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Strontium in PDB 7osy: Human Prolyl-Trna Synthetase in Complex with L-Proline

Enzymatic activity of Human Prolyl-Trna Synthetase in Complex with L-Proline

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

Protein crystallography data

The structure of Human Prolyl-Trna Synthetase in Complex with L-Proline, PDB code: 7osy 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) 44.20 / 2.23
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.89, 88.404, 83.745, 90, 110.2, 90
R / Rfree (%) 20.9 / 26.1

Other elements in 7osy:

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

Strontium binding site 1 out of 6 in 7osy

Go back to Strontium Binding Sites List in 7osy
Strontium binding site 1 out of 6 in the Human Prolyl-Trna Synthetase in Complex with L-Proline


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr1603

b:59.3
occ:1.00
 OE2 A:GLU1264 2.6 73.6 1.0
O A:HOH1762 2.6 63.1 1.0
O A:LYS1265 2.8 77.0 1.0
O A:HOH1727 2.9 54.2 1.0
CD A:GLU1264 3.8 79.0 1.0
C A:LYS1265 3.8 58.6 1.0
SR A:SR1605 3.9 54.3 1.0
CA A:GLN1266 4.4 67.9 1.0
CB A:GLN1266 4.4 63.8 1.0
N A:GLN1266 4.5 51.0 1.0
N A:LYS1265 4.5 69.6 1.0
OE1 A:GLU1264 4.7 75.9 1.0
CG A:GLU1264 4.7 80.1 1.0
CA A:LYS1265 4.8 60.7 1.0
CB A:GLU1264 4.9 60.5 1.0

Strontium binding site 2 out of 6 in 7osy

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Strontium binding site 2 out of 6 in the Human Prolyl-Trna Synthetase in Complex with L-Proline


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr1604

b:108.9
occ:1.00
 O A:GLY1072 2.7 46.2 1.0
OE2 A:GLU1074 2.7 92.1 1.0
O A:HOH1764 2.8 68.8 1.0
O A:HOH1737 2.8 49.8 1.0
O A:HOH1763 3.3 79.4 1.0
CD A:GLU1074 3.6 82.2 1.0
O A:HOH1704 3.6 60.0 1.0
C A:GLY1072 3.8 48.4 1.0
CG A:GLU1074 3.9 52.2 1.0
CA A:GLY1072 4.3 43.8 1.0
OE1 A:GLU1074 4.6 93.5 1.0
O A:LYS1143 4.9 45.0 1.0
N A:VAL1073 4.9 38.0 1.0

Strontium binding site 3 out of 6 in 7osy

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Strontium binding site 3 out of 6 in the Human Prolyl-Trna Synthetase in Complex with L-Proline


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr1605

b:54.3
occ:1.00
 OE2 A:GLU1264 2.7 73.6 1.0
OE1 A:GLU1264 2.7 75.9 1.0
O A:HOH1727 2.9 54.2 1.0
CD A:GLU1264 3.0 79.0 1.0
O A:HOH1731 3.5 66.0 1.0
SR A:SR1603 3.9 59.3 1.0
CG A:GLU1264 4.5 80.1 1.0

Strontium binding site 4 out of 6 in 7osy

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Strontium binding site 4 out of 6 in the Human Prolyl-Trna Synthetase in Complex with L-Proline


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr1603

b:56.5
occ:1.00
 OE1 B:GLU1264 2.6 56.7 1.0
O B:HOH1745 2.6 47.7 1.0
O B:HOH1739 2.7 39.2 1.0
O B:LYS1265 2.8 47.8 1.0
OE1 B:GLN1266 3.0 70.9 1.0
C B:LYS1265 3.8 52.6 1.0
CD B:GLU1264 3.8 57.9 1.0
SR B:SR1605 3.8 57.4 1.0
CD B:GLN1266 3.9 73.8 1.0
N B:LYS1265 4.4 48.2 1.0
CA B:GLN1266 4.4 60.6 1.0
N B:GLN1266 4.4 51.9 1.0
CB B:GLN1266 4.6 68.3 1.0
OE2 B:GLU1264 4.6 60.4 1.0
NE2 B:GLN1266 4.6 41.6 1.0
CG B:GLU1264 4.7 62.6 1.0
CA B:LYS1265 4.7 47.0 1.0
O B:HOH1742 4.8 51.8 1.0
CB B:GLU1264 4.8 45.1 1.0
CG B:GLN1266 4.8 74.9 1.0

Strontium binding site 5 out of 6 in 7osy

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Strontium binding site 5 out of 6 in the Human Prolyl-Trna Synthetase in Complex with L-Proline


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr1604

b:63.7
occ:1.00
 O B:GLY1072 2.6 34.0 1.0
O B:HOH1748 3.0 41.7 1.0
OE2 B:GLU1074 3.0 81.9 1.0
O B:HOH1756 3.3 56.9 1.0
C B:GLY1072 3.6 32.5 1.0
O B:HOH1720 3.6 26.2 1.0
CD B:GLU1074 3.7 68.4 1.0
CG B:GLU1074 3.8 57.3 1.0
O B:HOH1749 4.0 87.5 1.0
CA B:GLY1072 4.1 32.5 1.0
O B:HOH1754 4.6 36.9 1.0
N B:VAL1073 4.7 35.8 1.0
OE1 B:GLU1074 4.8 69.0 1.0
O B:LYS1143 5.0 40.4 1.0

Strontium binding site 6 out of 6 in 7osy

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr1605

b:57.4
occ:1.00
 OE2 B:GLU1264 2.6 60.4 1.0
O B:HOH1739 2.8 39.2 1.0
OE1 B:GLU1264 2.9 56.7 1.0
CD B:GLU1264 3.1 57.9 1.0
O B:HOH1742 3.3 51.8 1.0
SR B:SR1603 3.8 56.5 1.0
O B:HOH1717 4.1 42.4 1.0
CG B:GLU1264 4.6 62.6 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 07:06:08 2024

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