Fluorine in PDB 6kvq: S. Aureus Ftsz in Complex with Bofp (Compound 3)

The structure of S. Aureus Ftsz in Complex with Bofp (Compound 3), PDB code: 6kvq was solved by E.Ferrer-Gonzalez, J.Fujita, T.Yoshizawa, J.M.Nelson, A.J.Pilch, E.Hillman, M.Ozawa, N.Kuroda, A.K.Parhi, E.J.Lavoie, H.Matsumura, D.S.Pilch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.09 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	72.268, 49.686, 88.592, 90.00, 111.24, 90.00
R / Rfree (%)	19 / 21.4

The structure of S. Aureus Ftsz in Complex with Bofp (Compound 3) also contains other interesting chemical elements:

Bromine	(Br)	1 atom
Calcium	(Ca)	1 atom

The binding sites of Fluorine atom in the S. Aureus Ftsz in Complex with Bofp (Compound 3) (pdb code 6kvq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 7 binding sites of Fluorine where determined in the S. Aureus Ftsz in Complex with Bofp (Compound 3), PDB code: 6kvq:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Fluorine binding site 1 out of 7 in the S. Aureus Ftsz in Complex with Bofp (Compound 3)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of S. Aureus Ftsz in Complex with Bofp (Compound 3) within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:31.9 occ:0.60 F26 A:DVX403 0.0 31.9 0.6 C25 A:DVX403 1.3 28.0 0.6 C27 A:DVX403 2.3 30.7 0.6 C24 A:DVX403 2.4 17.2 0.6 O30 A:DVX403 2.7 29.9 0.6 C28 A:DVX403 2.8 30.2 0.6 CG2 A:VAL297 2.8 27.1 1.0 CB A:VAL203 3.2 27.0 1.0 CG1 A:VAL203 3.3 26.7 1.0 O A:VAL203 3.3 24.7 1.0 C31 A:DVX403 3.6 22.8 0.6 C23 A:DVX403 3.6 25.4 0.6 C A:VAL203 3.8 24.5 1.0 CA A:CA402 3.9 20.1 0.5 N29 A:DVX403 3.9 15.4 0.6 CB A:VAL297 4.0 28.1 1.0 N A:GLY205 4.0 24.6 1.0 CG1 A:VAL297 4.0 30.0 1.0 O A:ASP199 4.0 28.9 1.0 CA A:VAL203 4.1 24.8 1.0 CA A:GLY205 4.1 22.7 1.0 C22 A:DVX403 4.1 29.8 0.6 O A:HOH597 4.2 40.7 1.0 CG2 A:VAL203 4.4 29.2 1.0 O A:LEU200 4.6 27.5 1.0 C A:SER204 4.6 23.9 1.0 CA A:LEU200 4.6 27.6 1.0 N A:SER204 4.6 25.1 1.0 N A:VAL203 4.7 26.5 1.0 F32 A:DVX403 4.7 24.1 0.6 C A:ASP199 4.8 28.1 1.0 OD1 A:ASN208 4.9 23.7 1.0

Fluorine binding site 2 out of 7 in the S. Aureus Ftsz in Complex with Bofp (Compound 3)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of S. Aureus Ftsz in Complex with Bofp (Compound 3) within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:24.1 occ:0.60 F32 A:DVX403 0.0 24.1 0.6 C31 A:DVX403 1.3 22.8 0.6 C22 A:DVX403 2.3 29.8 0.6 C27 A:DVX403 2.4 30.7 0.6 O21 A:DVX403 2.6 28.6 0.6 OD1 A:ASN263 2.9 27.4 1.0 C28 A:DVX403 2.9 30.2 0.6 CG A:ASN263 3.0 32.9 1.0 N29 A:DVX403 3.1 15.4 0.6 CB A:ASN263 3.2 27.1 1.0 CD1 A:LEU209 3.2 25.4 1.0 CD1 A:LEU200 3.5 27.4 1.0 C23 A:DVX403 3.6 25.4 0.6 C25 A:DVX403 3.6 28.0 0.6 CG A:LEU200 3.6 34.6 1.0 CB A:LEU209 3.7 23.2 1.0 CG A:LEU209 3.8 21.3 1.0 O30 A:DVX403 3.8 29.9 0.6 ND2 A:ASN263 3.9 33.5 1.0 C20 A:DVX403 4.0 20.9 0.6 CB A:LEU200 4.0 32.0 1.0 C24 A:DVX403 4.1 17.2 0.6 O48 A:DVX403 4.2 29.0 0.6 C33 A:DVX403 4.5 25.6 0.6 CA A:LEU200 4.5 27.6 1.0 CA A:ASN263 4.5 22.4 1.0 CA A:LEU209 4.7 20.3 1.0 N A:LEU209 4.7 19.5 1.0 C19 A:DVX403 4.7 23.2 0.6 F26 A:DVX403 4.7 31.9 0.6 O A:LEU209 4.8 21.5 1.0

Fluorine binding site 3 out of 7 in the S. Aureus Ftsz in Complex with Bofp (Compound 3)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of S. Aureus Ftsz in Complex with Bofp (Compound 3) within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:33.9 occ:0.60 F41 A:DVX403 0.0 33.9 0.6 C40 A:DVX403 1.3 34.9 0.6 F42 A:DVX403 2.0 29.5 0.6 F43 A:DVX403 2.2 36.5 0.6 C39 A:DVX403 2.5 34.8 0.6 CE A:MET218 2.7 30.6 1.0 C44 A:DVX403 3.0 39.3 0.6 CD1 A:ILE311 3.3 46.3 1.0 SD A:MET218 3.5 28.9 1.0 C38 A:DVX403 3.7 28.4 0.6 CB A:MET226 3.9 49.2 1.0 CG1 A:ILE311 4.1 37.8 1.0 CG A:MET226 4.1 66.2 1.0 CD1 A:ILE162 4.1 30.7 1.0 C45 A:DVX403 4.4 35.5 0.6 CG1 A:VAL129 4.5 21.8 1.0 CB A:ILE311 4.6 37.6 1.0 CD1 A:ILE197 4.7 39.1 1.0 CG2 A:VAL129 4.8 25.0 1.0 C37 A:DVX403 4.9 27.9 0.6 CG A:MET218 4.9 24.1 1.0 CE2 A:PHE100 5.0 27.8 1.0

Fluorine binding site 4 out of 7 in the S. Aureus Ftsz in Complex with Bofp (Compound 3)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of S. Aureus Ftsz in Complex with Bofp (Compound 3) within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:29.5 occ:0.60 F42 A:DVX403 0.0 29.5 0.6 C40 A:DVX403 1.3 34.9 0.6 F41 A:DVX403 2.0 33.9 0.6 F43 A:DVX403 2.3 36.5 0.6 C39 A:DVX403 2.4 34.8 0.6 C38 A:DVX403 2.9 28.4 0.6 CG A:MET226 3.2 66.2 1.0 CB A:MET226 3.4 49.2 1.0 C44 A:DVX403 3.7 39.3 0.6 CD1 A:ILE162 4.0 30.7 1.0 CA A:GLY193 4.0 31.7 1.0 CE2 A:PHE100 4.2 27.8 1.0 SD A:MET226 4.3 85.1 1.0 C37 A:DVX403 4.3 27.9 0.6 C A:GLY193 4.4 32.9 1.0 CE A:MET218 4.6 30.6 1.0 O A:GLY193 4.6 31.7 1.0 C45 A:DVX403 4.8 35.5 0.6 CD1 A:ILE197 4.8 39.1 1.0 CD1 A:ILE311 4.9 46.3 1.0 CA A:MET226 4.9 30.7 1.0 CG1 A:VAL129 4.9 21.8 1.0

Fluorine binding site 5 out of 7 in the S. Aureus Ftsz in Complex with Bofp (Compound 3)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of S. Aureus Ftsz in Complex with Bofp (Compound 3) within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:36.5 occ:0.60 F43 A:DVX403 0.0 36.5 0.6 C40 A:DVX403 1.4 34.9 0.6 F41 A:DVX403 2.2 33.9 0.6 F42 A:DVX403 2.3 29.5 0.6 C39 A:DVX403 2.3 34.8 0.6 CD1 A:ILE197 3.0 39.1 1.0 C38 A:DVX403 3.0 28.4 0.6 CE2 A:PHE100 3.3 27.8 1.0 C44 A:DVX403 3.3 39.3 0.6 CE A:MET218 3.6 30.6 1.0 CZ A:PHE100 3.7 28.0 1.0 SD A:MET218 3.7 28.9 1.0 CE A:MET98 3.8 24.6 1.0 CG1 A:ILE197 4.2 33.0 1.0 C37 A:DVX403 4.3 27.9 0.6 CG2 A:VAL129 4.4 25.0 1.0 CD2 A:PHE100 4.4 22.2 1.0 C45 A:DVX403 4.5 35.5 0.6 CG1 A:VAL129 4.6 21.8 1.0 O A:GLY193 4.6 31.7 1.0 C36 A:DVX403 4.9 30.7 0.6 CB A:VAL129 4.9 20.8 1.0 C A:GLY193 4.9 32.9 1.0

Fluorine binding site 6 out of 7 in the S. Aureus Ftsz in Complex with Bofp (Compound 3)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of S. Aureus Ftsz in Complex with Bofp (Compound 3) within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:46.7 occ:0.60 F51 A:DVX403 0.0 46.7 0.6 B50 A:DVX403 1.6 39.8 0.6 N06 A:DVX403 2.5 41.8 0.6 N49 A:DVX403 2.5 32.7 0.6 F52 A:DVX403 2.6 40.0 0.6 C13 A:DVX403 3.0 37.3 0.6 C14 A:DVX403 3.1 39.4 0.6 C04 A:DVX403 3.1 40.6 0.6 C05 A:DVX403 3.3 39.3 0.6 C07 A:DVX403 3.5 40.1 0.6 C09 A:DVX403 3.6 31.4 0.6 CG2 A:VAL307 4.1 31.6 1.0 CG1 A:VAL307 4.1 32.6 1.0 C15 A:DVX403 4.2 32.1 0.6 C08 A:DVX403 4.2 34.6 0.6 C12 A:DVX403 4.3 34.2 0.6 C03 A:DVX403 4.5 42.2 0.6 C10 A:DVX403 4.5 26.1 0.6 CB A:VAL307 4.6 32.8 1.0 CD1 A:ILE228 4.6 48.6 1.0 O17 A:DVX403 4.7 30.0 0.6 C02 A:DVX403 4.7 40.6 0.6 CG2 A:VAL230 4.8 38.6 1.0 C16 A:DVX403 4.9 27.1 0.6

Fluorine binding site 7 out of 7 in the S. Aureus Ftsz in Complex with Bofp (Compound 3)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of S. Aureus Ftsz in Complex with Bofp (Compound 3) within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:40.0 occ:0.60 F52 A:DVX403 0.0 40.0 0.6 B50 A:DVX403 1.6 39.8 0.6 N06 A:DVX403 2.4 41.8 0.6 N49 A:DVX403 2.5 32.7 0.6 F51 A:DVX403 2.6 46.7 0.6 CG2 A:VAL230 2.9 38.6 1.0 C04 A:DVX403 3.0 40.6 0.6 C13 A:DVX403 3.1 37.3 0.6 C14 A:DVX403 3.2 39.4 0.6 C05 A:DVX403 3.2 39.3 0.6 CD1 A:ILE228 3.2 48.6 1.0 C07 A:DVX403 3.4 40.1 0.6 CG1 A:VAL307 3.6 32.6 1.0 C09 A:DVX403 3.6 31.4 0.6 CG1 A:ILE228 3.7 44.7 1.0 C08 A:DVX403 4.1 34.6 0.6 CG2 A:VAL307 4.1 31.6 1.0 C12 A:DVX403 4.3 34.2 0.6 C03 A:DVX403 4.3 42.2 0.6 CB A:VAL230 4.4 41.0 1.0 CB A:VAL307 4.5 32.8 1.0 C10 A:DVX403 4.6 26.1 0.6 C02 A:DVX403 4.6 40.6 0.6 C15 A:DVX403 4.7 32.1 0.6 CG1 A:VAL230 5.0 42.5 1.0 CB A:ILE228 5.0 39.5 1.0

E.Ferrer-Gonzalez, J.Fujita, T.Yoshizawa, J.M.Nelson, A.J.Pilch, E.Hillman, M.Ozawa, N.Kuroda, H.M.Al-Tameemi, J.M.Boyd, E.J.Lavoie, H.Matsumura, D.S.Pilch. Structure-Guided Design of A Fluorescent Probe For the Visualization of Ftsz in Clinically Important Gram-Positive and Gram-Negative Bacterial Pathogens. Sci Rep V. 9 20092 2019.
ISSN: ESSN 2045-2322
PubMed: 31882782
DOI: 10.1038/S41598-019-56557-X