Zinc in PDB 7y28: Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1

All present enzymatic activity of Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1:
6.1.1.15; 6.1.1.17;

The structure of Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1, PDB code: 7y28 was solved by S.Kim, I.Yoon, J.Son, S.Park, K.Y.Hwang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.43 / 2.29
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.563, 92.38, 86.059, 90, 108.72, 90
R / Rfree (%)	20.7 / 26.4

The structure of Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1 also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Fluorine	(F)	2 atoms

The binding sites of Zinc atom in the Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1 (pdb code 7y28). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1, PDB code: 7y28:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2603 b:64.6 occ:1.00 SG A:CYS1448 2.3 100.4 1.0 SG A:CYS1495 2.4 58.9 1.0 SG A:CYS1497 2.4 84.4 1.0 SG A:CYS1453 2.4 64.2 1.0 CB A:CYS1448 3.0 54.9 1.0 CB A:CYS1495 3.5 63.9 1.0 CB A:CYS1453 3.6 61.9 1.0 N A:CYS1448 3.6 56.1 1.0 CB A:CYS1497 3.9 86.1 1.0 CA A:CYS1448 3.9 52.4 1.0 CD1 A:PHE1447 4.0 40.2 1.0 CE1 A:PHE1447 4.0 53.8 1.0 N A:CYS1497 4.0 62.1 1.0 CA A:CYS1497 4.4 75.0 1.0 N A:VAL1496 4.6 70.4 1.0 C A:PHE1447 4.7 52.3 1.0 CA A:CYS1495 4.9 68.7 1.0 CA A:PHE1447 5.0 53.0 1.0 CA A:CYS1453 5.0 55.3 1.0

Zinc binding site 2 out of 2 in the Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2603 b:109.0 occ:1.00 SG B:CYS1448 2.2 160.7 1.0 SG B:CYS1453 2.4 79.5 1.0 O B:HOH2748 2.5 46.9 1.0 CB B:CYS1448 3.6 90.2 1.0 N B:CYS1448 3.7 63.1 1.0 O B:HOH2754 4.0 45.6 1.0 CB B:CYS1453 4.2 79.2 1.0 CA B:CYS1448 4.2 64.6 1.0 CD2 B:PHE1447 4.4 54.8 1.0 CE2 B:PHE1447 4.6 72.5 1.0 C B:PHE1447 4.7 66.2 1.0 CA B:PHE1447 4.8 70.1 1.0 CZ3 B:TRP1456 4.9 87.2 1.0

S.Kim, K.Hwang, I.Yoon. Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl-Trna Synthetase 1 To Be Published.