Atomistry » Magnesium » PDB 7xmb-7y4a » 7y1h
Atomistry »
  Magnesium »
    PDB 7xmb-7y4a »
      7y1h »

Magnesium in PDB 7y1h: Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1

Enzymatic activity of 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;

Protein crystallography data

The structure of Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1, PDB code: 7y1h 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) 37.90 / 1.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 71.698, 92.364, 87.504, 90, 108.2, 90
R / Rfree (%) 20.7 / 24.3

Other elements in 7y1h:

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

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1 (pdb code 7y1h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl- Trna Synthetase 1, PDB code: 7y1h:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7y1h

Go back to Magnesium Binding Sites List in 7y1h
Magnesium binding site 1 out of 4 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:Mg2604

b:22.5
occ:1.00
 O A:HOH2773 2.2 31.2 1.0
O2B A:ATP2602 2.2 31.0 1.0
O3G A:ATP2602 2.3 34.6 1.0
O A:HOH2710 2.3 30.3 1.0
O A:HOH2786 2.4 33.3 1.0
PB A:ATP2602 3.4 35.1 1.0
O3B A:ATP2602 3.5 38.3 1.0
PG A:ATP2602 3.5 42.8 1.0
NH1 A:ARG1163 3.9 28.3 1.0
NH1 A:ARG1152 4.0 27.1 1.0
O1G A:ATP2602 4.4 46.7 1.0
O1B A:ATP2602 4.4 39.5 1.0
OE2 A:GLU1154 4.5 34.9 1.0
N A:F992601 4.5 40.7 1.0
N7 A:ATP2602 4.5 29.8 1.0
O3A A:ATP2602 4.5 32.8 1.0
OE1 A:GLU1100 4.5 44.5 1.0
O2G A:ATP2602 4.7 39.1 1.0
OE1 A:GLU1154 4.7 37.6 1.0
C7 A:F992601 4.7 36.0 1.0
OE2 A:GLU1100 4.7 54.7 1.0
C8 A:ATP2602 4.9 32.6 1.0
CE1 A:PHE1097 4.9 50.4 1.0

Magnesium binding site 2 out of 4 in 7y1h

Go back to Magnesium Binding Sites List in 7y1h
Magnesium binding site 2 out of 4 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:Mg2605

b:29.0
occ:1.00
 O1B A:ATP2602 2.3 39.5 1.0
O1G A:ATP2602 2.4 46.7 1.0
NE2 A:GLN1237 2.7 37.6 1.0
PB A:ATP2602 3.4 35.1 1.0
PG A:ATP2602 3.5 42.8 1.0
O3B A:ATP2602 3.5 38.3 1.0
CD A:GLN1237 3.7 30.6 1.0
OE1 A:GLN1237 3.8 45.3 1.0
O2B A:ATP2602 4.2 31.0 1.0
O3G A:ATP2602 4.3 34.6 1.0
OE1 A:GLU1214 4.4 45.9 1.0
O A:GLU1214 4.5 41.6 1.0
O3A A:ATP2602 4.7 32.8 1.0
O2G A:ATP2602 4.7 39.1 1.0
CE A:LYS1210 4.8 41.3 1.0
NZ A:LYS1210 4.8 39.0 1.0

Magnesium binding site 3 out of 4 in 7y1h

Go back to Magnesium Binding Sites List in 7y1h
Magnesium binding site 3 out of 4 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 3 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:Mg2604

b:41.9
occ:1.00
 O B:HOH2713 2.3 52.3 1.0
O2B B:ATP2602 2.3 61.3 1.0
O B:HOH2722 2.6 46.0 1.0
O3G B:ATP2602 3.6 77.0 1.0
PB B:ATP2602 3.8 71.8 1.0
N B:F992601 4.0 39.2 1.0
NH1 B:ARG1152 4.0 32.9 1.0
O3B B:ATP2602 4.2 72.7 1.0
PG B:ATP2602 4.3 76.4 1.0
C7 B:F992601 4.4 35.4 1.0
OE1 B:GLU1100 4.4 69.7 1.0
CE1 B:PHE1097 4.4 61.5 1.0
OE1 B:GLU1154 4.5 54.3 1.0
NH1 B:ARG1163 4.5 58.6 1.0
O1G B:ATP2602 4.6 77.1 1.0
OE2 B:GLU1100 4.6 69.5 1.0
O3A B:ATP2602 4.6 67.0 1.0
OE2 B:GLU1154 4.6 56.8 1.0
N7 B:ATP2602 4.7 49.6 1.0
O1B B:ATP2602 4.7 64.5 1.0
CZ B:PHE1097 4.7 56.5 1.0
CD B:ARG1152 4.8 35.7 1.0
CD B:GLU1100 4.9 71.7 1.0

Magnesium binding site 4 out of 4 in 7y1h

Go back to Magnesium Binding Sites List in 7y1h
Magnesium binding site 4 out of 4 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 4 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:Mg2605

b:80.9
occ:1.00
 O1B B:ATP2602 2.9 64.5 1.0
OE1 B:GLU1214 3.2 59.7 1.0
O1G B:ATP2602 3.3 77.1 1.0
NE2 B:GLN1237 3.5 49.2 1.0
O B:GLU1214 3.9 46.0 1.0
PB B:ATP2602 4.0 71.8 1.0
O3B B:ATP2602 4.2 72.7 1.0
PG B:ATP2602 4.3 76.4 1.0
CD B:GLU1214 4.4 59.0 1.0
NZ B:LYS1210 4.5 51.6 1.0
CD B:GLN1237 4.6 49.8 1.0
CE B:LYS1210 4.6 46.2 1.0
O2B B:ATP2602 4.6 61.3 1.0
OE1 B:GLN1237 4.8 59.4 1.0
O B:HOH2775 4.8 38.7 1.0

Reference:

S.Kim, K.Hwang, I.Yoon. Controlling Fibrosis Using Compound with Novel Binding Mode to Prolyl-Trna Synthetase 1 To Be Published.
Page generated: Thu Aug 14 18:54:43 2025

Last articles

Mg in 7Z9M
Mg in 7Z9K
Mg in 7Z9G
Mg in 7Z9C
Mg in 7Z8I
Mg in 7Z8M
Mg in 7Z8U
Mg in 7Z8Q
Mg in 7Z8L
Mg in 7Z8H
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy