Zinc in PDB 7ot3: Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B

All present enzymatic activity of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B:
6.1.1.15; 6.1.1.17;

The structure of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B, PDB code: 7ot3 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)	54.77 / 2.53
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.871, 92.422, 87.26, 90, 108.88, 90
R / Rfree (%)	21.8 / 27.6

The structure of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Strontium	(Sr)	4 atoms

The binding sites of Zinc atom in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B (pdb code 7ot3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B, PDB code: 7ot3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1603 b:119.0 occ:1.00 SG A:CYS1448 2.4 130.1 1.0 SG A:CYS1453 2.5 136.9 1.0 SG A:CYS1497 2.5 138.5 1.0 SG A:CYS1495 2.5 140.6 1.0 CB A:CYS1497 2.8 140.8 1.0 CB A:CYS1448 3.6 136.5 1.0 CB A:CYS1453 3.6 131.4 1.0 CB A:CYS1495 3.7 140.0 1.0 N A:CYS1497 3.7 135.9 1.0 CA A:CYS1497 3.9 145.0 1.0 N A:CYS1448 4.0 139.1 1.0 CE1 A:PHE1447 4.3 98.7 1.0 CD1 A:PHE1447 4.4 108.3 1.0 CA A:CYS1448 4.4 137.1 1.0 OD1 A:ASN1500 4.6 172.8 1.0 N A:VAL1496 4.7 129.4 1.0 C A:VAL1496 4.9 129.7 1.0 CA A:CYS1495 4.9 130.7 1.0 CB A:ASN1500 4.9 168.6 1.0 C A:CYS1495 4.9 126.2 1.0 C A:CYS1497 5.0 170.7 1.0

Zinc binding site 2 out of 2 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1603 b:172.7 occ:1.00 SG B:CYS1453 2.4 161.1 1.0 SG B:CYS1495 2.4 159.2 1.0 SG B:CYS1448 2.5 160.5 1.0 SG B:CYS1497 2.5 175.8 1.0 CB B:CYS1495 3.2 168.9 1.0 CB B:CYS1453 3.2 167.8 1.0 CB B:CYS1497 3.3 177.9 1.0 CB B:CYS1448 3.7 168.3 1.0 N B:CYS1497 4.0 169.9 1.0 N B:CYS1448 4.1 154.2 1.0 CA B:CYS1497 4.3 188.7 1.0 CA B:CYS1448 4.5 162.1 1.0 CD2 B:PHE1447 4.6 147.3 1.0 CE2 B:PHE1447 4.6 150.2 1.0 CA B:CYS1495 4.6 172.9 1.0 CA B:CYS1453 4.7 159.9 1.0 N B:VAL1496 4.7 170.8 1.0 C B:CYS1495 4.8 175.0 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