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Zinc in PDB 7cbi: Crystal Structure of Threonyl-Trna Synthetase (Thrrs) From Salmonella Enterica in Complex with An Inhibitor

Enzymatic activity of Crystal Structure of Threonyl-Trna Synthetase (Thrrs) From Salmonella Enterica in Complex with An Inhibitor

All present enzymatic activity of Crystal Structure of Threonyl-Trna Synthetase (Thrrs) From Salmonella Enterica in Complex with An Inhibitor:
6.1.1.3;

Protein crystallography data

The structure of Crystal Structure of Threonyl-Trna Synthetase (Thrrs) From Salmonella Enterica in Complex with An Inhibitor, PDB code: 7cbi was solved by J.Guo, B.Chen, H.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.36 / 1.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.077, 101.162, 103.548, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 20.8

Other elements in 7cbi:

The structure of Crystal Structure of Threonyl-Trna Synthetase (Thrrs) From Salmonella Enterica in Complex with An Inhibitor also contains other interesting chemical elements:

Bromine (Br) 2 atoms
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Threonyl-Trna Synthetase (Thrrs) From Salmonella Enterica in Complex with An Inhibitor (pdb code 7cbi). 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 Threonyl-Trna Synthetase (Thrrs) From Salmonella Enterica in Complex with An Inhibitor, PDB code: 7cbi:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7cbi

Go back to Zinc Binding Sites List in 7cbi
Zinc binding site 1 out of 2 in the Crystal Structure of Threonyl-Trna Synthetase (Thrrs) From Salmonella Enterica in Complex with An Inhibitor


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 Threonyl-Trna Synthetase (Thrrs) From Salmonella Enterica in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:11.9
occ:1.00
 NE2 A:HIS385 2.1 11.7 1.0
ND1 A:HIS511 2.1 11.3 1.0
N25 A:FQU702 2.2 19.9 1.0
O26 A:FQU702 2.3 18.3 1.0
SG A:CYS334 2.3 12.4 1.0
CE1 A:HIS511 2.9 12.2 1.0
CE1 A:HIS385 3.0 11.4 1.0
C21 A:FQU702 3.1 20.6 1.0
CD2 A:HIS385 3.1 11.1 1.0
CG A:HIS511 3.1 11.7 1.0
C23 A:FQU702 3.2 19.9 1.0
CB A:CYS334 3.3 11.8 1.0
CB A:HIS511 3.6 11.4 1.0
O A:HOH845 3.8 13.9 1.0
NE2 A:HIS511 4.1 12.2 1.0
ND1 A:HIS385 4.1 11.1 1.0
CA A:CYS334 4.1 11.4 1.0
CG A:HIS385 4.2 11.4 1.0
CD2 A:HIS511 4.2 11.7 1.0
N A:CYS334 4.3 11.2 1.0
OD2 A:ASP383 4.3 13.0 1.0
OD1 A:ASP383 4.4 12.8 1.0
C24 A:FQU702 4.4 19.4 1.0
C20 A:FQU702 4.5 22.3 1.0
O A:HOH1126 4.5 33.0 1.0
CA A:HIS511 4.5 11.3 1.0
CG A:ASP383 4.8 12.9 1.0
O22 A:FQU702 5.0 22.8 1.0

Zinc binding site 2 out of 2 in 7cbi

Go back to Zinc Binding Sites List in 7cbi
Zinc binding site 2 out of 2 in the Crystal Structure of Threonyl-Trna Synthetase (Thrrs) From Salmonella Enterica in Complex with An Inhibitor


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 Threonyl-Trna Synthetase (Thrrs) From Salmonella Enterica in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:12.7
occ:1.00
 NE2 B:HIS385 2.1 12.5 1.0
ND1 B:HIS511 2.1 11.9 1.0
O26 B:FQU703 2.2 12.6 1.0
N25 B:FQU703 2.3 13.6 1.0
SG B:CYS334 2.4 14.0 1.0
CE1 B:HIS511 3.0 12.3 1.0
C21 B:FQU703 3.0 13.8 1.0
CE1 B:HIS385 3.1 12.1 1.0
CD2 B:HIS385 3.1 12.1 1.0
C23 B:FQU703 3.1 12.9 1.0
CG B:HIS511 3.2 12.2 1.0
CB B:CYS334 3.3 13.4 1.0
CB B:HIS511 3.6 12.0 1.0
O B:HOH895 3.7 11.6 1.0
NE2 B:HIS511 4.1 12.4 1.0
ND1 B:HIS385 4.2 11.9 1.0
OD2 B:ASP383 4.2 11.4 1.0
OD1 B:ASP383 4.2 11.3 1.0
CD2 B:HIS511 4.2 12.6 1.0
CG B:HIS385 4.2 12.3 1.0
CA B:CYS334 4.3 12.8 1.0
C24 B:FQU703 4.4 12.8 1.0
N B:CYS334 4.4 12.7 1.0
OH B:TYR462 4.5 17.3 1.0
C20 B:FQU703 4.5 14.7 1.0
O B:HOH1011 4.5 26.5 1.0
CA B:HIS511 4.5 12.1 1.0
CG B:ASP383 4.7 11.2 1.0
OE1 B:GLN484 4.8 16.4 1.0
O22 B:FQU703 5.0 14.6 1.0

Reference:

J.Guo, B.Chen, Y.Yu, B.Cheng, Y.Ju, J.Tang, Z.Cai, Q.Gu, J.Xu, H.Zhou. Structure-Guided Optimization and Mechanistic Study of A Class of Quinazolinone-Threonine Hybrids As Antibacterial Thrrs Inhibitors. Eur.J.Med.Chem. V. 207 12848 2020.
ISSN: ISSN 0223-5234
PubMed: 32980741
DOI: 10.1016/J.EJMECH.2020.112848
Page generated: Tue Oct 29 18:08:00 2024

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