Zinc in PDB 7osz: Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4D

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

The structure of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4D, PDB code: 7osz 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)	78.03 / 2.46
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.671, 86.696, 83.117, 90, 110.14, 90
R / Rfree (%)	22 / 27.8

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

Strontium

(Sr)

7 atoms

The binding sites of Zinc atom in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4D (pdb code 7osz). 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 4D, PDB code: 7osz:
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 4D


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 4D within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1603 b:73.7 occ:1.00 SG A:CYS1497 2.4 91.1 1.0 SG A:CYS1448 2.5 63.5 1.0 SG A:CYS1453 2.5 75.9 1.0 SG A:CYS1495 2.5 75.7 1.0 CB A:CYS1497 3.2 86.5 1.0 CB A:CYS1448 3.2 54.0 1.0 CB A:CYS1495 3.2 79.2 1.0 CB A:CYS1453 3.7 76.6 1.0 N A:CYS1448 3.9 64.5 1.0 N A:CYS1497 4.0 80.0 1.0 CA A:CYS1448 4.2 63.6 1.0 CA A:CYS1497 4.2 81.3 1.0 ND2 A:ASN1500 4.3 94.9 1.0 CE1 A:PHE1447 4.5 71.7 1.0 CD1 A:PHE1447 4.5 59.8 1.0 CA A:CYS1495 4.6 81.3 1.0 N A:VAL1496 4.7 73.1 1.0 CB A:ASN1500 4.8 100.0 1.0 C A:CYS1495 4.8 78.1 1.0 O A:ASN1500 4.9 95.3 1.0

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


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 4D within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1603 b:54.7 occ:1.00 SG B:CYS1497 2.4 65.9 1.0 SG B:CYS1495 2.5 52.9 1.0 SG B:CYS1448 2.5 55.8 1.0 SG B:CYS1453 2.6 59.5 1.0 CB B:CYS1448 2.9 44.3 1.0 CB B:CYS1497 3.0 68.2 1.0 CB B:CYS1495 3.4 54.7 1.0 CB B:CYS1453 3.5 66.7 1.0 N B:CYS1448 3.7 49.0 1.0 N B:CYS1497 3.9 75.9 1.0 CA B:CYS1448 3.9 50.1 1.0 CA B:CYS1497 4.1 77.4 1.0 CE1 B:PHE1447 4.2 43.0 1.0 CD1 B:PHE1447 4.3 42.3 1.0 CA B:CYS1495 4.7 59.8 1.0 C B:PHE1447 4.9 42.3 1.0 C B:CYS1448 4.9 54.6 1.0 N B:VAL1496 4.9 52.3 1.0 C B:CYS1495 4.9 65.5 1.0 CA B:CYS1453 4.9 55.2 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