Zinc in PDB 7wmi: Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor

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

The structure of Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor, PDB code: 7wmi was solved by Z.Cai, B.Chen, Y.Yu, H.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	85.394, 102.618, 102.851, 90, 90, 90
R / Rfree (%)	20.8 / 24.3

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

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

The binding sites of Zinc atom in the Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor (pdb code 7wmi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor, PDB code: 7wmi:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Threonyl-Trna Synthetase 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 Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:20.2 occ:1.00 NE2 A:HIS385 2.0 18.7 1.0 ND1 A:HIS511 2.1 18.4 1.0 O20 A:9IC703 2.2 21.0 1.0 N19 A:9IC703 2.3 22.4 1.0 SG A:CYS334 2.4 19.3 1.0 CE1 A:HIS511 3.0 18.7 1.0 C16 A:9IC703 3.0 22.4 1.0 CE1 A:HIS385 3.0 18.8 1.0 CD2 A:HIS385 3.0 19.0 1.0 C18 A:9IC703 3.1 21.7 1.0 CG A:HIS511 3.2 18.6 1.0 CB A:CYS334 3.4 19.2 1.0 CB A:HIS511 3.5 18.7 1.0 O A:HOH875 3.8 17.8 1.0 ND1 A:HIS385 4.1 18.6 1.0 NE2 A:HIS511 4.2 18.7 1.0 CG A:HIS385 4.2 18.9 1.0 CA A:CYS334 4.2 19.5 1.0 CD2 A:HIS511 4.3 18.9 1.0 OD2 A:ASP383 4.3 20.0 1.0 C21 A:9IC703 4.3 21.0 1.0 OD1 A:ASP383 4.3 19.3 1.0 N A:CYS334 4.3 19.6 1.0 C15 A:9IC703 4.4 23.5 1.0 CA A:HIS511 4.5 19.0 1.0 O A:HOH1037 4.6 32.6 1.0 CG A:ASP383 4.8 19.2 1.0 O17 A:9IC703 4.9 23.4 1.0

Zinc binding site 2 out of 2 in the Threonyl-Trna Synthetase 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 Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:25.4 occ:1.00 NE2 B:HIS385 2.0 21.9 1.0 O20 B:9IC702 2.2 25.4 1.0 ND1 B:HIS511 2.2 26.9 1.0 N19 B:9IC702 2.3 25.5 1.0 SG B:CYS334 2.5 25.6 1.0 C16 B:9IC702 3.0 25.7 1.0 CE1 B:HIS385 3.0 22.3 1.0 CD2 B:HIS385 3.0 22.1 1.0 C18 B:9IC702 3.1 25.4 1.0 CE1 B:HIS511 3.1 26.8 1.0 CG B:HIS511 3.2 26.5 1.0 CB B:CYS334 3.3 25.2 1.0 CB B:HIS511 3.6 26.0 1.0 O B:HOH850 3.8 25.7 1.0 ND1 B:HIS385 4.1 22.1 1.0 CG B:HIS385 4.1 22.4 1.0 CA B:CYS334 4.2 25.2 1.0 OD2 B:ASP383 4.2 23.1 1.0 NE2 B:HIS511 4.2 26.4 1.0 N B:CYS334 4.3 25.1 1.0 C21 B:9IC702 4.3 25.6 1.0 CD2 B:HIS511 4.3 26.3 1.0 OD1 B:ASP383 4.3 22.7 1.0 C15 B:9IC702 4.4 26.2 1.0 CA B:HIS511 4.4 25.8 1.0 CG B:ASP383 4.7 22.8 1.0 O17 B:9IC702 5.0 26.3 1.0

Z.Cai, B.Chen, Y.Yu, J.Guo, Z.Luo, B.Cheng, J.Xu, Q.Gu, H.Zhou. Design, Synthesis, and Proof-of-Concept of Triple-Site Inhibitors Against Aminoacyl-Trna Synthetases. J.Med.Chem. V. 65 5800 2022.
ISSN: ISSN 0022-2623
PubMed: 35363470
DOI: 10.1021/ACS.JMEDCHEM.2C00134