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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

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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

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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

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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

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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

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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

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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

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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: Sat Aug 21 17:34:13 2021

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