Zinc in PDB 5vad: Crystal Structure of Human Prolyl-Trna Synthetase (Prs) in Complex with Inhibitor

All present enzymatic activity of Crystal Structure of Human Prolyl-Trna Synthetase (Prs) in Complex with Inhibitor:
6.1.1.15; 6.1.1.17;

The structure of Crystal Structure of Human Prolyl-Trna Synthetase (Prs) in Complex with Inhibitor, PDB code: 5vad was solved by K.Okada, R.J.Skene, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.93 / 2.36
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.089, 92.278, 84.832, 90.00, 111.18, 90.00
R / Rfree (%)	19.6 / 26.2

The binding sites of Zinc atom in the Crystal Structure of Human Prolyl-Trna Synthetase (Prs) in Complex with Inhibitor (pdb code 5vad). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Human Prolyl-Trna Synthetase (Prs) in Complex with Inhibitor, PDB code: 5vad:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human Prolyl-Trna Synthetase (Prs) in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human Prolyl-Trna Synthetase (Prs) in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1603 b:0.0 occ:1.00 SG A:CYS1453 2.2 0.9 1.0 SG A:CYS1495 2.4 95.9 1.0 SG A:CYS1448 2.9 0.9 1.0 CB A:CYS1497 3.0 0.9 1.0 SG A:CYS1497 3.2 0.4 1.0 CB A:CYS1495 3.2 0.5 1.0 CB A:CYS1448 3.3 0.3 1.0 CB A:CYS1453 3.6 0.8 1.0 N A:CYS1497 3.7 0.3 1.0 N A:CYS1448 3.8 0.6 1.0 CA A:CYS1497 3.9 0.5 1.0 CB A:ASN1500 4.0 99.5 1.0 CA A:CYS1448 4.2 0.4 1.0 CD1 A:PHE1447 4.3 95.1 1.0 CE1 A:PHE1447 4.5 93.7 1.0 N A:VAL1496 4.6 0.6 1.0 CA A:CYS1495 4.6 1.0 1.0 C A:VAL1496 4.8 0.7 1.0 C A:CYS1495 4.8 0.1 1.0 O A:ASN1500 4.9 0.6 1.0 C A:PHE1447 4.9 0.2 1.0 CA A:CYS1453 5.0 0.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human Prolyl-Trna Synthetase (Prs) in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human Prolyl-Trna Synthetase (Prs) in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1603 b:0.2 occ:1.00 SG B:CYS1453 1.8 0.5 1.0 SG B:CYS1448 2.4 0.9 1.0 SG B:CYS1495 2.5 0.9 1.0 CB B:CYS1453 3.2 0.9 1.0 CB B:CYS1497 3.3 0.7 1.0 SG B:CYS1497 3.3 0.9 1.0 CB B:CYS1495 3.3 0.7 1.0 CB B:CYS1448 4.0 0.8 1.0 CE1 B:PHE1447 4.5 0.5 1.0 CA B:CYS1453 4.5 0.1 1.0 N B:CYS1448 4.6 0.4 1.0 CD1 B:PHE1447 4.6 0.6 1.0 CA B:CYS1495 4.7 0.9 1.0 O B:VAL1496 4.7 1.0 1.0 CA B:CYS1497 4.7 0.7 1.0 C B:CYS1495 4.8 0.5 1.0 CA B:CYS1448 4.9 0.2 1.0 O B:CYS1453 4.9 0.2 1.0

R.Adachi, K.Okada, R.Skene, K.Ogawa, M.Miwa, K.Tsuchinaga, S.Ohkubo, T.Henta, T.Kawamoto. Discovery of A Novel Prolyl-Trna Synthetase Inhibitor and Elucidation of Its Binding Mode to the Atp Site in Complex with L-Proline. Biochem. Biophys. Res. V. 488 393 2017COMMUN..
ISSN: ESSN 1090-2104
PubMed: 28501621
DOI: 10.1016/J.BBRC.2017.05.064