Zinc in PDB 7osy: Human Prolyl-Trna Synthetase in Complex with L-Proline

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

The structure of Human Prolyl-Trna Synthetase in Complex with L-Proline, PDB code: 7osy 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)	44.20 / 2.23
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.89, 88.404, 83.745, 90, 110.2, 90
R / Rfree (%)	20.9 / 26.1

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

Strontium

(Sr)

6 atoms

The binding sites of Zinc atom in the Human Prolyl-Trna Synthetase in Complex with L-Proline (pdb code 7osy). 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, PDB code: 7osy:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1602 b:71.8 occ:1.00 SG A:CYS1495 2.4 75.9 1.0 SG A:CYS1453 2.4 81.0 1.0 SG A:CYS1448 2.4 71.0 1.0 SG A:CYS1497 2.6 88.3 1.0 CB A:CYS1495 3.3 74.4 1.0 CB A:CYS1497 3.3 86.4 1.0 CB A:CYS1448 3.4 75.9 1.0 CB A:CYS1453 3.5 76.4 1.0 N A:CYS1448 3.9 66.4 1.0 CE1 A:PHE1447 4.1 70.2 1.0 CD1 A:PHE1447 4.1 68.3 1.0 N A:CYS1497 4.1 77.2 1.0 CA A:CYS1448 4.3 59.2 1.0 CA A:CYS1497 4.3 77.8 1.0 CA A:CYS1495 4.7 70.7 1.0 ND2 A:ASN1500 4.9 110.3 1.0 CA A:CYS1453 4.9 76.8 1.0 N A:VAL1496 4.9 66.9 1.0 C A:CYS1495 5.0 67.5 1.0 CB A:ASN1500 5.0 101.6 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1602 b:69.4 occ:1.00 SG B:CYS1453 2.4 74.3 1.0 SG B:CYS1495 2.4 73.1 1.0 SG B:CYS1497 2.5 79.4 1.0 SG B:CYS1448 2.5 71.1 1.0 CB B:CYS1497 3.2 80.7 1.0 CB B:CYS1453 3.3 73.1 1.0 CB B:CYS1495 3.4 81.2 1.0 CB B:CYS1448 3.6 71.3 1.0 N B:CYS1497 4.0 85.7 1.0 N B:CYS1448 4.1 68.1 1.0 CE1 B:PHE1447 4.2 70.9 1.0 CA B:CYS1497 4.3 82.8 1.0 CD1 B:PHE1447 4.3 73.8 1.0 CA B:CYS1448 4.5 70.5 1.0 CA B:CYS1453 4.8 77.7 1.0 CA B:CYS1495 4.8 85.8 1.0 N B:VAL1496 4.9 83.8 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