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Strontium in PDB 7ot1: Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3C

Enzymatic activity of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3C

All present enzymatic activity of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3C:
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 3C, PDB code: 7ot1 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) 65.89 / 2.71
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.273, 88.968, 84.749, 90, 110.34, 90
R / Rfree (%) 21.4 / 28.3

Other elements in 7ot1:

The structure of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3C 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 3C (pdb code 7ot1). 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 and Compound 3C, PDB code: 7ot1:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6;

Strontium binding site 1 out of 6 in 7ot1

Go back to Strontium Binding Sites List in 7ot1
Strontium binding site 1 out of 6 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3C


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 3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr1604

b:81.7
occ:1.00
 OE2 A:GLU1264 2.5 64.7 1.0
OE1 A:GLN1266 2.6 47.4 1.0
CD A:GLU1264 3.3 80.7 1.0
OE1 A:GLU1264 3.5 84.5 1.0
O A:LYS1265 3.6 69.3 1.0
CD A:GLN1266 3.6 35.3 1.0
O A:HOH1722 3.7 21.6 1.0
CA A:GLN1266 4.2 31.3 1.0
C A:LYS1265 4.3 44.4 1.0
NE2 A:GLN1266 4.4 36.8 1.0
CB A:GLN1266 4.4 32.9 1.0
SR A:SR1605 4.5 122.1 1.0
CG A:GLN1266 4.6 37.3 1.0
N A:GLN1266 4.6 30.7 1.0
CG A:GLU1264 4.7 71.8 1.0

Strontium binding site 2 out of 6 in 7ot1

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Strontium binding site 2 out of 6 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3C


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 3C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr1605

b:122.1
occ:1.00
 OE1 A:GLU1264 2.6 84.5 1.0
CD A:GLU1264 3.5 80.7 1.0
CG A:GLU1264 4.2 71.8 1.0
OE2 A:GLU1264 4.3 64.7 1.0
SR A:SR1604 4.5 81.7 1.0

Strontium binding site 3 out of 6 in 7ot1

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


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 3C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr1604

b:68.4
occ:1.00
 OE1 B:GLU1264 2.5 56.4 1.0
OE1 B:GLN1266 2.7 96.7 1.0
O B:LYS1265 3.1 61.0 1.0
OE2 B:GLU1264 3.3 70.4 1.0
CD B:GLU1264 3.3 61.7 1.0
O B:HOH1720 3.8 55.8 1.0
CD B:GLN1266 4.0 90.6 1.0
C B:LYS1265 4.1 42.3 1.0
CA B:GLN1266 4.3 47.1 1.0
SR B:SR1607 4.5 120.8 1.0
N B:GLN1266 4.6 52.3 1.0
CG B:GLU1264 4.7 40.0 1.0
NE2 B:GLN1266 4.8 87.1 1.0
CB B:GLN1266 4.8 63.1 1.0
CG B:GLN1266 4.9 78.2 1.0

Strontium binding site 4 out of 6 in 7ot1

Go back to Strontium Binding Sites List in 7ot1
Strontium binding site 4 out of 6 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3C


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 3C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr1605

b:135.9
occ:1.00
 O B:GLY1072 2.7 37.0 1.0
C B:GLY1072 3.6 36.9 1.0
CG B:GLU1074 3.8 34.0 1.0
CA B:GLY1072 4.0 38.6 1.0
O A:HOH1741 4.3 59.0 1.0
O B:HOH1727 4.4 52.3 1.0
O B:HOH1726 4.4 43.2 1.0
N B:VAL1073 4.7 36.7 1.0

Strontium binding site 5 out of 6 in 7ot1

Go back to Strontium Binding Sites List in 7ot1
Strontium binding site 5 out of 6 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3C


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 3C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr1606

b:117.6
occ:1.00
 O B:LYS1499 2.6 75.2 1.0
O B:HOH1728 2.7 62.3 1.0
C B:LYS1499 3.8 67.2 1.0
CA B:ASN1500 4.6 56.9 1.0
CB B:LYS1499 4.6 65.5 1.0
N B:ASN1500 4.6 62.4 1.0
CA B:LYS1499 4.7 60.5 1.0
CB B:ASN1500 4.7 55.3 1.0

Strontium binding site 6 out of 6 in 7ot1

Go back to Strontium Binding Sites List in 7ot1
Strontium binding site 6 out of 6 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3C


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 3C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr1607

b:120.8
occ:1.00
 OE1 B:GLU1264 3.0 56.4 1.0
CG B:GLU1264 3.2 40.0 1.0
CD B:GLU1264 3.3 61.7 1.0
O B:HOH1722 3.9 37.7 1.0
OE2 B:GLU1264 4.3 70.4 1.0
SR B:SR1604 4.5 68.4 1.0
CB B:GLU1264 4.6 37.9 1.0
CA B:GLU1264 4.8 44.5 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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