Fluorine in PDB 8w8l: Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38

The structure of Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38, PDB code: 8w8l was solved by Z.Luo, H.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	97.05 / 1.82
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.484, 103.06, 194.095, 90, 90, 90
R / Rfree (%)	21.1 / 24.1

The structure of Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38 also contains other interesting chemical elements:

Magnesium

(Mg)

9 atoms

The binding sites of Fluorine atom in the Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38 (pdb code 8w8l). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38, PDB code: 8w8l:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:23.1 occ:1.00 F29 A:W20601 0.0 23.1 1.0 C10 A:W20601 1.3 22.3 1.0 C9 A:W20601 2.3 22.9 1.0 C11 A:W20601 2.4 22.3 1.0 N14 A:W20601 3.0 23.1 1.0 S13 A:W20601 3.0 23.7 1.0 O27 A:W20601 3.1 23.8 1.0 CB A:HIS411 3.3 18.1 1.0 O A:HIS411 3.6 17.6 1.0 O A:GLY443 3.6 17.4 1.0 C8 A:W20601 3.6 23.2 1.0 C12 A:W20601 3.6 21.4 1.0 CA A:GLY443 3.6 17.7 1.0 C15 A:W20601 3.7 22.8 1.0 N A:HIS411 3.7 17.8 1.0 C18 A:W20601 3.8 21.7 1.0 C A:GLY443 3.8 17.5 1.0 CA A:HIS411 3.9 18.1 1.0 N A:GLY443 4.1 18.0 1.0 C7 A:W20601 4.1 21.1 1.0 C A:HIS411 4.2 19.4 1.0 CE2 A:PHE413 4.2 24.5 1.0 C16 A:W20601 4.3 22.2 1.0 O28 A:W20601 4.4 22.2 1.0 O17 A:W20601 4.4 21.8 1.0 OE2 A:GLU408 4.4 34.3 1.0 CG A:HIS411 4.5 18.4 1.0 CE A:MET157 4.5 24.8 1.0 C19 A:W20601 4.6 21.6 1.0 C A:GLY410 4.6 18.8 1.0 CZ A:PHE413 4.7 24.3 1.0 N A:ILE444 4.8 17.5 1.0 ND1 A:HIS411 4.9 19.1 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38 within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:20.3 occ:1.00 F30 A:W20601 0.0 20.3 1.0 C3 A:W20601 1.3 19.7 1.0 C1 A:W20601 2.3 18.7 1.0 C4 A:W20601 2.4 20.2 1.0 N25 A:W20601 2.7 19.2 1.0 C8 A:W20601 2.7 23.2 1.0 C7 A:W20601 2.9 21.1 1.0 O A:HOH917 3.0 17.7 1.0 CA A:GLY445 3.1 19.6 1.0 CE2 A:PHE155 3.6 17.7 1.0 C5 A:W20601 3.6 19.2 1.0 C2 A:W20601 3.6 18.8 1.0 CD2 A:PHE155 3.7 17.7 1.0 CD A:ARG448 3.9 26.7 1.0 N A:GLY445 3.9 19.3 1.0 C9 A:W20601 4.0 22.9 1.0 C24 A:W20601 4.0 18.9 1.0 NH1 A:ARG448 4.0 27.7 1.0 C6 A:W20601 4.1 18.7 1.0 NE A:ARG448 4.2 27.4 1.0 C12 A:W20601 4.3 21.4 1.0 C A:GLY445 4.3 19.6 1.0 CZ A:ARG448 4.3 27.0 1.0 CE A:MET157 4.3 24.8 1.0 CG A:ARG448 4.4 25.9 1.0 CZ A:PHE155 4.4 18.0 1.0 CG A:PHE155 4.6 17.9 1.0 CB A:ARG448 4.7 25.1 1.0 C A:ILE444 4.7 18.7 1.0 C22 A:W20601 4.8 18.8 1.0 O A:ILE156 4.8 16.9 1.0 O A:ILE444 4.9 18.6 1.0 N23 A:W20601 4.9 18.9 1.0 O A:GLY445 4.9 19.2 1.0 CB A:MET157 5.0 20.3 1.0 N A:VAL446 5.0 19.8 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38 within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:26.1 occ:1.00 F29 B:W20601 0.0 26.1 1.0 C10 B:W20601 1.4 22.7 1.0 C9 B:W20601 2.4 22.7 1.0 C11 B:W20601 2.4 21.2 1.0 N14 B:W20601 2.9 19.8 1.0 S13 B:W20601 3.0 20.7 1.0 O27 B:W20601 3.2 21.8 1.0 CB B:HIS411 3.3 20.8 1.0 CA B:GLY443 3.5 18.4 1.0 O B:GLY443 3.5 18.9 1.0 C8 B:W20601 3.6 22.1 1.0 O B:HIS411 3.6 19.4 1.0 C12 B:W20601 3.6 21.0 1.0 C15 B:W20601 3.7 19.6 1.0 C18 B:W20601 3.7 19.7 1.0 C B:GLY443 3.7 18.1 1.0 N B:HIS411 3.8 20.0 1.0 CA B:HIS411 3.9 20.2 1.0 N B:GLY443 4.0 18.5 1.0 C7 B:W20601 4.1 21.3 1.0 C B:HIS411 4.2 19.6 1.0 C16 B:W20601 4.3 19.6 1.0 O17 B:W20601 4.3 20.0 1.0 CE2 B:PHE413 4.3 22.5 1.0 O28 B:W20601 4.3 20.1 1.0 CG B:HIS411 4.5 21.8 1.0 C19 B:W20601 4.5 20.0 1.0 CE B:MET157 4.7 22.3 1.0 C B:GLY410 4.7 20.1 1.0 N B:ILE444 4.8 18.2 1.0 OE2 B:GLU408 4.8 29.6 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Bacterial Prolyl-Trna Synthetase in Complex with Inhibitor Paa-38 within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:23.6 occ:1.00 F30 B:W20601 0.0 23.6 1.0 C3 B:W20601 1.3 21.1 1.0 C1 B:W20601 2.3 20.2 1.0 C4 B:W20601 2.4 21.2 1.0 N25 B:W20601 2.7 19.4 1.0 C8 B:W20601 2.7 22.1 1.0 C7 B:W20601 2.9 21.3 1.0 CA B:GLY445 3.0 17.8 1.0 O B:HOH929 3.1 18.0 1.0 C5 B:W20601 3.6 20.6 1.0 C2 B:W20601 3.6 20.1 1.0 N B:GLY445 3.8 17.7 1.0 CE2 B:PHE155 3.9 18.6 1.0 CD2 B:PHE155 4.0 18.4 1.0 C24 B:W20601 4.0 18.3 1.0 C9 B:W20601 4.0 22.7 1.0 NE B:ARG448 4.1 21.9 1.0 C6 B:W20601 4.1 20.7 1.0 CZ B:ARG448 4.1 22.6 1.0 C B:GLY445 4.2 18.0 1.0 C12 B:W20601 4.3 21.0 1.0 NH1 B:ARG448 4.3 23.5 1.0 CB B:ARG448 4.4 23.0 1.0 CD B:ARG448 4.4 22.5 1.0 CE B:MET157 4.5 22.3 1.0 NH2 B:ARG448 4.5 22.4 1.0 CZ B:PHE155 4.7 19.0 1.0 C B:ILE444 4.8 18.2 1.0 C22 B:W20601 4.8 19.5 1.0 O B:GLY445 4.8 18.5 1.0 CG B:PHE155 4.8 17.8 1.0 N23 B:W20601 4.9 18.7 1.0 O B:ILE444 5.0 17.8 1.0 N B:VAL446 5.0 17.8 1.0 O B:ILE156 5.0 19.3 1.0

Z.Luo, H.Zhou. Structure-Guided Fluorine Scanning Accelerates the Discovery of Potent and Selective Inhibitors Against Bacterial Prolyl-Trna Synthetase To Be Published.