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Magnesium in PDB 7y3s: 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: 7y3s 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) 41.25 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 71.897, 92.017, 87.326, 90, 108.16, 90
R / Rfree (%) 20.3 / 25

Other elements in 7y3s:

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

Bromine (Br) 2 atoms
Zinc (Zn) 1 atom

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 7y3s). 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: 7y3s:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7y3s

Go back to Magnesium Binding Sites List in 7y3s
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:Mg2603

b:21.6
occ:1.00
 O1B A:ATP2602 2.6 26.9 1.0
O1G A:ATP2602 2.9 31.5 1.0
O2B A:ATP2602 3.4 62.0 1.0
PB A:ATP2602 3.4 44.1 1.0
OE2 A:GLU1154 3.7 47.1 1.0
NH1 A:ARG1152 3.8 34.3 1.0
O3B A:ATP2602 3.9 112.5 1.0
PG A:ATP2602 4.0 59.0 1.0
OE1 A:GLU1100 4.2 39.8 1.0
N1 A:F9C2601 4.3 39.4 1.0
CE1 A:PHE1097 4.3 42.0 1.0
NH1 A:ARG1163 4.3 31.4 1.0
OE2 A:GLU1100 4.4 37.5 1.0
OE1 A:GLU1154 4.4 45.4 1.0
CD A:GLU1154 4.5 40.9 1.0
C6 A:F9C2601 4.7 41.7 1.0
N7 A:ATP2602 4.7 23.8 1.0
CD A:GLU1100 4.8 38.8 1.0
CD A:ARG1152 4.8 30.6 1.0
CZ A:ARG1152 4.9 35.7 1.0
O3A A:ATP2602 4.9 36.8 1.0
O3G A:ATP2602 4.9 34.1 1.0
CZ A:PHE1097 5.0 43.0 1.0
O2G A:ATP2602 5.0 73.4 1.0

Magnesium binding site 2 out of 4 in 7y3s

Go back to Magnesium Binding Sites List in 7y3s
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:Mg2604

b:28.8
occ:1.00
 O2G A:ATP2602 2.5 73.4 1.0
O3B A:ATP2602 2.7 112.5 1.0
OE1 A:GLN1237 2.9 39.7 1.0
PG A:ATP2602 3.2 59.0 1.0
PB A:ATP2602 3.7 44.1 1.0
CD A:GLN1237 3.9 31.9 1.0
O3A A:ATP2602 4.0 36.8 1.0
O1B A:ATP2602 4.1 26.9 1.0
NE2 A:GLN1237 4.1 35.4 1.0
O1G A:ATP2602 4.3 31.5 1.0
OE1 A:GLU1214 4.3 58.2 1.0
O3G A:ATP2602 4.3 34.1 1.0
O A:GLU1214 4.6 65.4 1.0
O2B A:ATP2602 4.9 62.0 1.0

Magnesium binding site 3 out of 4 in 7y3s

Go back to Magnesium Binding Sites List in 7y3s
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:40.5
occ:1.00
 O2B B:ATP2602 2.2 53.9 1.0
O B:HOH2719 2.4 33.4 1.0
O3G B:ATP2602 3.1 74.7 1.0
PB B:ATP2602 3.5 69.7 1.0
O3B B:ATP2602 3.7 73.2 1.0
PG B:ATP2602 3.7 69.3 1.0
O1G B:ATP2602 3.8 75.9 1.0
NH1 B:ARG1163 4.1 50.7 1.0
O1B B:ATP2602 4.2 58.8 1.0
OE2 B:GLU1154 4.3 56.4 1.0
NH1 B:ARG1152 4.4 41.7 1.0
OE2 B:GLU1100 4.4 61.2 1.0
OE1 B:GLU1154 4.4 56.6 1.0
N7 B:ATP2602 4.5 40.0 1.0
O3A B:ATP2602 4.7 64.1 1.0
N1 B:F9C2601 4.8 41.1 1.0
CD B:GLU1154 4.8 58.0 1.0
CE1 B:PHE1097 4.8 45.9 1.0
C8 B:ATP2602 4.9 49.4 1.0
NZ B:LYS1156 4.9 68.2 1.0
OE1 B:GLU1100 5.0 55.3 1.0

Magnesium binding site 4 out of 4 in 7y3s

Go back to Magnesium Binding Sites List in 7y3s
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:53.6
occ:1.00
 O1B B:ATP2602 2.5 58.8 1.0
OE1 B:GLU1214 3.0 53.0 1.0
O B:HOH2709 3.0 38.1 1.0
NE2 B:GLN1237 3.3 39.0 1.0
O1G B:ATP2602 3.5 75.9 1.0
PB B:ATP2602 3.8 69.7 1.0
CE B:LYS1210 4.0 49.3 1.0
O3B B:ATP2602 4.0 73.2 1.0
O B:GLU1214 4.1 45.1 1.0
CD B:GLU1214 4.1 59.4 1.0
PG B:ATP2602 4.3 69.3 1.0
NZ B:LYS1210 4.3 49.8 1.0
CD B:GLN1237 4.4 38.1 1.0
CD B:LYS1210 4.4 46.8 1.0
OE1 B:GLN1237 4.6 45.0 1.0
OE2 B:GLU1214 4.7 65.9 1.0
O2B B:ATP2602 4.8 53.9 1.0
O3A B:ATP2602 4.9 64.1 1.0
O2G B:ATP2602 4.9 59.6 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 Jul 27 20:40:56 2023

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