Zinc in PDB 7wmf: 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: 7wmf 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 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	85.792, 102.521, 103.171, 90, 90, 90
R / Rfree (%)	22.4 / 26.7

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

Chlorine	(Cl)	4 atoms
Fluorine	(F)	6 atoms

The binding sites of Zinc atom in the Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor (pdb code 7wmf). 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: 7wmf:
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:Zn703 b:30.0 occ:1.00 NE2 A:HIS385 2.0 26.8 1.0 ND1 A:HIS511 2.1 26.4 1.0 N4 A:9I9701 2.2 33.4 1.0 O2 A:9I9701 2.2 31.5 1.0 SG A:CYS334 2.4 31.1 1.0 CE1 A:HIS511 2.9 27.7 1.0 CE1 A:HIS385 3.0 26.9 1.0 C14 A:9I9701 3.0 34.2 1.0 CD2 A:HIS385 3.0 27.3 1.0 CG A:HIS511 3.1 27.5 1.0 C15 A:9I9701 3.1 33.2 1.0 CB A:CYS334 3.4 30.2 1.0 CB A:HIS511 3.6 27.6 1.0 O A:HOH838 3.7 27.9 1.0 NE2 A:HIS511 4.1 28.1 1.0 ND1 A:HIS385 4.1 26.3 1.0 CG A:HIS385 4.1 27.4 1.0 CD2 A:HIS511 4.2 28.1 1.0 CA A:CYS334 4.2 30.6 1.0 OD2 A:ASP383 4.3 31.8 1.0 OD1 A:ASP383 4.3 29.8 1.0 C16 A:9I9701 4.4 32.8 1.0 N A:CYS334 4.4 30.7 1.0 C13 A:9I9701 4.4 36.7 1.0 CA A:HIS511 4.5 28.2 1.0 CG A:ASP383 4.7 30.1 1.0 O3 A:9I9701 4.9 36.6 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:Zn702 b:42.6 occ:1.00 NE2 B:HIS385 1.9 33.1 1.0 N4 B:9I9701 2.2 45.0 1.0 ND1 B:HIS511 2.2 47.4 1.0 O2 B:9I9701 2.2 45.4 1.0 SG B:CYS334 2.5 42.5 1.0 CE1 B:HIS385 2.9 36.9 1.0 CD2 B:HIS385 3.0 34.8 1.0 C14 B:9I9701 3.0 45.6 1.0 C15 B:9I9701 3.1 44.6 1.0 CE1 B:HIS511 3.1 47.1 1.0 CG B:HIS511 3.2 47.2 1.0 CB B:CYS334 3.4 42.2 1.0 CB B:HIS511 3.5 46.8 1.0 ND1 B:HIS385 4.0 36.0 1.0 CG B:HIS385 4.1 36.4 1.0 OD2 B:ASP383 4.1 42.0 1.0 CA B:CYS334 4.2 42.7 1.0 O B:HOH863 4.2 51.0 1.0 N B:CYS334 4.3 41.3 1.0 NE2 B:HIS511 4.3 47.0 1.0 OD1 B:ASP383 4.3 42.5 1.0 CA B:HIS511 4.3 46.9 1.0 CD2 B:HIS511 4.3 47.2 1.0 C16 B:9I9701 4.3 44.9 1.0 C13 B:9I9701 4.4 46.2 1.0 CG B:ASP383 4.6 42.6 1.0 O3 B:9I9701 4.8 45.1 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