna Synthetase Glurs From Borrelia Burgdorferi Bound to Glutamic Acid and Zinc (pdb code 4gri). 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 A Glutamyl-Trna Synthetase Glurs From Borrelia Burgdorferi Bound to Glutamic Acid and Zinc, PDB code: 4gri:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4gri

Go back to Zinc Binding Sites List in 4gri
Zinc binding site 1 out of 2 in the Crystal Structure of A Glutamyl-Trna Synthetase Glurs From Borrelia Burgdorferi Bound to Glutamic Acid and Zinc


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 A Glutamyl-Trna Synthetase Glurs From Borrelia Burgdorferi Bound to Glutamic Acid and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:44.8
occ:1.00
 OH A:TYR130 2.1 7.1 1.0
SG A:CYS109 2.3 38.8 1.0
SG A:CYS134 2.4 39.6 1.0
SG A:CYS107 2.4 32.0 1.0
N A:CYS109 3.0 4.2 1.0
CB A:CYS109 3.0 6.4 1.0
CZ A:TYR130 3.2 50.7 1.0
N A:TYR108 3.2 23.9 1.0
CB A:CYS134 3.4 11.8 1.0
CB A:CYS107 3.4 24.2 1.0
CA A:CYS109 3.5 22.2 1.0
CA A:CYS107 3.6 10.6 1.0
CE1 A:TYR130 3.7 31.7 1.0
C A:CYS107 3.8 31.5 1.0
C A:TYR108 3.9 50.8 1.0
CA A:TYR108 4.2 37.6 1.0
N A:CYS134 4.2 23.5 1.0
CE2 A:TYR130 4.3 45.2 1.0
ND1 A:HIS133 4.3 24.3 1.0
CA A:CYS134 4.4 20.2 1.0
CB A:HIS133 4.6 11.8 1.0
O A:CYS107 4.8 39.2 1.0
C A:CYS109 4.8 24.3 1.0
C A:HIS133 4.9 29.5 1.0
CG A:HIS133 4.9 36.4 1.0
O A:TYR108 5.0 18.6 1.0

Zinc binding site 2 out of 2 in 4gri

Go back to Zinc Binding Sites List in 4gri
Zinc binding site 2 out of 2 in the Crystal Structure of A Glutamyl-Trna Synthetase Glurs From Borrelia Burgdorferi Bound to Glutamic Acid and Zinc


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 A Glutamyl-Trna Synthetase Glurs From Borrelia Burgdorferi Bound to Glutamic Acid and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:45.6
occ:1.00
 OH B:TYR130 2.1 15.5 1.0
SG B:CYS107 2.3 37.0 1.0
SG B:CYS134 2.4 42.4 1.0
SG B:CYS109 2.4 37.7 1.0
N B:CYS109 2.9 11.9 1.0
CB B:CYS109 3.0 12.0 1.0
N B:TYR108 3.1 20.2 1.0
CZ B:TYR130 3.3 88.6 1.0
CB B:CYS134 3.3 15.6 1.0
CB B:CYS107 3.4 24.4 1.0
CA B:CYS109 3.5 12.0 1.0
CA B:CYS107 3.6 22.4 1.0
C B:CYS107 3.6 31.5 1.0
C B:TYR108 3.8 48.7 1.0
CE1 B:TYR130 3.8 80.8 1.0
CA B:TYR108 4.0 31.1 1.0
N B:CYS134 4.3 35.4 1.0
CE2 B:TYR130 4.3 36.0 1.0
CA B:CYS134 4.4 38.8 1.0
ND1 B:HIS133 4.5 39.5 1.0
O B:CYS107 4.6 34.9 1.0
CB B:HIS133 4.7 19.8 1.0
C B:CYS109 4.8 12.8 1.0
O B:TYR108 4.8 49.1 1.0
CB B:TYR108 4.9 11.8 1.0
C B:HIS133 5.0 39.5 1.0

Reference:

S.O.Moen, T.E.Edwards, D.M.Dranow, M.C.Clifton, B.Sankaran, W.C.Van Voorhis, A.Sharma, C.Manoil, B.L.Staker, P.J.Myler, D.D.Lorimer. Ligand Co-Crystallization of Aminoacyl-Trna Synthetases From Infectious Disease Organisms. Sci Rep V. 7 223 2017.
ISSN: ESSN 2045-2322
PubMed: 28303005
DOI: 10.1038/S41598-017-00367-6
Page generated: Sat Oct 26 23:28:06 2024

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