Magnesium 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:

Chlorine	(Cl)	4 atoms
Zinc	(Zn)	2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1, PDB code: 7y1w:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1604 b:52.5 occ:1.00 O2B A:ATP1603 2.3 103.2 1.0 O3G A:ATP1603 3.0 113.3 1.0 OE2 A:GLU1154 3.4 87.8 1.0 O3B A:ATP1603 3.5 107.1 1.0 PB A:ATP1603 3.5 97.4 1.0 OE1 A:GLU1154 3.9 90.3 1.0 PG A:ATP1603 3.9 120.5 1.0 CD A:GLU1154 4.1 90.9 1.0 NH1 A:ARG1152 4.1 70.5 1.0 OE1 A:GLU1100 4.2 88.0 1.0 OE2 A:GLU1100 4.4 98.0 1.0 O3A A:ATP1603 4.4 80.0 1.0 NH1 A:ARG1163 4.5 77.6 1.0 N2 A:F9O1602 4.6 65.0 1.0 O1B A:ATP1603 4.7 107.8 1.0 O2G A:ATP1603 4.7 171.5 1.0 CD A:GLU1100 4.7 92.1 1.0 N7 A:ATP1603 4.8 58.7 1.0 CE1 A:PHE1097 4.9 80.8 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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 A:Mg1605 b:86.5 occ:1.00 O2G A:ATP1603 2.2 171.5 1.0 OE1 A:GLN1237 2.5 89.8 1.0 O1B A:ATP1603 3.0 107.8 1.0 OE1 A:GLU1214 3.4 95.2 1.0 NZ A:LYS1210 3.4 84.0 1.0 PG A:ATP1603 3.6 120.5 1.0 CD A:GLN1237 3.7 74.9 1.0 O3B A:ATP1603 4.0 107.1 1.0 PB A:ATP1603 4.1 97.4 1.0 O1G A:ATP1603 4.4 109.6 1.0 NE2 A:GLN1237 4.5 62.6 1.0 O3G A:ATP1603 4.5 113.3 1.0 O A:GLU1214 4.6 82.0 1.0 CE A:LYS1210 4.6 74.4 1.0 CD A:GLU1214 4.6 91.6 1.0 CG A:GLN1237 4.7 70.7 1.0 O2B A:ATP1603 4.9 103.2 1.0

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