Zinc in PDB 7ot1: Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3C

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

The structure of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3C, PDB code: 7ot1 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)	65.89 / 2.71
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	70.273, 88.968, 84.749, 90, 110.34, 90
R / Rfree (%)	21.4 / 28.3

The structure of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3C 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 and Compound 3C (pdb code 7ot1). 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 3C, PDB code: 7ot1:
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 3C


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 3C within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1603 b:72.2 occ:1.00 SG A:CYS1448 2.4 65.7 1.0 SG A:CYS1495 2.4 63.4 1.0 SG A:CYS1453 2.5 56.0 1.0 SG A:CYS1497 2.5 97.9 1.0 CB A:CYS1448 3.1 65.2 1.0 CB A:CYS1495 3.2 64.0 1.0 CB A:CYS1497 3.5 68.2 1.0 CB A:CYS1453 3.5 56.3 1.0 N A:CYS1448 3.8 42.3 1.0 CA A:CYS1448 4.1 43.5 1.0 N A:CYS1497 4.1 62.3 1.0 CE1 A:PHE1447 4.3 44.2 1.0 CD1 A:PHE1447 4.3 38.2 1.0 CA A:CYS1497 4.4 62.8 1.0 CB A:ASN1500 4.5 66.7 1.0 CA A:CYS1495 4.6 55.8 1.0 N A:VAL1496 4.7 69.4 1.0 OD1 A:ASN1500 4.8 91.4 1.0 C A:CYS1495 4.9 60.4 1.0 O A:ASN1500 4.9 73.4 1.0 CA A:CYS1453 4.9 56.3 1.0 C A:CYS1448 5.0 46.3 1.0 C A:PHE1447 5.0 42.2 1.0

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


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 3C within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1603 b:88.6 occ:1.00 SG B:CYS1497 2.4 76.0 1.0 SG B:CYS1453 2.4 75.3 1.0 SG B:CYS1448 2.5 60.7 1.0 SG B:CYS1495 2.5 61.5 1.0 CB B:CYS1497 3.1 73.0 1.0 CB B:CYS1495 3.2 58.2 1.0 CB B:CYS1453 3.3 63.5 1.0 CB B:CYS1448 3.4 66.6 1.0 N B:CYS1497 4.0 64.2 1.0 N B:CYS1448 4.1 50.8 1.0 CA B:CYS1497 4.2 70.6 1.0 CA B:CYS1448 4.4 50.9 1.0 CE1 B:PHE1447 4.5 49.1 1.0 CD1 B:PHE1447 4.6 49.3 1.0 CA B:CYS1495 4.6 58.9 1.0 CA B:CYS1453 4.8 65.2 1.0 N B:VAL1496 4.9 58.3 1.0 CB B:ASN1500 4.9 55.3 1.0 C B:CYS1495 4.9 59.9 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