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Chlorine in PDB 7ot3: Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B

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

All present enzymatic activity of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B:
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 3B, PDB code: 7ot3 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) 54.77 / 2.53
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 71.871, 92.422, 87.26, 90, 108.88, 90
R / Rfree (%) 21.8 / 27.6

Other elements in 7ot3:

The structure of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B also contains other interesting chemical elements:

Strontium (Sr) 4 atoms
Zinc (Zn) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B (pdb code 7ot3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B, PDB code: 7ot3:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 7ot3

Go back to Chlorine Binding Sites List in 7ot3
Chlorine binding site 1 out of 4 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1602

b:82.0
occ:1.00
 CL1 A:0W41602 0.0 82.0 1.0
C13 A:0W41602 1.7 82.2 1.0
C14 A:0W41602 2.7 80.4 1.0
C12 A:0W41602 2.7 81.4 1.0
C11 A:0W41602 3.0 74.8 1.0
O A:GLY1238 3.5 61.5 1.0
C A:GLY1238 3.6 78.3 1.0
CA A:GLY1239 3.7 60.8 1.0
N A:GLY1239 3.7 91.3 1.0
NE2 A:GLN1237 3.7 98.5 1.0
O A:GLN1237 3.7 77.5 1.0
C15 A:0W41602 4.0 78.0 1.0
C17 A:0W41602 4.0 82.1 1.0
OG1 A:THR1276 4.0 60.9 1.0
CG A:GLN1237 4.3 85.6 1.0
CG2 A:THR1276 4.3 51.6 1.0
C A:GLN1237 4.4 75.8 1.0
CD A:ARG1278 4.4 54.7 1.0
CA A:GLY1238 4.4 57.1 1.0
C16 A:0W41602 4.5 72.0 1.0
NH1 A:ARG1278 4.5 77.3 1.0
N10 A:0W41602 4.5 82.4 1.0
CD A:GLN1237 4.5 93.2 1.0
N A:THR1276 4.6 57.2 1.0
C A:GLY1239 4.6 80.1 1.0
CB A:THR1276 4.7 67.5 1.0
N A:GLY1238 4.7 72.5 1.0
NE A:ARG1278 4.9 62.4 1.0
CZ A:ARG1278 4.9 74.8 1.0
O A:GLY1274 4.9 66.2 1.0
CA A:LEU1275 5.0 55.2 1.0

Chlorine binding site 2 out of 4 in 7ot3

Go back to Chlorine Binding Sites List in 7ot3
Chlorine binding site 2 out of 4 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1602

b:100.4
occ:1.00
 CL2 A:0W41602 0.0 100.4 1.0
C21 A:0W41602 1.7 108.7 1.0
C22 A:0W41602 2.7 93.1 1.0
C20 A:0W41602 2.7 100.0 1.0
C19 A:0W41602 3.0 96.8 1.0
CB A:ARG1163 3.4 88.5 1.0
CG A:ARG1163 3.4 105.1 1.0
N9 A:0W41602 3.6 98.9 1.0
O8 A:0W41602 3.7 98.7 1.0
CE A:LYS1156 3.8 128.1 1.0
C7 A:0W41602 3.8 99.6 1.0
C23 A:0W41602 4.0 90.2 1.0
C25 A:0W41602 4.0 102.3 1.0
CA A:ARG1163 4.1 60.0 1.0
CZ A:ARG1163 4.1 127.4 1.0
NH1 A:ARG1163 4.2 114.6 1.0
NE A:ARG1163 4.2 129.9 1.0
NZ A:LYS1156 4.4 120.0 1.0
CD A:ARG1163 4.4 118.2 1.0
C24 A:0W41602 4.5 88.6 1.0
NH2 A:ARG1163 4.6 121.5 1.0
C A:ARG1163 4.8 78.6 1.0
C2 A:0W41602 4.9 90.7 1.0
CB A:GLU1154 4.9 94.8 1.0
NH2 A:ARG1278 5.0 69.5 1.0

Chlorine binding site 3 out of 4 in 7ot3

Go back to Chlorine Binding Sites List in 7ot3
Chlorine binding site 3 out of 4 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1602

b:108.7
occ:1.00
 CL1 B:0W41602 0.0 108.7 1.0
C13 B:0W41602 1.7 90.5 1.0
C14 B:0W41602 2.7 90.8 1.0
C12 B:0W41602 2.7 89.1 1.0
C11 B:0W41602 3.0 93.5 1.0
O B:GLN1237 3.5 114.5 1.0
NE2 B:GLN1237 3.6 113.0 1.0
C B:GLY1238 3.7 92.0 1.0
N B:GLY1239 3.7 114.1 1.0
O B:GLY1238 3.7 110.2 1.0
CA B:GLY1239 3.8 98.1 1.0
C15 B:0W41602 4.0 97.8 1.0
C17 B:0W41602 4.0 94.7 1.0
OG1 B:THR1276 4.1 79.0 1.0
NH1 B:ARG1278 4.2 110.4 1.0
C B:GLN1237 4.2 110.8 1.0
CG2 B:THR1276 4.2 62.4 1.0
CD B:ARG1278 4.3 80.3 1.0
CA B:GLY1238 4.4 89.1 1.0
CG B:GLN1237 4.5 103.7 1.0
N10 B:0W41602 4.5 102.3 1.0
C16 B:0W41602 4.5 98.9 1.0
CD B:GLN1237 4.6 106.9 1.0
N B:GLY1238 4.6 101.6 1.0
CZ B:ARG1278 4.6 94.8 1.0
NE B:ARG1278 4.7 94.6 1.0
C B:GLY1239 4.8 91.3 1.0
N B:THR1276 4.8 62.8 1.0
CB B:THR1276 4.8 73.3 1.0
N4 B:0W41602 4.9 109.6 1.0
CB B:ARG1278 5.0 83.4 1.0
CB B:GLN1237 5.0 110.3 1.0

Chlorine binding site 4 out of 4 in 7ot3

Go back to Chlorine Binding Sites List in 7ot3
Chlorine binding site 4 out of 4 in the Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Human Prolyl-Trna Synthetase in Complex with L-Proline and Compound 3B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1602

b:144.6
occ:1.00
 CL2 B:0W41602 0.0 144.6 1.0
C21 B:0W41602 1.7 138.1 1.0
C22 B:0W41602 2.7 129.4 1.0
C20 B:0W41602 2.7 134.8 1.0
C19 B:0W41602 3.0 129.9 1.0
CG B:ARG1163 3.5 92.1 1.0
N9 B:0W41602 3.6 122.2 1.0
CB B:ARG1163 3.8 83.0 1.0
C23 B:0W41602 4.0 135.0 1.0
C25 B:0W41602 4.0 134.8 1.0
O8 B:0W41602 4.0 100.3 1.0
C7 B:0W41602 4.0 115.7 1.0
CD B:ARG1163 4.1 103.2 1.0
CA B:ARG1163 4.3 91.1 1.0
OE2 B:GLU1154 4.3 150.3 1.0
CD B:GLU1154 4.3 154.5 1.0
OE1 B:GLU1154 4.4 130.6 1.0
C24 B:0W41602 4.5 131.1 1.0
NH2 B:ARG1278 4.9 98.3 1.0
O B:TYR1512 4.9 117.2 1.0
CG B:GLU1154 4.9 155.0 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: Sun Jul 13 05:26:11 2025

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