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Zinc in PDB 7cbh: 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: 7cbh 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 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.183, 101.267, 103.427, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 21.5

Other elements in 7cbh:

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) 1 atom
Chlorine (Cl) 1 atom

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 7cbh). 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: 7cbh:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7cbh

Go back to Zinc Binding Sites List in 7cbh
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:Zn702

b:19.9
occ:1.00
 NE2 A:HIS385 2.0 18.1 1.0
N7 A:FQR701 2.1 27.9 1.0
ND1 A:HIS511 2.1 19.3 1.0
O8 A:FQR701 2.2 25.7 1.0
SG A:CYS334 2.3 20.4 1.0
CE1 A:HIS385 2.9 18.8 1.0
C3 A:FQR701 2.9 28.7 1.0
CE1 A:HIS511 3.0 19.6 1.0
CD2 A:HIS385 3.1 19.2 1.0
C5 A:FQR701 3.1 28.1 1.0
CG A:HIS511 3.2 19.7 1.0
CB A:CYS334 3.3 19.3 1.0
CB A:HIS511 3.5 19.2 1.0
O A:HOH827 3.8 20.3 1.0
ND1 A:HIS385 4.1 18.0 1.0
CA A:CYS334 4.1 18.9 1.0
CG A:HIS385 4.2 18.6 1.0
NE2 A:HIS511 4.2 18.9 1.0
CD2 A:HIS511 4.3 19.7 1.0
OD2 A:ASP383 4.3 21.9 1.0
N A:CYS334 4.3 19.0 1.0
C6 A:FQR701 4.3 27.8 1.0
OD1 A:ASP383 4.3 22.2 1.0
C2 A:FQR701 4.4 30.8 1.0
CA A:HIS511 4.5 19.1 1.0
O A:HOH978 4.6 25.1 1.0
CG A:ASP383 4.8 21.6 1.0
O4 A:FQR701 4.9 30.6 1.0

Zinc binding site 2 out of 2 in 7cbh

Go back to Zinc Binding Sites List in 7cbh
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:Zn701

b:24.3
occ:1.00
 NE2 B:HIS385 2.0 19.5 1.0
ND1 B:HIS511 2.2 22.5 1.0
SG B:CYS334 2.3 24.6 1.0
CE1 B:HIS385 3.0 19.5 1.0
CE1 B:HIS511 3.0 23.8 1.0
CD2 B:HIS385 3.0 19.6 1.0
CG B:HIS511 3.2 23.1 1.0
CB B:CYS334 3.3 23.3 1.0
CB B:HIS511 3.5 23.5 1.0
O B:HOH810 3.7 22.8 1.0
ND1 B:HIS385 4.1 19.2 1.0
NE2 B:HIS511 4.2 23.6 1.0
CG B:HIS385 4.2 20.0 1.0
CA B:CYS334 4.2 23.1 1.0
CD2 B:HIS511 4.2 24.7 1.0
OD2 B:ASP383 4.3 24.3 1.0
N B:CYS334 4.3 21.9 1.0
CE B:MET332 4.3 40.1 1.0
OH B:TYR462 4.3 28.7 1.0
OD1 B:ASP383 4.4 22.9 1.0
CA B:HIS511 4.6 22.7 1.0
CG B:ASP383 4.8 22.5 1.0
OE1 B:GLN484 4.8 26.9 1.0
CZ B:TYR462 5.0 27.9 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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