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Magnesium in PDB 7y28: 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: 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

Other elements in 7y28:

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

Fluorine (F) 2 atoms
Zinc (Zn) 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 7y28). 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: 7y28:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7y28

Go back to Magnesium Binding Sites List in 7y28
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:29.6
occ:1.00
 O A:HOH2745 2.0 43.9 1.0
O1G A:ATP2602 2.4 36.8 1.0
O2B A:ATP2602 2.4 32.0 1.0
PG A:ATP2602 3.6 45.5 1.0
PB A:ATP2602 3.6 44.2 1.0
O3B A:ATP2602 3.7 38.3 1.0
NH1 A:ARG1163 4.1 35.6 1.0
OE2 A:GLU1154 4.1 59.4 1.0
OE2 A:GLU1100 4.4 52.2 1.0
O2G A:ATP2602 4.4 52.3 1.0
O1B A:ATP2602 4.4 54.3 1.0
NH1 A:ARG1152 4.5 24.4 1.0
CE2 A:PHE1097 4.6 48.2 1.0
N2 A:F962601 4.7 39.1 1.0
OE1 A:GLU1154 4.7 54.4 1.0
OE1 A:GLU1100 4.8 39.7 1.0
O3G A:ATP2602 4.8 46.6 1.0
O3A A:ATP2602 4.8 40.2 1.0
CD A:GLU1154 4.9 43.5 1.0
N7 A:ATP2602 4.9 31.0 1.0

Magnesium binding site 2 out of 4 in 7y28

Go back to Magnesium Binding Sites List in 7y28
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:35.0
occ:1.00
 O1B A:ATP2602 2.4 54.3 1.0
O2G A:ATP2602 2.5 52.3 1.0
OE1 A:GLN1237 2.6 39.3 1.0
PB A:ATP2602 3.5 44.2 1.0
O3B A:ATP2602 3.6 38.3 1.0
CD A:GLN1237 3.6 34.4 1.0
PG A:ATP2602 3.7 45.5 1.0
OE1 A:GLU1214 3.8 53.4 1.0
NE2 A:GLN1237 3.9 39.9 1.0
NZ A:LYS1210 4.3 38.3 1.0
O2B A:ATP2602 4.4 32.0 1.0
O1G A:ATP2602 4.4 36.8 1.0
O A:GLU1214 4.5 59.4 1.0
CE A:LYS1210 4.6 37.1 1.0
O3A A:ATP2602 4.7 40.2 1.0
O3G A:ATP2602 4.8 46.6 1.0
NZ A:LYS1477 4.9 51.7 1.0
CG A:GLN1237 4.9 36.1 1.0

Magnesium binding site 3 out of 4 in 7y28

Go back to Magnesium Binding Sites List in 7y28
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:72.5
occ:1.00
 O1B B:ATP2602 2.7 133.2 1.0
O3G B:ATP2602 2.8 96.4 1.0
OE2 B:GLU1154 3.3 80.9 1.0
N2 B:F962601 3.9 59.3 1.0
PB B:ATP2602 4.0 126.6 1.0
OE1 B:GLU1100 4.1 62.8 1.0
PG B:ATP2602 4.1 100.5 1.0
OE2 B:GLU1100 4.2 66.0 1.0
CD B:GLU1154 4.2 63.8 1.0
O3B B:ATP2602 4.2 114.2 1.0
NH1 B:ARG1152 4.2 46.0 1.0
OE1 B:GLU1154 4.3 70.5 1.0
O1A B:ATP2602 4.4 101.8 1.0
NH1 B:ARG1163 4.4 73.9 1.0
N7 B:ATP2602 4.5 54.4 1.0
CD B:GLU1100 4.6 54.9 1.0
C8 B:F962601 4.7 47.9 1.0
CD B:ARG1152 4.8 28.3 1.0
C9 B:F962601 4.9 41.7 1.0
O1G B:ATP2602 5.0 97.6 1.0
C8 B:ATP2602 5.0 66.5 1.0

Magnesium binding site 4 out of 4 in 7y28

Go back to Magnesium Binding Sites List in 7y28
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:83.0
occ:1.00
 O2B B:ATP2602 2.6 128.9 1.0
OE1 B:GLU1214 3.3 65.4 1.0
O1G B:ATP2602 3.3 97.6 1.0
PB B:ATP2602 3.7 126.6 1.0
O3B B:ATP2602 4.0 114.2 1.0
CD B:GLU1214 4.2 53.1 1.0
PG B:ATP2602 4.2 100.5 1.0
OE1 B:GLN1237 4.2 67.0 1.0
NZ B:LYS1477 4.3 73.5 1.0
O1B B:ATP2602 4.4 133.2 1.0
OE2 B:GLU1214 4.6 71.9 1.0
O B:GLU1214 4.7 56.4 1.0
O3G B:ATP2602 4.8 96.4 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 18:58:02 2025

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