Atomistry » Strontium » PDB 6p5t-8cvc » 7osz
Atomistry »
  Strontium »
    PDB 6p5t-8cvc »
      7osz »

Strontium in PDB 7osz: Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4D

Enzymatic activity of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4D

All present enzymatic activity of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4D:
6.1.1.15; 6.1.1.17;

Protein crystallography data

The structure of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4D, PDB code: 7osz was solved by L.Pang, J.Zitko, S.V.Strelkov, S.D.Weeks, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 78.03 / 2.46
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.671, 86.696, 83.117, 90, 110.14, 90
R / Rfree (%) 22 / 27.8

Other elements in 7osz:

The structure of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4D also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Strontium Binding Sites:

The binding sites of Strontium atom in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4D (pdb code 7osz). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 7 binding sites of Strontium where determined in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4D, PDB code: 7osz:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7;

Strontium binding site 1 out of 7 in 7osz

Go back to Strontium Binding Sites List in 7osz
Strontium binding site 1 out of 7 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4D


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr1604

b:60.9
occ:1.00
 OE1 A:GLU1264 2.5 69.8 1.0
O A:HOH1723 2.5 38.6 1.0
O A:LYS1265 2.7 64.3 1.0
OE1 A:GLN1266 3.1 100.6 1.0
CD A:GLU1264 3.5 67.2 1.0
O A:HOH1727 3.6 46.9 1.0
C A:LYS1265 3.8 57.4 1.0
CD A:GLN1266 3.8 95.0 1.0
OE2 A:GLU1264 4.1 49.9 1.0
CA A:GLN1266 4.3 59.6 1.0
NE2 A:GLN1266 4.4 85.0 1.0
CB A:GLN1266 4.4 67.4 1.0
N A:GLN1266 4.5 56.7 1.0
SR A:SR1606 4.5 156.4 1.0
N A:LYS1265 4.6 61.7 1.0
CG A:GLU1264 4.7 50.4 1.0
CG A:GLN1266 4.7 75.7 1.0
CA A:LYS1265 4.8 48.9 1.0
CB A:GLU1264 4.9 49.9 1.0

Strontium binding site 2 out of 7 in 7osz

Go back to Strontium Binding Sites List in 7osz
Strontium binding site 2 out of 7 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4D


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr1605

b:191.7
occ:1.00
 OE1 A:GLU1074 2.7 128.5 1.0
O A:HOH1731 2.7 86.0 1.0
O A:GLY1072 2.9 44.6 1.0
CD A:GLU1074 3.5 116.2 1.0
OE2 A:GLU1074 3.7 127.3 1.0
O A:HOH1741 3.9 56.1 1.0
C A:GLY1072 4.1 43.9 1.0
O A:LYS1143 4.6 44.1 1.0
CA A:GLY1072 4.7 40.2 1.0
O A:PRO1141 4.7 51.7 1.0
N A:LYS1143 4.7 47.3 1.0
CB A:LYS1143 4.8 56.1 1.0
CG A:GLU1074 4.9 85.3 1.0

Strontium binding site 3 out of 7 in 7osz

Go back to Strontium Binding Sites List in 7osz
Strontium binding site 3 out of 7 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4D


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr1606

b:156.4
occ:1.00
 OE2 A:GLU1264 2.5 49.9 1.0
CD A:GLU1264 3.6 67.2 1.0
O A:HOH1727 3.7 46.9 1.0
OE1 A:GLU1264 3.9 69.8 1.0
O A:HOH1732 3.9 52.7 1.0
SR A:SR1604 4.5 60.9 1.0
CG A:GLU1264 4.9 50.4 1.0

Strontium binding site 4 out of 7 in 7osz

Go back to Strontium Binding Sites List in 7osz
Strontium binding site 4 out of 7 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4D


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr1604

b:65.1
occ:1.00
 OE1 B:GLU1264 2.5 76.0 1.0
O B:LYS1265 2.5 83.9 1.0
OE2 B:GLU1264 2.6 83.0 1.0
CD B:GLU1264 2.8 78.2 1.0
OE1 B:GLN1266 2.9 49.1 1.0
O B:HOH1701 3.2 53.9 1.0
O B:HOH1723 3.3 36.2 1.0
C B:LYS1265 3.6 60.3 1.0
CD B:GLN1266 3.6 69.8 1.0
CB B:GLN1266 4.1 57.4 1.0
CA B:GLN1266 4.1 60.2 1.0
SR B:SR1605 4.1 65.8 1.0
N B:GLN1266 4.3 56.6 1.0
NE2 B:GLN1266 4.3 59.8 1.0
CG B:GLU1264 4.3 55.7 1.0
CG B:GLN1266 4.5 71.4 1.0
N B:LYS1265 4.5 57.3 1.0
CA B:LYS1265 4.7 67.6 1.0

Strontium binding site 5 out of 7 in 7osz

Go back to Strontium Binding Sites List in 7osz
Strontium binding site 5 out of 7 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4D


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr1605

b:65.8
occ:1.00
 OE2 B:GLU1264 2.6 83.0 1.0
O B:HOH1723 3.2 36.2 1.0
O B:HOH1731 3.3 54.4 1.0
CD B:GLU1264 3.5 78.2 1.0
CG B:GLU1264 4.0 55.7 1.0
SR B:SR1604 4.1 65.1 1.0
OE1 B:GLU1264 4.6 76.0 1.0
O B:LYS1265 4.8 83.9 1.0

Strontium binding site 6 out of 7 in 7osz

Go back to Strontium Binding Sites List in 7osz
Strontium binding site 6 out of 7 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4D


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr1606

b:84.9
occ:1.00
 OE2 B:GLU1074 2.5 116.1 1.0
O B:GLY1072 2.6 51.7 1.0
CD B:GLU1074 3.3 108.0 1.0
O B:HOH1713 3.5 69.8 1.0
C B:GLY1072 3.6 53.2 1.0
OE1 B:GLU1074 3.7 118.4 1.0
O B:HOH1732 3.8 71.9 1.0
O B:HOH1725 3.9 25.4 1.0
O B:HOH1733 4.0 52.7 1.0
CA B:GLY1072 4.0 53.5 1.0
CG B:GLU1074 4.4 82.4 1.0
O B:PRO1141 4.8 59.4 1.0
N B:VAL1073 4.8 48.7 1.0
CB B:LYS1143 4.9 51.9 1.0

Strontium binding site 7 out of 7 in 7osz

Go back to Strontium Binding Sites List in 7osz
Strontium binding site 7 out of 7 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4D


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr1607

b:93.2
occ:1.00
 O B:LYS1499 2.6 70.4 1.0
C B:LYS1499 3.5 50.9 1.0
O B:HOH1704 3.9 50.2 1.0
N B:ASN1500 4.2 54.3 1.0
CA B:ASN1500 4.2 56.4 1.0
CA B:LYS1499 4.3 52.9 1.0
CB B:LYS1499 4.3 52.6 1.0
CB B:ASN1500 4.5 46.0 1.0

Reference:

L.Pang, S.D.Weeks, S.V.Strelkov, J.Zitko, A.Van Aerschot. Towards Novel 3-Aminopyrazinamide-Based Prolyl-Trna Synthetase Inhibitors: in Silico Modelling, Thermal Shift Assay and Structural Studies Int J Mol Sci 2021.
ISSN: ESSN 1422-0067
DOI: 10.3390/IJMS22157793
Page generated: Fri Oct 11 07:07:28 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy