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Fluorine in PDB 7ot2: Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4J

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

All present enzymatic activity of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4J:
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 4J, PDB code: 7ot2 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) 54.91 / 2.48
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.017, 92.839, 87.933, 90, 108.99, 90
R / Rfree (%) 19.4 / 25.3

Other elements in 7ot2:

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

Zinc (Zn) 2 atoms
Strontium (Sr) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4J (pdb code 7ot2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4J, PDB code: 7ot2:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7ot2

Go back to Fluorine Binding Sites List in 7ot2
Fluorine binding site 1 out of 6 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4J


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4J within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1602

b:70.0
occ:1.00
 F19 A:1FI1602 0.0 70.0 1.0
C18 A:1FI1602 1.3 76.0 1.0
F21 A:1FI1602 2.1 78.0 1.0
F20 A:1FI1602 2.1 73.4 1.0
C13 A:1FI1602 2.4 68.6 1.0
C11 A:1FI1602 3.0 60.8 1.0
C12 A:1FI1602 3.0 71.4 1.0
OG1 A:THR1276 3.1 54.5 1.0
C14 A:1FI1602 3.4 62.0 1.0
O A:GLY1238 3.7 56.0 1.0
O A:GLN1237 3.7 65.5 1.0
CD A:ARG1278 3.8 45.0 1.0
C A:GLY1238 3.9 61.6 1.0
CG2 A:THR1276 4.0 51.5 1.0
N A:THR1276 4.1 49.1 1.0
CB A:THR1276 4.1 52.4 1.0
CB A:ARG1278 4.3 54.4 1.0
NE A:ARG1278 4.3 54.4 1.0
C17 A:1FI1602 4.3 71.0 1.0
N10 A:1FI1602 4.4 57.7 1.0
N4 A:1FI1602 4.4 68.5 1.0
N A:GLY1239 4.4 71.3 1.0
CA A:GLY1238 4.5 50.2 1.0
CG A:ARG1278 4.6 53.5 1.0
NH1 A:ARG1278 4.6 60.6 1.0
C15 A:1FI1602 4.6 57.9 1.0
C A:GLN1237 4.6 65.1 1.0
CA A:THR1276 4.6 39.8 1.0
CZ A:ARG1278 4.7 56.9 1.0
CA A:GLY1239 4.7 56.5 1.0
CA A:LEU1275 4.9 57.2 1.0
C A:LEU1275 4.9 64.9 1.0
C3 A:1FI1602 4.9 67.6 1.0
N A:GLY1238 4.9 58.9 1.0
C16 A:1FI1602 5.0 65.7 1.0

Fluorine binding site 2 out of 6 in 7ot2

Go back to Fluorine Binding Sites List in 7ot2
Fluorine binding site 2 out of 6 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4J


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4J within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1602

b:73.4
occ:1.00
 F20 A:1FI1602 0.0 73.4 1.0
C18 A:1FI1602 1.3 76.0 1.0
F21 A:1FI1602 2.1 78.0 1.0
F19 A:1FI1602 2.1 70.0 1.0
C13 A:1FI1602 2.4 68.6 1.0
C11 A:1FI1602 3.0 60.8 1.0
C12 A:1FI1602 3.0 71.4 1.0
O A:GLN1237 3.0 65.5 1.0
NE2 A:GLN1237 3.1 81.2 1.0
C14 A:1FI1602 3.4 62.0 1.0
CG A:GLN1237 3.5 73.3 1.0
NH1 A:ARG1278 3.5 60.6 1.0
C A:GLN1237 3.6 65.1 1.0
CD A:GLN1237 3.7 77.4 1.0
CB A:GLN1237 3.8 68.5 1.0
CZ A:ARG1278 4.1 56.9 1.0
N A:GLY1239 4.2 71.3 1.0
C A:GLY1238 4.2 61.6 1.0
CD A:ARG1278 4.2 45.0 1.0
C17 A:1FI1602 4.3 71.0 1.0
N A:GLY1238 4.3 58.9 1.0
N10 A:1FI1602 4.4 57.7 1.0
CA A:GLN1237 4.4 77.5 1.0
NE A:ARG1278 4.4 54.4 1.0
CA A:GLY1238 4.5 50.2 1.0
O A:GLY1238 4.6 56.0 1.0
C15 A:1FI1602 4.6 57.9 1.0
CA A:GLY1239 4.7 56.5 1.0
OE1 A:GLN1237 4.8 77.5 1.0
NH2 A:ARG1278 4.9 50.3 1.0
C16 A:1FI1602 5.0 65.7 1.0

Fluorine binding site 3 out of 6 in 7ot2

Go back to Fluorine Binding Sites List in 7ot2
Fluorine binding site 3 out of 6 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4J


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4J within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1602

b:78.0
occ:1.00
 F21 A:1FI1602 0.0 78.0 1.0
C18 A:1FI1602 1.3 76.0 1.0
F19 A:1FI1602 2.1 70.0 1.0
F20 A:1FI1602 2.1 73.4 1.0
C13 A:1FI1602 2.4 68.6 1.0
C14 A:1FI1602 2.7 62.0 1.0
CA A:GLY1239 3.0 56.5 1.0
N A:GLY1239 3.0 71.3 1.0
C A:GLY1238 3.3 61.6 1.0
O A:GLY1238 3.3 56.0 1.0
C A:GLY1239 3.6 66.4 1.0
C12 A:1FI1602 3.7 71.4 1.0
N A:THR1240 3.8 56.4 1.0
O A:GLY1274 4.0 63.4 1.0
C15 A:1FI1602 4.1 57.9 1.0
O A:GLN1237 4.1 65.5 1.0
CA A:GLY1238 4.2 50.2 1.0
C11 A:1FI1602 4.3 60.8 1.0
CG A:GLN1237 4.3 73.3 1.0
NE2 A:GLN1237 4.3 81.2 1.0
O A:GLY1239 4.3 73.5 1.0
OG1 A:THR1240 4.4 72.6 1.0
C A:GLN1237 4.5 65.1 1.0
N A:GLY1238 4.5 58.9 1.0
CD A:GLN1237 4.6 77.4 1.0
CA A:LEU1275 4.6 57.2 1.0
C A:GLY1274 4.8 60.0 1.0
C17 A:1FI1602 4.8 71.0 1.0
CG2 A:THR1240 4.8 78.4 1.0
N A:THR1276 4.9 49.1 1.0
C16 A:1FI1602 4.9 65.7 1.0
CA A:THR1240 5.0 57.7 1.0
CB A:THR1240 5.0 62.4 1.0

Fluorine binding site 4 out of 6 in 7ot2

Go back to Fluorine Binding Sites List in 7ot2
Fluorine binding site 4 out of 6 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4J


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4J within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1602

b:87.9
occ:1.00
 F19 B:1FI1602 0.0 87.9 1.0
C18 B:1FI1602 1.3 82.8 1.0
F20 B:1FI1602 2.1 83.4 1.0
F21 B:1FI1602 2.1 85.9 1.0
C13 B:1FI1602 2.4 73.8 1.0
C12 B:1FI1602 3.0 60.7 1.0
C11 B:1FI1602 3.0 63.3 1.0
NE2 B:GLN1237 3.1 81.3 1.0
O B:GLN1237 3.2 74.2 1.0
NH1 B:ARG1278 3.2 55.8 1.0
CG B:GLN1237 3.2 87.9 1.0
C14 B:1FI1602 3.4 56.9 1.0
CB B:GLN1237 3.6 86.4 1.0
CD B:GLN1237 3.6 83.2 1.0
C B:GLN1237 3.7 74.8 1.0
CZ B:ARG1278 4.1 70.9 1.0
CA B:GLN1237 4.2 77.6 1.0
C17 B:1FI1602 4.3 51.6 1.0
CD B:ARG1278 4.3 67.9 1.0
C B:GLY1238 4.4 59.2 1.0
N B:GLY1238 4.4 67.2 1.0
N10 B:1FI1602 4.4 72.8 1.0
O B:GLY1238 4.5 64.8 1.0
N B:GLY1239 4.5 68.2 1.0
NE B:ARG1278 4.5 73.0 1.0
C15 B:1FI1602 4.6 60.9 1.0
CA B:GLY1238 4.7 69.7 1.0
OE1 B:GLN1237 4.8 90.5 1.0
CA B:GLY1239 4.9 57.2 1.0
C16 B:1FI1602 4.9 65.4 1.0
NH2 B:ARG1278 4.9 64.5 1.0
N B:GLN1237 5.0 86.6 1.0

Fluorine binding site 5 out of 6 in 7ot2

Go back to Fluorine Binding Sites List in 7ot2
Fluorine binding site 5 out of 6 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4J


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4J within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1602

b:83.4
occ:1.00
 F20 B:1FI1602 0.0 83.4 1.0
C18 B:1FI1602 1.3 82.8 1.0
F21 B:1FI1602 2.1 85.9 1.0
F19 B:1FI1602 2.1 87.9 1.0
C13 B:1FI1602 2.3 73.8 1.0
C14 B:1FI1602 2.7 56.9 1.0
CA B:GLY1239 3.0 57.2 1.0
N B:GLY1239 3.0 68.2 1.0
O B:GLY1238 3.1 64.8 1.0
C B:GLY1238 3.1 59.2 1.0
C B:GLY1239 3.4 57.7 1.0
C12 B:1FI1602 3.7 60.7 1.0
CG B:GLN1237 3.7 87.9 1.0
N B:THR1240 3.8 61.1 1.0
NE2 B:GLN1237 4.0 81.3 1.0
O B:GLN1237 4.0 74.2 1.0
O B:GLY1239 4.0 67.8 1.0
C15 B:1FI1602 4.1 60.9 1.0
CA B:GLY1238 4.1 69.7 1.0
OG1 B:THR1240 4.2 78.5 1.0
CD B:GLN1237 4.2 83.2 1.0
O B:GLY1274 4.2 80.2 1.0
C B:GLN1237 4.2 74.8 1.0
N B:GLY1238 4.2 67.2 1.0
C11 B:1FI1602 4.3 63.3 1.0
CB B:GLN1237 4.7 86.4 1.0
C17 B:1FI1602 4.7 51.6 1.0
CG2 B:THR1240 4.8 82.0 1.0
CB B:THR1240 4.9 70.2 1.0
C16 B:1FI1602 4.9 65.4 1.0
CA B:THR1240 4.9 76.0 1.0

Fluorine binding site 6 out of 6 in 7ot2

Go back to Fluorine Binding Sites List in 7ot2
Fluorine binding site 6 out of 6 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4J


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 4J within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1602

b:85.9
occ:1.00
 F21 B:1FI1602 0.0 85.9 1.0
C18 B:1FI1602 1.3 82.8 1.0
F20 B:1FI1602 2.1 83.4 1.0
F19 B:1FI1602 2.1 87.9 1.0
C13 B:1FI1602 2.4 73.8 1.0
C11 B:1FI1602 3.0 63.3 1.0
C12 B:1FI1602 3.0 60.7 1.0
O B:GLY1238 3.3 64.8 1.0
C14 B:1FI1602 3.4 56.9 1.0
O B:GLN1237 3.4 74.2 1.0
OG1 B:THR1276 3.4 63.1 1.0
CD B:ARG1278 3.5 67.9 1.0
C B:GLY1238 3.7 59.2 1.0
NH1 B:ARG1278 4.0 55.8 1.0
NE B:ARG1278 4.1 73.0 1.0
CG2 B:THR1276 4.1 53.5 1.0
C B:GLN1237 4.3 74.8 1.0
CA B:GLY1238 4.3 69.7 1.0
CZ B:ARG1278 4.3 70.9 1.0
N B:GLY1239 4.3 68.2 1.0
C17 B:1FI1602 4.4 51.6 1.0
N10 B:1FI1602 4.4 72.8 1.0
CB B:THR1276 4.4 59.7 1.0
CG B:ARG1278 4.4 71.1 1.0
CB B:ARG1278 4.5 70.9 1.0
N4 B:1FI1602 4.5 69.1 1.0
N B:THR1276 4.6 59.1 1.0
N B:GLY1238 4.6 67.2 1.0
C15 B:1FI1602 4.6 60.9 1.0
CA B:GLY1239 4.7 57.2 1.0
CG B:GLN1237 4.9 87.9 1.0
C3 B:1FI1602 5.0 73.1 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: Tue Jul 15 22:37:48 2025

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