Zinc in PDB 7cbg: 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: 7cbg 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) 50.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.793, 101.796, 105.633, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 26.1

Other elements in 7cbg:

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

Chlorine (Cl) 4 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 7cbg). 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: 7cbg:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7cbg

Go back to Zinc Binding Sites List in 7cbg
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:12.9
occ:1.00
 O24 A:FQL701 2.0 20.1 1.0
NE2 A:HIS385 2.0 14.7 1.0
ND1 A:HIS511 2.1 15.9 1.0
SG A:CYS334 2.3 15.6 1.0
N22 A:FQL701 2.3 20.4 1.0
CE1 A:HIS385 3.0 14.8 1.0
C23 A:FQL701 3.0 20.3 1.0
CE1 A:HIS511 3.0 15.9 1.0
CD2 A:HIS385 3.1 14.8 1.0
C26 A:FQL701 3.1 20.3 1.0
CG A:HIS511 3.1 16.0 1.0
C21 A:FQL701 3.2 20.4 1.0
CB A:CYS334 3.4 15.6 1.0
CB A:HIS511 3.5 16.0 1.0
O A:HOH802 3.8 12.3 1.0
ND1 A:HIS385 4.1 14.8 1.0
NE2 A:HIS511 4.2 16.0 1.0
CG A:HIS385 4.2 14.8 1.0
OD2 A:ASP383 4.2 14.8 1.0
CD2 A:HIS511 4.2 16.0 1.0
C25 A:FQL701 4.3 20.3 1.0
CA A:CYS334 4.3 15.5 1.0
OD1 A:ASP383 4.3 14.8 1.0
CA A:HIS511 4.4 16.1 1.0
N A:CYS334 4.4 15.7 1.0
C19 A:FQL701 4.5 20.7 1.0
CG A:ASP383 4.7 14.8 1.0
O20 A:FQL701 4.9 20.7 1.0

Zinc binding site 2 out of 2 in 7cbg

Go back to Zinc Binding Sites List in 7cbg
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:18.8
occ:1.00
 O24 B:FQL701 2.0 21.7 1.0
NE2 B:HIS385 2.1 16.2 1.0
ND1 B:HIS511 2.1 19.4 1.0
SG B:CYS334 2.3 18.7 1.0
N22 B:FQL701 2.3 22.0 1.0
CE1 B:HIS511 3.0 19.5 1.0
CE1 B:HIS385 3.0 16.2 1.0
C21 B:FQL701 3.1 22.0 1.0
C23 B:FQL701 3.1 21.8 1.0
CD2 B:HIS385 3.1 16.2 1.0
CG B:HIS511 3.1 19.4 1.0
C26 B:FQL701 3.2 22.1 1.0
CB B:CYS334 3.4 18.6 1.0
CB B:HIS511 3.5 19.4 1.0
O B:HOH802 3.5 13.2 1.0
NE2 B:HIS511 4.1 19.5 1.0
ND1 B:HIS385 4.1 16.2 1.0
CD2 B:HIS511 4.2 19.5 1.0
C25 B:FQL701 4.2 21.8 1.0
CG B:HIS385 4.2 16.2 1.0
OD2 B:ASP383 4.3 14.7 1.0
CA B:CYS334 4.3 18.6 1.0
OD1 B:ASP383 4.3 14.7 1.0
CA B:HIS511 4.4 19.5 1.0
N B:CYS334 4.4 18.6 1.0
C19 B:FQL701 4.5 22.3 1.0
CG B:ASP383 4.8 14.8 1.0
CE B:MET509 4.8 25.1 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: Wed Dec 16 13:39:45 2020

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