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: Fri Aug 2 14:52:34 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy