Zinc in PDB 7wm7: 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: 7wm7 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 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	85.473, 102.049, 103.01, 90, 90, 90
R / Rfree (%)	22.8 / 27.4

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 7wm7). 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: 7wm7:
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:Zn701 b:43.2 occ:1.00 NE2 A:HIS385 2.0 37.0 1.0 ND1 A:HIS511 2.1 41.7 1.0 N30 A:9I6702 2.1 47.2 1.0 O29 A:9I6702 2.3 45.8 1.0 SG A:CYS334 2.4 39.5 1.0 CE1 A:HIS511 2.8 42.8 1.0 C25 A:9I6702 2.9 48.0 1.0 CE1 A:HIS385 3.0 37.0 1.0 CD2 A:HIS385 3.0 37.2 1.0 CG A:HIS511 3.2 41.2 1.0 C27 A:9I6702 3.2 47.3 1.0 CB A:CYS334 3.4 38.5 1.0 CB A:HIS511 3.7 40.1 1.0 O A:HOH807 3.8 32.7 1.0 NE2 A:HIS511 4.0 43.5 1.0 ND1 A:HIS385 4.1 37.4 1.0 CG A:HIS385 4.2 36.8 1.0 CD2 A:HIS511 4.2 41.9 1.0 CA A:CYS334 4.2 38.7 1.0 OD2 A:ASP383 4.2 44.3 1.0 C28 A:9I6702 4.3 45.7 1.0 N A:CYS334 4.3 39.1 1.0 C24 A:9I6702 4.4 50.2 1.0 OD1 A:ASP383 4.4 44.6 1.0 CA A:HIS511 4.5 40.6 1.0 CG A:ASP383 4.7 43.0 1.0 O26 A:9I6702 4.8 50.2 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:58.4 occ:1.00 NE2 B:HIS385 2.0 47.2 1.0 N30 B:9I6702 2.2 54.4 1.0 SG B:CYS334 2.3 56.8 1.0 O29 B:9I6702 2.4 52.7 1.0 ND1 B:HIS511 2.5 46.9 1.0 CE1 B:HIS385 2.8 48.4 1.0 CG B:HIS511 3.1 46.6 1.0 CE1 B:HIS511 3.1 47.5 1.0 CD2 B:HIS385 3.2 48.6 1.0 C25 B:9I6702 3.2 56.4 1.0 CB B:CYS334 3.3 56.3 1.0 C27 B:9I6702 3.4 55.3 1.0 CB B:HIS511 3.5 46.5 1.0 CD2 B:HIS511 4.0 48.0 1.0 NE2 B:HIS511 4.0 50.1 1.0 ND1 B:HIS385 4.0 48.2 1.0 OD2 B:ASP383 4.0 53.4 1.0 CA B:CYS334 4.1 57.5 1.0 CG B:HIS385 4.2 50.2 1.0 N B:CYS334 4.3 57.4 1.0 OD1 B:ASP383 4.3 54.8 1.0 CA B:HIS511 4.4 47.0 1.0 C28 B:9I6702 4.5 55.4 1.0 C24 B:9I6702 4.5 59.6 1.0 CG B:ASP383 4.6 53.5 1.0 O26 B:9I6702 4.8 61.2 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