Chlorine in PDB 7ot0: Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4H

All present enzymatic activity of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4H:
6.1.1.15; 6.1.1.17;

The structure of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4H, PDB code: 7ot0 was solved by L.Pang, J.Zitko, S.V.Strelkov, S.D.Weeks, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.44 / 2.32
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.163, 93.458, 87.484, 90, 108.61, 90
R / Rfree (%)	19.7 / 25

The structure of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4H also contains other interesting chemical elements:

Strontium	(Sr)	2 atoms
Zinc	(Zn)	2 atoms

The binding sites of Chlorine atom in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4H (pdb code 7ot0). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4H, PDB code: 7ot0:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4H


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4H within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1602 b:61.6 occ:1.00 CL1 A:0YI1602 0.0 61.6 1.0 C13 A:0YI1602 1.7 58.4 1.0 C14 A:0YI1602 2.7 49.6 1.0 C12 A:0YI1602 2.7 61.2 1.0 C11 A:0YI1602 3.1 60.1 1.0 O A:GLN1237 3.4 60.5 1.0 C A:GLY1238 3.5 57.5 1.0 O A:GLY1238 3.5 55.5 1.0 N A:GLY1239 3.6 61.0 1.0 CA A:GLY1239 3.7 50.4 1.0 C15 A:0YI1602 4.0 50.9 1.0 C17 A:0YI1602 4.0 53.4 1.0 NE2 A:GLN1237 4.0 57.7 1.0 OG1 A:THR1276 4.0 41.8 1.0 C A:GLN1237 4.2 60.1 1.0 CG A:GLN1237 4.2 51.2 1.0 CA A:GLY1238 4.2 44.3 1.0 CG2 A:THR1276 4.3 39.7 1.0 NH1 A:ARG1278 4.3 50.0 1.0 CD A:ARG1278 4.4 42.2 1.0 C16 A:0YI1602 4.5 54.6 1.0 N10 A:0YI1602 4.5 65.5 1.0 N A:GLY1238 4.5 54.2 1.0 N A:THR1276 4.6 41.4 1.0 CD A:GLN1237 4.6 65.8 1.0 C A:GLY1239 4.7 55.2 1.0 O A:GLY1274 4.7 46.2 1.0 CB A:THR1276 4.7 42.3 1.0 NE A:ARG1278 4.9 45.2 1.0 CZ A:ARG1278 4.9 54.6 1.0 CB A:GLN1237 5.0 52.5 1.0 CB A:ARG1278 5.0 50.4 1.0

Chlorine binding site 2 out of 2 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4H


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4H within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1602 b:91.5 occ:1.00 CL1 B:0YI1602 0.0 91.5 1.0 C13 B:0YI1602 1.7 74.1 1.0 C14 B:0YI1602 2.7 76.6 1.0 C12 B:0YI1602 2.7 64.6 1.0 C11 B:0YI1602 3.1 73.0 1.0 O B:GLN1237 3.3 67.2 1.0 C B:GLY1238 3.7 52.5 1.0 NE2 B:GLN1237 3.7 66.4 1.0 O B:GLY1238 3.7 58.4 1.0 N B:GLY1239 3.7 66.8 1.0 CA B:GLY1239 3.9 56.6 1.0 C15 B:0YI1602 4.0 75.3 1.0 C17 B:0YI1602 4.0 65.2 1.0 NH1 B:ARG1278 4.1 55.5 1.0 CG B:GLN1237 4.1 70.5 1.0 C B:GLN1237 4.1 62.7 1.0 CD B:ARG1278 4.2 62.4 1.0 OG1 B:THR1276 4.2 48.5 1.0 CA B:GLY1238 4.4 54.0 1.0 CD B:GLN1237 4.4 70.8 1.0 CG2 B:THR1276 4.5 35.3 1.0 C16 B:0YI1602 4.5 76.8 1.0 N10 B:0YI1602 4.5 80.7 1.0 CZ B:ARG1278 4.6 68.9 1.0 N B:GLY1238 4.6 59.2 1.0 NE B:ARG1278 4.6 65.5 1.0 C B:GLY1239 4.7 56.9 1.0 CB B:GLN1237 4.8 75.4 1.0 N4 B:0YI1602 5.0 58.7 1.0 CB B:THR1276 5.0 52.5 1.0 N B:THR1276 5.0 37.8 1.0

L.Pang, S.D.Weeks, S.V.Strelkov, J.Zitko, A.Van Aerschot. Towards Novel 3-Aminopyrazinamide-Based Prolyl-Trna Synthetase Inhibitors: in Silico Modelling, Thermal Shift Assay and Structural Studies Int J Mol Sci 2021.
ISSN: ESSN 1422-0067
DOI: 10.3390/IJMS22157793