Fluorine in PDB 7wmf: Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor

Enzymatic activity of Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor

All present enzymatic activity of Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor:
6.1.1.3;

Protein crystallography data

The structure of Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor, PDB code: 7wmf was solved by Z.Cai, B.Chen, Y.Yu, H.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.792, 102.521, 103.171, 90, 90, 90
R / Rfree (%) 22.4 / 26.7

Other elements in 7wmf:

The structure of Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Chlorine (Cl) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor (pdb code 7wmf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor, PDB code: 7wmf:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7wmf

Go back to Fluorine Binding Sites List in 7wmf
Fluorine binding site 1 out of 6 in the Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:68.0
occ:1.00
 F2 A:9I9701 0.0 68.0 1.0
C24 A:9I9701 1.3 71.1 1.0
F1 A:9I9701 2.1 71.5 1.0
F A:9I9701 2.1 72.9 1.0
C23 A:9I9701 2.4 68.2 1.0
C22 A:9I9701 2.8 65.2 1.0
O A:VAL376 3.2 39.6 1.0
C25 A:9I9701 3.6 66.1 1.0
C21 A:9I9701 4.2 62.4 1.0
CG A:GLU365 4.3 54.4 1.0
N A:VAL376 4.3 43.5 1.0
C A:VAL376 4.3 41.2 1.0
CD1 A:PHE379 4.4 38.4 1.0
CD A:GLU365 4.4 56.9 1.0
CE1 A:PHE379 4.5 39.1 1.0
OE1 A:GLU365 4.6 57.0 1.0
C26 A:9I9701 4.7 63.9 1.0
CG2 A:VAL376 4.7 42.5 1.0
CA A:VAL376 4.9 42.8 1.0
OE2 A:GLU365 4.9 62.4 1.0

Fluorine binding site 2 out of 6 in 7wmf

Go back to Fluorine Binding Sites List in 7wmf
Fluorine binding site 2 out of 6 in the Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:72.9
occ:1.00
 F A:9I9701 0.0 72.9 1.0
C24 A:9I9701 1.3 71.1 1.0
F1 A:9I9701 2.1 71.5 1.0
F2 A:9I9701 2.1 68.0 1.0
C23 A:9I9701 2.4 68.2 1.0
C25 A:9I9701 2.8 66.1 1.0
O A:MET374 3.4 45.9 1.0
C22 A:9I9701 3.6 65.2 1.0
N A:VAL376 3.8 43.5 1.0
CA A:ARG375 3.9 48.6 1.0
C26 A:9I9701 4.2 63.9 1.0
O A:VAL376 4.2 39.6 1.0
C A:MET374 4.3 46.9 1.0
CG A:ARG375 4.4 54.2 1.0
C A:ARG375 4.4 45.6 1.0
CG2 A:VAL376 4.5 42.5 1.0
N A:ARG375 4.5 46.1 1.0
CB A:ARG375 4.7 51.2 1.0
C21 A:9I9701 4.7 62.4 1.0
CA A:VAL376 4.9 42.8 1.0
C A:VAL376 5.0 41.2 1.0
C20 A:9I9701 5.0 61.1 1.0

Fluorine binding site 3 out of 6 in 7wmf

Go back to Fluorine Binding Sites List in 7wmf
Fluorine binding site 3 out of 6 in the Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:71.5
occ:1.00
 F1 A:9I9701 0.0 71.5 1.0
C24 A:9I9701 1.3 71.1 1.0
F A:9I9701 2.1 72.9 1.0
F2 A:9I9701 2.1 68.0 1.0
C23 A:9I9701 2.4 68.2 1.0
CG2 A:VAL376 3.1 42.5 1.0
C25 A:9I9701 3.2 66.1 1.0
C22 A:9I9701 3.2 65.2 1.0
O A:VAL376 3.4 39.6 1.0
CD1 A:PHE379 3.7 38.4 1.0
N A:VAL376 3.7 43.5 1.0
CG A:PHE379 3.8 38.1 1.0
CB A:PHE379 3.8 36.3 1.0
C A:VAL376 4.0 41.2 1.0
CA A:VAL376 4.2 42.8 1.0
CB A:VAL376 4.2 42.4 1.0
CE1 A:PHE379 4.4 39.1 1.0
C26 A:9I9701 4.4 63.9 1.0
C21 A:9I9701 4.5 62.4 1.0
OG A:SER517 4.6 42.2 1.0
O A:MET374 4.6 45.9 1.0
CD2 A:PHE379 4.6 38.9 1.0
C A:ARG375 4.8 45.6 1.0
CB A:SER517 4.8 41.2 1.0
CA A:ARG375 4.9 48.6 1.0
C20 A:9I9701 5.0 61.1 1.0

Fluorine binding site 4 out of 6 in 7wmf

Go back to Fluorine Binding Sites List in 7wmf
Fluorine binding site 4 out of 6 in the Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:75.7
occ:1.00
 F2 B:9I9701 0.0 75.7 1.0
C24 B:9I9701 1.3 76.8 1.0
F1 B:9I9701 2.1 78.3 1.0
F B:9I9701 2.1 76.6 1.0
C23 B:9I9701 2.4 73.7 1.0
C25 B:9I9701 2.8 72.2 1.0
OE1 B:GLU365 3.0 60.5 1.0
O B:VAL376 3.0 41.7 1.0
C22 B:9I9701 3.6 71.3 1.0
CG B:GLU365 3.8 58.2 1.0
CD B:GLU365 3.8 59.2 1.0
C26 B:9I9701 4.2 70.9 1.0
C B:VAL376 4.2 42.0 1.0
CD1 B:PHE379 4.4 45.8 1.0
N B:VAL376 4.5 42.0 1.0
CE1 B:PHE379 4.5 47.8 1.0
CB B:ARG363 4.5 47.1 1.0
CG B:ARG363 4.5 49.6 1.0
C21 B:9I9701 4.8 69.5 1.0
CA B:VAL376 5.0 42.3 1.0

Fluorine binding site 5 out of 6 in 7wmf

Go back to Fluorine Binding Sites List in 7wmf
Fluorine binding site 5 out of 6 in the Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:76.6
occ:1.00
 F B:9I9701 0.0 76.6 1.0
C24 B:9I9701 1.3 76.8 1.0
F1 B:9I9701 2.1 78.3 1.0
F2 B:9I9701 2.1 75.7 1.0
C23 B:9I9701 2.4 73.7 1.0
C22 B:9I9701 3.2 71.3 1.0
C25 B:9I9701 3.3 72.2 1.0
N B:VAL376 3.4 42.0 1.0
O B:VAL376 3.5 41.7 1.0
CA B:ARG375 3.9 44.3 1.0
O B:MET374 4.0 47.2 1.0
CG2 B:VAL376 4.1 42.8 1.0
C B:ARG375 4.2 42.1 1.0
C B:VAL376 4.3 42.0 1.0
CG B:ARG375 4.3 45.9 1.0
CA B:VAL376 4.4 42.3 1.0
C21 B:9I9701 4.4 69.5 1.0
C26 B:9I9701 4.5 70.9 1.0
OE1 B:GLU365 4.6 60.5 1.0
CB B:ARG375 4.7 44.4 1.0
C B:MET374 4.8 46.1 1.0
CB B:VAL376 4.8 42.8 1.0
N B:ARG375 4.9 44.4 1.0
C20 B:9I9701 5.0 67.3 1.0

Fluorine binding site 6 out of 6 in 7wmf

Go back to Fluorine Binding Sites List in 7wmf
Fluorine binding site 6 out of 6 in the Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Threonyl-Trna Synthetase From Salmonella Enterica in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:78.3
occ:1.00
 F1 B:9I9701 0.0 78.3 1.0
C24 B:9I9701 1.3 76.8 1.0
F2 B:9I9701 2.1 75.7 1.0
F B:9I9701 2.1 76.6 1.0
C23 B:9I9701 2.4 73.7 1.0
C22 B:9I9701 2.8 71.3 1.0
O B:VAL376 2.9 41.7 1.0
CD1 B:PHE379 3.1 45.8 1.0
CG2 B:VAL376 3.2 42.8 1.0
C B:VAL376 3.5 42.0 1.0
C25 B:9I9701 3.6 72.2 1.0
CG B:PHE379 3.7 43.6 1.0
CE1 B:PHE379 3.7 47.8 1.0
N B:VAL376 3.9 42.0 1.0
CB B:PHE379 3.9 41.0 1.0
CA B:VAL376 4.1 42.3 1.0
C21 B:9I9701 4.2 69.5 1.0
CB B:VAL376 4.2 42.8 1.0
N B:ARG377 4.4 40.4 1.0
O B:ARG377 4.7 38.1 1.0
C B:ARG377 4.7 39.0 1.0
C26 B:9I9701 4.7 70.9 1.0
CA B:ARG377 4.7 40.2 1.0
CD2 B:PHE379 4.8 45.5 1.0
CZ B:PHE379 4.8 46.9 1.0
C20 B:9I9701 5.0 67.3 1.0

Reference:

Z.Cai, B.Chen, Y.Yu, J.Guo, Z.Luo, B.Cheng, J.Xu, Q.Gu, H.Zhou. Design, Synthesis, and Proof-of-Concept of Triple-Site Inhibitors Against Aminoacyl-Trna Synthetases. J.Med.Chem. V. 65 5800 2022.
ISSN: ISSN 0022-2623
PubMed: 35363470
DOI: 10.1021/ACS.JMEDCHEM.2C00134
Page generated: Wed Apr 5 01:47:31 2023

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