Zinc in PDB 7y1w: 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: 7y1w 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)	33.22 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.556, 92.147, 86.728, 90, 108.77, 90
R / Rfree (%)	22.9 / 28.9

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

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Zinc atom in the Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1 (pdb code 7y1w). 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: 7y1w:
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:Zn1601 b:116.9 occ:1.00 SG A:CYS1453 2.3 202.7 1.0 SG A:CYS1448 2.3 210.1 1.0 SG A:CYS1495 2.3 197.9 1.0 CB A:CYS1448 2.9 117.8 1.0 CB A:CYS1495 2.9 111.7 1.0 CG1 A:VAL1496 3.1 96.8 1.0 N A:CYS1448 3.6 81.5 1.0 N A:VAL1496 3.6 110.6 1.0 CB A:CYS1453 3.7 130.7 1.0 CA A:CYS1448 3.8 83.0 1.0 CA A:CYS1495 4.2 82.2 1.0 CB A:VAL1496 4.2 92.5 1.0 C A:CYS1495 4.2 84.8 1.0 CA A:VAL1496 4.5 103.6 1.0 CD1 A:PHE1447 4.5 65.7 1.0 CE1 A:PHE1447 4.6 70.1 1.0 N A:CYS1497 4.6 112.0 1.0 C A:PHE1447 4.8 75.6 1.0 N A:CYS1495 4.8 77.0 1.0 CA A:CYS1453 5.0 98.4 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:Zn1601 b:139.9 occ:1.00 SG B:CYS1495 2.3 202.4 1.0 SG B:CYS1448 2.3 210.9 1.0 SG B:CYS1453 2.3 148.4 1.0 CB B:CYS1497 2.5 126.8 1.0 CB B:CYS1453 2.6 122.8 1.0 CB B:CYS1448 3.0 133.2 1.0 CB B:CYS1495 3.4 123.0 1.0 N B:CYS1497 3.6 121.0 1.0 CA B:CYS1497 3.7 123.0 1.0 SG B:CYS1497 3.7 129.5 1.0 N B:CYS1448 3.8 90.6 1.0 CA B:CYS1448 3.9 98.8 1.0 CA B:CYS1453 4.0 116.7 1.0 C B:CYS1453 4.7 115.2 1.0 O B:CYS1453 4.8 117.5 1.0 C B:CYS1497 4.8 130.8 1.0 CA B:CYS1495 4.8 102.0 1.0 C B:VAL1496 4.9 117.7 1.0 N B:VAL1496 4.9 120.1 1.0 CE2 B:PHE1447 4.9 95.0 1.0 C B:PHE1447 5.0 99.4 1.0 N B:CYS1453 5.0 109.7 1.0 CD2 B:PHE1447 5.0 88.6 1.0

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