Fluorine in PDB 8c41: High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin

The structure of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin, PDB code: 8c41 was solved by S.Najmudin, X.S.Pan, B.Wang, N.E.Cheyen, L.M.Fisher, M.R.Sanderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	115.01 / 2.39
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	157.471, 157.471, 212.339, 90, 90, 120
R / Rfree (%)	19.2 / 24.3

The structure of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin also contains other interesting chemical elements:

Magnesium	(Mg)	6 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Fluorine atom in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin (pdb code 8c41). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin, PDB code: 8c41:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin within 5.0Å range: probe atom residue distance (Å) B Occ F:F101 b:63.4 occ:1.00 F1 F:TE9101 0.0 63.4 1.0 C9 F:TE9101 1.4 62.4 1.0 C8 F:TE9101 2.3 60.3 1.0 C10 F:TE9101 2.4 62.4 1.0 H4 F:TE9101 2.5 60.6 1.0 H5 F:TE9101 2.7 61.7 1.0 N7 F:DA5 2.8 59.3 1.0 C2 F:DC4 2.8 73.0 1.0 N4 F:TE9101 2.8 62.6 1.0 C11 F:TE9101 2.9 61.7 1.0 N3 F:DC4 3.0 71.3 1.0 H6 F:TE9101 3.0 62.6 1.0 N1 F:DC4 3.0 77.8 1.0 H2' F:DC4 3.0 86.4 1.0 C8 F:DA5 3.1 61.8 1.0 H8 F:DA5 3.2 61.4 1.0 C4 F:DC4 3.3 69.5 1.0 C6 F:DC4 3.3 76.0 1.0 O2 F:DC4 3.3 69.4 1.0 C5 F:DA5 3.4 59.1 1.0 C5 F:DC4 3.5 71.5 1.0 C14 F:TE9101 3.6 61.9 1.0 C7 F:TE9101 3.6 59.0 1.0 C1' F:DC4 3.7 84.7 1.0 C2' F:DC4 3.7 87.5 1.0 H62 F:DA5 3.8 61.2 1.0 H22 H:DG1 3.8 80.5 1.0 H1' F:DC4 3.8 84.4 1.0 H6 F:DC4 3.9 75.0 1.0 N9 F:DA5 3.9 62.1 1.0 H1 H:DG1 4.1 79.4 1.0 C4 F:DA5 4.1 60.3 1.0 H5 F:DC4 4.1 72.2 1.0 N4 F:DC4 4.1 68.1 1.0 H2'' F:DC4 4.1 86.5 1.0 C15 F:TE9101 4.1 60.2 1.0 C6 F:DA5 4.2 59.6 1.0 C13 F:TE9101 4.2 62.9 1.0 N6 F:DA5 4.3 61.5 1.0 C12 F:TE9101 4.4 61.7 1.0 H41 F:DC4 4.4 68.4 1.0 H9 F:TE9101 4.5 62.0 1.0 N2 H:DG1 4.6 80.6 1.0 N1 H:DG1 4.6 79.4 1.0 H42 F:DC4 4.6 69.2 1.0 C6 F:TE9101 4.8 59.0 1.0 H10 F:TE9101 4.9 62.8 1.0 C2 H:DG1 4.9 81.1 1.0 H3' F:DC4 4.9 87.8 1.0 H7 F:TE9101 4.9 61.5 1.0 O4' F:DA5 4.9 61.6 1.0 O3 F:TE9101 4.9 57.4 1.0 C1' F:DA5 5.0 61.5 1.0 C3' F:DC4 5.0 88.4 1.0

Fluorine binding site 2 out of 6 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin within 5.0Å range: probe atom residue distance (Å) B Occ F:F101 b:61.3 occ:1.00 F2 F:TE9101 0.0 61.3 1.0 C16 F:TE9101 1.3 56.9 1.0 C17 F:TE9101 2.4 55.6 1.0 C2 F:TE9101 2.4 56.7 1.0 H2' E:DT7 2.4 50.5 1.0 H11 F:TE9101 2.5 55.6 1.0 C2 E:DT7 2.8 45.3 1.0 N1 E:DT7 2.8 45.2 1.0 H2'' E:DT7 2.9 50.9 1.0 H3 F:TE9101 2.9 60.0 1.0 N3 F:TE9101 2.9 58.8 1.0 C2' E:DT7 2.9 50.1 1.0 N3 E:DT7 3.2 46.1 1.0 C3 F:TE9101 3.2 59.6 1.0 O2 E:DT7 3.2 45.4 1.0 C6 E:DT7 3.2 45.6 1.0 C1' E:DT7 3.4 47.0 1.0 HA3 A:GLY457 3.4 55.8 1.0 N2 F:TE9101 3.6 53.6 1.0 C18 F:TE9101 3.6 53.8 1.0 H3 E:DT7 3.6 46.1 1.0 C4 E:DT7 3.6 45.9 1.0 C5 E:DT7 3.6 45.6 1.0 H6 E:DT7 3.7 45.7 1.0 H1' E:DT7 3.8 46.9 1.0 C1 F:TE9101 4.1 53.5 1.0 C15 F:TE9101 4.1 60.2 1.0 O5' H:DG1 4.2 97.3 1.0 CL1 F:TE9101 4.2 65.9 1.0 CA A:GLY457 4.2 56.5 1.0 HA2 A:GLY457 4.3 55.9 1.0 OP1 H:DG1 4.3 99.6 1.0 C3' E:DT7 4.4 50.9 1.0 C4 F:TE9101 4.4 60.0 1.0 O4 E:DT7 4.5 44.7 1.0 H3' E:DT7 4.6 52.0 1.0 H73 E:DT7 4.6 46.7 1.0 O4' E:DT7 4.6 46.5 1.0 C14 F:TE9101 4.6 61.9 1.0 N A:GLY457 4.6 55.4 1.0 N1 F:DA5 4.7 59.9 1.0 F3 F:TE9101 4.7 54.4 1.0 H2 F:DA5 4.7 59.8 1.0 C7 E:DT7 4.7 45.7 1.0 HO3' E:DT7 4.9 72.2 0.0 H A:LYS458 4.9 53.6 1.0 O A:ARG456 4.9 53.0 1.0 P H:DG1 5.0 97.7 1.0 C A:ARG456 5.0 56.5 1.0 O4' H:DG1 5.0 95.3 1.0 O2 F:TE9101 5.0 59.1 1.0

Fluorine binding site 3 out of 6 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin within 5.0Å range: probe atom residue distance (Å) B Occ F:F101 b:54.4 occ:1.00 F3 F:TE9101 0.0 54.4 1.0 C18 F:TE9101 1.3 53.8 1.0 C17 F:TE9101 2.4 55.6 1.0 C1 F:TE9101 2.4 53.5 1.0 H11 F:TE9101 2.6 55.6 1.0 H1 F:TE9101 2.6 54.2 1.0 HA2 A:GLY434 2.6 57.0 1.0 H A:ASP435 2.6 54.2 1.0 HA A:ARG456 2.7 57.9 1.0 N1 F:TE9101 2.8 53.1 1.0 H4' H:DG1 3.1 97.0 1.0 N A:ASP435 3.5 54.2 1.0 HD2 A:ARG456 3.5 62.0 1.0 OD2 A:ASP435 3.5 57.5 1.0 H A:GLY457 3.5 56.0 1.0 OP2 H:DG1 3.5 93.8 1.0 CA A:GLY434 3.6 58.0 1.0 H2 F:TE9101 3.6 53.3 1.0 N2 F:TE9101 3.6 53.6 1.0 C16 F:TE9101 3.6 56.9 1.0 CA A:ARG456 3.6 58.0 1.0 O A:LEU455 3.8 55.8 1.0 HD3 A:ARG456 3.8 62.3 1.0 N A:GLY457 3.9 55.4 1.0 OP1 H:DG1 4.0 99.6 1.0 HA3 A:GLY434 4.0 57.0 1.0 C A:GLY434 4.0 55.4 1.0 C4' H:DG1 4.0 95.4 1.0 P H:DG1 4.0 97.7 1.0 C A:ARG456 4.1 56.5 1.0 HB2 A:ASP435 4.1 54.2 1.0 O5' H:DG1 4.1 97.3 1.0 C2 F:TE9101 4.1 56.7 1.0 CG A:ASP435 4.1 55.6 1.0 CD A:ARG456 4.1 62.5 1.0 O4' H:DG1 4.2 95.3 1.0 N A:ARG456 4.4 58.2 1.0 C A:LEU455 4.4 58.2 1.0 CB A:ASP435 4.4 54.2 1.0 N A:GLY434 4.5 57.4 1.0 H A:GLY434 4.5 58.1 1.0 CA A:ASP435 4.5 53.9 1.0 HB3 A:ARG456 4.6 59.4 1.0 CB A:ARG456 4.6 59.5 1.0 C5' H:DG1 4.7 93.8 1.0 F2 F:TE9101 4.7 61.3 1.0 H A:SER436 4.8 54.3 1.0 CL1 F:TE9101 4.8 65.9 1.0 O3' H:DG1 4.8 104.5 1.0 HA2 A:GLY457 4.9 55.9 1.0 CA A:GLY457 4.9 56.5 1.0 O A:ARG456 4.9 53.0 1.0 HA3 A:GLY457 4.9 55.8 1.0 CG A:ARG456 5.0 61.5 1.0 OD1 A:ASP435 5.0 56.2 1.0

Fluorine binding site 4 out of 6 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin within 5.0Å range: probe atom residue distance (Å) B Occ H:F101 b:52.6 occ:1.00 F1 H:TE9101 0.0 52.6 1.0 C9 H:TE9101 1.3 54.2 1.0 C8 H:TE9101 2.3 54.4 1.0 C10 H:TE9101 2.4 56.4 1.0 H4 H:TE9101 2.5 54.4 1.0 H5 H:TE9101 2.7 58.5 1.0 N4 H:TE9101 2.8 59.3 1.0 N7 H:DA5 2.9 55.1 1.0 C11 H:TE9101 2.9 58.2 1.0 C2 H:DT4 2.9 86.9 1.0 H2' H:DT4 2.9 81.7 1.0 H6 H:TE9101 2.9 59.4 1.0 N1 H:DT4 3.0 86.1 1.0 N3 H:DT4 3.0 86.8 1.0 C8 H:DA5 3.2 56.9 1.0 C6 H:DT4 3.2 85.3 1.0 C4 H:DT4 3.3 85.3 1.0 H8 H:DA5 3.3 56.8 1.0 C5 H:DT4 3.4 85.3 1.0 C5 H:DA5 3.5 55.2 1.0 H3 H:DT4 3.5 87.1 1.0 O2 H:DT4 3.5 82.3 1.0 C7 H:TE9101 3.6 54.0 1.0 C14 H:TE9101 3.6 56.8 1.0 C2' H:DT4 3.7 82.4 1.0 C1' H:DT4 3.7 84.3 1.0 H6 H:DT4 3.7 85.1 1.0 N9 H:DA5 3.9 58.2 1.0 H1' H:DT4 4.0 84.0 1.0 C4 H:DA5 4.1 56.3 1.0 H2'' H:DT4 4.1 81.5 1.0 O4 H:DT4 4.1 88.2 1.0 C15 H:TE9101 4.1 55.0 1.0 C6 H:DA5 4.2 55.1 1.0 C13 H:TE9101 4.2 61.2 1.0 C12 H:TE9101 4.4 59.7 1.0 N6 H:DA5 4.4 56.2 1.0 H73 H:DT4 4.4 83.9 1.0 C7 H:DT4 4.4 83.4 1.0 N1 F:DA1 4.4 78.1 1.0 H62 H:DA5 4.5 55.8 1.0 H9 H:TE9101 4.6 60.0 1.0 H71 H:DT4 4.6 83.7 1.0 H61 H:DA5 4.7 56.2 1.0 C6 H:TE9101 4.8 53.2 1.0 H2 F:DA1 4.8 78.0 1.0 H3' H:DT4 4.8 80.2 1.0 O4' H:DA5 4.8 59.3 1.0 H10 H:TE9101 4.9 61.0 1.0 C3' H:DT4 4.9 79.9 1.0 H7 H:TE9101 4.9 59.0 1.0 O3 H:TE9101 4.9 50.2 1.0 C1' H:DA5 4.9 58.6 1.0 C2 F:DA1 4.9 77.5 1.0

Fluorine binding site 5 out of 6 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin within 5.0Å range: probe atom residue distance (Å) B Occ H:F101 b:52.4 occ:1.00 F2 H:TE9101 0.0 52.4 1.0 C16 H:TE9101 1.4 51.7 1.0 C17 H:TE9101 2.4 52.4 1.0 C2 H:TE9101 2.4 52.0 1.0 H2' G:DT7 2.5 44.6 1.0 H11 H:TE9101 2.5 52.8 1.0 H3 H:TE9101 2.8 55.3 1.0 N1 G:DT7 2.8 40.6 1.0 H2'' G:DT7 2.9 44.4 1.0 C2 G:DT7 2.9 40.2 1.0 N3 H:TE9101 2.9 53.5 1.0 C2' G:DT7 3.0 43.6 1.0 C3 H:TE9101 3.1 54.6 1.0 C6 G:DT7 3.1 40.7 1.0 N3 G:DT7 3.2 40.0 1.0 C1' G:DT7 3.4 41.0 1.0 O2 G:DT7 3.4 40.6 1.0 C5 G:DT7 3.5 40.5 1.0 C4 G:DT7 3.6 40.1 1.0 H6 G:DT7 3.6 41.1 1.0 N2 H:TE9101 3.6 50.7 1.0 C18 H:TE9101 3.6 52.7 1.0 HA3 B:GLY457 3.7 57.8 1.0 H3 G:DT7 3.7 40.2 1.0 H1' G:DT7 3.8 40.6 1.0 O A:HOH1702 3.8 37.0 1.0 HA2 B:GLY457 4.0 57.7 1.0 C1 H:TE9101 4.1 51.2 1.0 C15 H:TE9101 4.1 55.0 1.0 OP1 F:DA1 4.2 86.7 1.0 CA B:GLY457 4.3 58.0 1.0 O5' F:DA1 4.3 89.2 1.0 C4 H:TE9101 4.4 55.1 1.0 CL1 H:TE9101 4.4 62.0 1.0 H73 G:DT7 4.4 42.4 1.0 O4 G:DT7 4.4 40.2 1.0 C3' G:DT7 4.5 43.7 1.0 O F:HOH204 4.5 24.0 1.0 C7 G:DT7 4.6 41.0 1.0 O4' G:DT7 4.7 40.3 1.0 H3' G:DT7 4.7 45.1 1.0 H2 H:DA5 4.7 56.0 1.0 C14 H:TE9101 4.8 56.8 1.0 F3 H:TE9101 4.8 53.6 1.0 O1 H:TE9101 4.8 60.4 1.0 N B:GLY457 4.8 60.6 1.0 N1 H:DA5 4.8 54.7 1.0 H71 G:DT7 5.0 41.0 1.0 HO3' G:DT7 5.0 62.4 0.0

Fluorine binding site 6 out of 6 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin within 5.0Å range: probe atom residue distance (Å) B Occ H:F101 b:53.6 occ:1.00 F3 H:TE9101 0.0 53.6 1.0 C18 H:TE9101 1.4 52.7 1.0 C1 H:TE9101 2.4 51.2 1.0 C17 H:TE9101 2.4 52.4 1.0 HA2 B:GLY434 2.5 47.6 1.0 H B:ASP435 2.5 48.3 1.0 H1 H:TE9101 2.5 51.5 1.0 H11 H:TE9101 2.6 52.8 1.0 N1 H:TE9101 2.8 50.6 1.0 HA B:ARG456 2.9 66.2 1.0 H4' F:DA1 3.2 90.3 1.0 N B:ASP435 3.3 48.5 1.0 CA B:GLY434 3.3 47.7 1.0 OP2 F:DA1 3.4 84.2 1.0 HA3 B:GLY434 3.5 47.6 1.0 O B:LEU455 3.5 58.2 1.0 H2 H:TE9101 3.6 51.3 1.0 N2 H:TE9101 3.6 50.7 1.0 C16 H:TE9101 3.6 51.7 1.0 O F:HOH204 3.7 24.0 1.0 H B:GLY457 3.7 60.6 1.0 OD2 B:ASP435 3.7 55.2 1.0 OP1 F:DA1 3.8 86.7 1.0 HD3 B:ARG456 3.8 79.5 1.0 CA B:ARG456 3.8 65.9 1.0 C B:GLY434 3.8 47.8 1.0 HB2 B:ASP435 3.9 49.7 1.0 P F:DA1 3.9 88.0 1.0 N B:GLY457 4.0 60.6 1.0 O5' F:DA1 4.0 89.2 1.0 C4' F:DA1 4.1 88.9 1.0 O4' F:DA1 4.1 89.7 1.0 C2 H:TE9101 4.1 52.0 1.0 C B:ARG456 4.2 63.5 1.0 HD2 B:ARG456 4.3 79.4 1.0 CG B:ASP435 4.3 52.0 1.0 C B:LEU455 4.4 60.7 1.0 CB B:ASP435 4.4 49.3 1.0 CA B:ASP435 4.4 48.7 1.0 N B:GLY434 4.5 47.3 1.0 CD B:ARG456 4.5 79.8 1.0 N B:ARG456 4.5 62.9 1.0 H B:GLY434 4.6 48.1 1.0 HB3 B:ARG456 4.6 73.0 1.0 HA2 B:GLY457 4.7 57.7 1.0 C5' F:DA1 4.7 87.4 1.0 H B:SER436 4.7 46.9 1.0 F2 H:TE9101 4.8 52.4 1.0 CB B:ARG456 4.8 74.4 1.0 CA B:GLY457 4.9 58.0 1.0 O3' F:DA1 4.9 97.2 1.0 CL1 H:TE9101 4.9 62.0 1.0 HA B:ASP435 5.0 48.8 1.0

S.Najmudin, X.S.Pan, B.Wang, N.E.Cheyen, L.M.Fisher, M.R.Sanderson. The Nature of the Molecular Interactions at High Resolution of the Streptococcus Pneumoniae Topoisomerase IV-Dna Complex with the Novel Fluoroquinolone Delafloxacin. To Be Published.