Zinc in PDB 6l2q: 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: 6l2q 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)	22.18 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.231, 101.917, 105.641, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 25.4

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

Chlorine

(Cl)

4 atoms

The binding sites of Zinc atom in the Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor (pdb code 6l2q). 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: 6l2q:
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:16.7 occ:1.00 NE2 A:HIS385 2.2 13.6 1.0 O25 A:E4O702 2.3 15.2 1.0 ND1 A:HIS511 2.3 17.9 1.0 N24 A:E4O702 2.4 16.3 1.0 SG A:CYS334 2.4 14.8 1.0 CE1 A:HIS385 2.9 13.7 1.0 C20 A:E4O702 3.1 16.4 1.0 CE1 A:HIS511 3.1 18.0 1.0 C22 A:E4O702 3.2 16.1 1.0 CD2 A:HIS385 3.3 13.9 1.0 CG A:HIS511 3.3 17.8 1.0 CB A:CYS334 3.3 14.6 1.0 O A:HOH841 3.5 14.6 1.0 CB A:HIS511 3.7 17.6 1.0 ND1 A:HIS385 4.1 13.7 1.0 CA A:CYS334 4.2 14.7 1.0 NE2 A:HIS511 4.2 18.2 1.0 OD2 A:ASP383 4.3 13.2 1.0 O A:HOH902 4.3 27.6 1.0 N A:CYS334 4.3 14.9 1.0 CG A:HIS385 4.3 13.8 1.0 CD2 A:HIS511 4.4 18.0 1.0 OD1 A:ASP383 4.4 13.2 1.0 C23 A:E4O702 4.4 15.6 1.0 C19 A:E4O702 4.5 17.4 1.0 CA A:HIS511 4.6 17.6 1.0 CG A:ASP383 4.8 13.0 1.0 SD A:MET332 4.9 24.0 1.0 O21 A:E4O702 4.9 17.8 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:20.3 occ:1.00 NE2 B:HIS385 2.2 19.0 1.0 ND1 B:HIS511 2.2 25.4 1.0 SG B:CYS334 2.2 20.8 1.0 O25 B:E4O702 2.3 22.5 1.0 N24 B:E4O702 2.7 23.7 1.0 CE1 B:HIS385 2.8 18.7 1.0 CE1 B:HIS511 2.9 25.8 1.0 CB B:CYS334 3.3 21.1 1.0 C20 B:E4O702 3.3 23.2 1.0 CG B:HIS511 3.3 25.3 1.0 C22 B:E4O702 3.3 23.1 1.0 CD2 B:HIS385 3.4 19.0 1.0 O B:HOH820 3.5 15.3 1.0 CB B:HIS511 3.9 24.7 1.0 NE2 B:HIS511 4.0 25.8 1.0 ND1 B:HIS385 4.0 18.7 1.0 CA B:CYS334 4.1 21.1 1.0 OD2 B:ASP383 4.2 16.5 1.0 N B:CYS334 4.2 21.1 1.0 CD2 B:HIS511 4.2 25.6 1.0 OD1 B:ASP383 4.3 16.6 1.0 CG B:HIS385 4.3 18.9 1.0 C23 B:E4O702 4.5 22.5 1.0 O B:HOH888 4.5 21.1 1.0 CA B:HIS511 4.7 24.3 1.0 CG B:ASP383 4.7 16.3 1.0 C19 B:E4O702 4.7 23.9 1.0 SD B:MET332 4.9 27.6 1.0

J.Guo, B.Chen, Y.Yu, B.Cheng, Y.Cheng, Y.Ju, Q.Gu, J.Xu, H.Zhou. Discovery of Novel Trna-Amino Acid Dual-Site Inhibitors Against Threonyl-Trna Synthetase By Fragment-Based Target Hopping. Eur.J.Med.Chem. V. 187 11941 2019.
ISSN: ISSN 0223-5234
PubMed: 31821989
DOI: 10.1016/J.EJMECH.2019.111941