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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 Oct 3 13:25:03 2024

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