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Fluorine in PDB 8qmc: High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin

Enzymatic activity of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin

All present enzymatic activity of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin:
5.6.2.2;

Protein crystallography data

The structure of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin, PDB code: 8qmc was solved by S.Najmudin, X.S.Pan, B.Wang, N.E.Chayen, 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) 64.86 / 2.40
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.14, 157.14, 211.636, 90, 90, 120
R / Rfree (%) 24.1 / 29.9

Other elements in 8qmc:

The structure of High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin (pdb code 8qmc). 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-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin, PDB code: 8qmc:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8qmc

Go back to Fluorine Binding Sites List in 8qmc
Fluorine binding site 1 out of 6 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and 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-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F101

b:29.0
occ:1.00
F1 F:TE9101 0.0 29.0 1.0
C9 F:TE9101 1.4 27.5 1.0
C8 F:TE9101 2.3 27.0 1.0
C10 F:TE9101 2.4 26.8 1.0
H4 F:TE9101 2.5 27.9 1.0
H5 F:TE9101 2.7 29.8 1.0
H6 F:TE9101 2.7 29.8 1.0
C2 F:DT4 2.8 39.3 1.0
N4 F:TE9101 2.8 27.5 1.0
C11 F:TE9101 2.8 29.2 1.0
N3 F:DT4 2.8 39.1 1.0
N7 F:DA5 2.8 24.7 1.0
C8 F:DA5 2.9 25.9 1.0
H8 F:DA5 2.9 27.0 1.0
N1 F:DT4 3.1 40.5 1.0
H2' F:DT4 3.1 40.1 1.0
H3 F:DT4 3.2 38.3 1.0
C4 F:DT4 3.2 39.5 1.0
O2 F:DT4 3.3 38.3 1.0
C6 F:DT4 3.3 41.4 1.0
C5 F:DT4 3.5 40.9 1.0
C5 F:DA5 3.5 23.5 1.0
N9 F:DA5 3.6 25.5 1.0
C14 F:TE9101 3.6 25.5 1.0
C7 F:TE9101 3.6 25.6 1.0
C1' F:DT4 3.9 41.6 1.0
C2' F:DT4 3.9 41.3 1.0
O4 F:DT4 3.9 38.8 1.0
C4 F:DA5 4.0 23.8 1.0
H6 F:DT4 4.0 42.2 1.0
H1' F:DT4 4.0 40.8 1.0
C15 F:TE9101 4.1 24.7 1.0
C13 F:TE9101 4.2 27.5 1.0
H62 F:DA5 4.3 23.3 1.0
N1 H:DA1 4.3 53.8 1.0
C12 F:TE9101 4.3 29.0 1.0
H2'' F:DT4 4.4 41.0 1.0
C6 F:DA5 4.4 22.4 1.0
H73 F:DT4 4.4 41.0 1.0
H2 H:DA1 4.5 55.5 1.0
C1' F:DA5 4.6 26.6 1.0
C7 F:DT4 4.6 41.9 1.0
H9 F:TE9101 4.6 27.2 1.0
O4' F:DA5 4.6 28.9 1.0
H1' F:DA5 4.6 26.3 1.0
C2 H:DA1 4.7 55.0 1.0
N6 F:DA5 4.7 22.8 1.0
H3' F:DT4 4.8 43.0 1.0
C6 F:TE9101 4.8 26.0 1.0
H7 F:TE9101 4.8 29.5 1.0
H10 F:TE9101 4.8 26.9 1.0
O3 F:TE9101 4.9 27.0 1.0
C3' F:DT4 5.0 43.0 1.0

Fluorine binding site 2 out of 6 in 8qmc

Go back to Fluorine Binding Sites List in 8qmc
Fluorine binding site 2 out of 6 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and 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-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F101

b:23.2
occ:1.00
F2 F:TE9101 0.0 23.2 1.0
C16 F:TE9101 1.3 22.9 1.0
H2' E:DT15 2.2 22.3 1.0
C17 F:TE9101 2.3 22.8 1.0
C2 F:TE9101 2.4 23.2 1.0
H11 F:TE9101 2.5 22.6 1.0
H3 F:TE9101 2.8 23.7 1.0
N1 E:DT15 2.8 19.7 1.0
C2 E:DT15 2.9 21.1 1.0
C2' E:DT15 2.9 21.2 1.0
N3 F:TE9101 3.0 23.7 1.0
H2'' E:DT15 3.0 22.4 1.0
C6 E:DT15 3.2 19.5 1.0
C3 F:TE9101 3.2 24.0 1.0
N3 E:DT15 3.2 21.7 1.0
O2 E:DT15 3.4 22.0 1.0
C1' E:DT15 3.4 19.3 1.0
C5 E:DT15 3.5 20.1 1.0
C4 E:DT15 3.6 21.1 1.0
N2 F:TE9101 3.6 23.7 1.0
C18 F:TE9101 3.6 23.2 1.0
H6 E:DT15 3.6 18.9 1.0
HA3 A:GLY457 3.6 26.6 1.0
H3 E:DT15 3.7 22.7 1.0
OP1 H:DA1 3.7 61.3 1.0
H1' E:DT15 3.9 19.4 1.0
C1 F:TE9101 4.1 23.6 1.0
C15 F:TE9101 4.2 24.7 1.0
C3' E:DT15 4.3 20.2 1.0
CL1 F:TE9101 4.3 25.2 1.0
H3' E:DT15 4.3 20.9 1.0
C4 F:TE9101 4.4 25.1 1.0
O4 E:DT15 4.4 21.7 1.0
CA A:GLY457 4.5 27.3 1.0
O4' E:DT15 4.6 17.6 1.0
HA2 A:GLY457 4.6 27.3 1.0
C7 E:DT15 4.6 20.0 1.0
H73 E:DT15 4.7 21.7 1.0
F3 F:TE9101 4.7 23.9 1.0
C14 F:TE9101 4.7 25.5 1.0
H71 E:DT15 4.7 19.9 1.0
O2 F:TE9101 4.7 24.6 1.0
N1 F:DA5 4.8 21.2 1.0
N A:GLY457 4.8 28.0 1.0
O5' H:DA1 4.9 60.4 1.0
O A:ARG456 4.9 27.4 1.0
HO3' E:DT15 4.9 30.0 0.0
P H:DA1 4.9 61.5 1.0

Fluorine binding site 3 out of 6 in 8qmc

Go back to Fluorine Binding Sites List in 8qmc
Fluorine binding site 3 out of 6 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and 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-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F101

b:23.9
occ:1.00
F3 F:TE9101 0.0 23.9 1.0
C18 F:TE9101 1.4 23.2 1.0
HA2 A:GLY434 2.4 31.3 1.0
C17 F:TE9101 2.4 22.8 1.0
C1 F:TE9101 2.4 23.6 1.0
H1 F:TE9101 2.5 24.1 1.0
HA A:ARG456 2.5 29.2 1.0
H11 F:TE9101 2.6 22.6 1.0
N1 F:TE9101 2.8 24.0 1.0
H A:ASP435 2.9 29.9 1.0
CA A:GLY434 3.2 31.8 1.0
H4' H:DA1 3.2 62.2 1.0
OP2 H:DA1 3.3 63.1 1.0
HA3 A:GLY434 3.3 31.0 1.0
O5' H:DA1 3.4 60.4 1.0
CA A:ARG456 3.5 29.2 1.0
H A:GLY457 3.5 28.5 1.0
H5' H:DA1 3.6 62.6 1.0
OD2 A:ASP435 3.6 30.4 1.0
N2 F:TE9101 3.6 23.7 1.0
N A:ASP435 3.6 30.5 1.0
C16 F:TE9101 3.6 22.9 1.0
H2 F:TE9101 3.6 24.5 1.0
O A:LEU455 3.7 30.0 1.0
P H:DA1 3.7 61.5 1.0
C5' H:DA1 3.8 61.4 1.0
N A:GLY457 3.8 28.0 1.0
C A:ARG456 3.8 28.1 1.0
C4' H:DA1 3.8 61.2 1.0
OP1 H:DA1 3.9 61.3 1.0
C A:GLY434 4.0 31.6 1.0
O4' H:DA1 4.1 60.1 1.0
C2 F:TE9101 4.1 23.2 1.0
HB3 A:ARG456 4.1 28.8 1.0
HG2 A:ARG456 4.1 31.3 1.0
CB A:ARG456 4.3 29.4 1.0
HD3 A:ARG456 4.3 30.4 1.0
N A:GLY434 4.3 32.9 1.0
N A:ARG456 4.4 30.4 1.0
C A:LEU455 4.4 31.1 1.0
CG A:ASP435 4.4 31.3 1.0
H A:GLY434 4.4 33.2 1.0
CG A:ARG456 4.6 31.0 1.0
O A:ARG456 4.6 27.4 1.0
CL1 F:TE9101 4.7 25.2 1.0
HB2 A:ASP435 4.7 30.3 1.0
F2 F:TE9101 4.7 23.2 1.0
H5'' H:DA1 4.8 60.6 1.0
H A:SER436 4.8 27.8 1.0
CA A:GLY457 4.8 27.3 1.0
HA3 A:GLY457 4.8 26.6 1.0
HE A:ARG456 4.8 32.5 1.0
CA A:ASP435 4.8 31.0 1.0
CD A:ARG456 4.9 31.2 1.0
HA2 A:GLY457 4.9 27.3 1.0
CB A:ASP435 4.9 31.0 1.0

Fluorine binding site 4 out of 6 in 8qmc

Go back to Fluorine Binding Sites List in 8qmc
Fluorine binding site 4 out of 6 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and 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-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F101

b:45.4
occ:1.00
F1 H:TE9101 0.0 45.4 1.0
C9 H:TE9101 1.4 44.5 1.0
C8 H:TE9101 2.3 44.4 1.0
C10 H:TE9101 2.4 43.8 1.0
H4 H:TE9101 2.5 45.2 1.0
H5 H:TE9101 2.7 45.8 1.0
N7 H:DG5 2.8 46.0 1.0
N4 H:TE9101 2.9 44.2 1.0
C2 H:DC4 2.9 54.6 1.0
C11 H:TE9101 2.9 45.2 1.0
H6 H:TE9101 2.9 45.6 1.0
C8 H:DG5 2.9 46.5 1.0
N3 H:DC4 2.9 54.7 1.0
H8 H:DG5 3.1 47.3 1.0
H2' H:DC4 3.1 54.6 1.0
N1 H:DC4 3.2 55.4 1.0
C4 H:DC4 3.3 55.3 1.0
O2 H:DC4 3.4 53.4 1.0
C5 H:DG5 3.4 44.9 1.0
C6 H:DC4 3.5 56.2 1.0
C5 H:DC4 3.5 56.2 1.0
N9 H:DG5 3.6 45.7 1.0
C7 H:TE9101 3.6 43.3 1.0
C14 H:TE9101 3.6 42.7 1.0
C4 H:DG5 3.8 44.6 1.0
C2' H:DC4 3.9 55.0 1.0
C1' H:DC4 4.0 55.6 1.0
N4 H:DC4 4.0 55.2 1.0
H6 H:DC4 4.1 56.9 1.0
C15 H:TE9101 4.1 42.4 1.0
H1 F:DG1 4.2 43.3 1.0
H5 H:DC4 4.2 56.9 1.0
H42 H:DC4 4.2 54.6 1.0
C6 H:DG5 4.2 44.2 1.0
H1' H:DC4 4.3 55.0 1.0
C13 H:TE9101 4.3 43.5 1.0
H2'' H:DC4 4.3 54.4 1.0
C12 H:TE9101 4.4 44.4 1.0
O6 H:DG5 4.6 44.7 1.0
C1' H:DG5 4.6 45.5 1.0
N1 F:DG1 4.6 43.7 1.0
H1' H:DG5 4.6 44.9 1.0
H41 H:DC4 4.6 55.9 1.0
N2 F:DG1 4.6 46.8 1.0
H22 F:DG1 4.6 45.8 1.0
H9 H:TE9101 4.7 43.3 1.0
H21 F:DG1 4.7 48.6 1.0
O4' H:DG5 4.7 46.6 1.0
C6 H:TE9101 4.8 43.4 1.0
N3 H:DG5 4.9 43.5 1.0
O3 H:TE9101 4.9 44.5 1.0
C2 F:DG1 4.9 46.1 1.0
H7 H:TE9101 4.9 44.5 1.0
H10 H:TE9101 4.9 42.9 1.0
H3' H:DC4 5.0 56.7 1.0

Fluorine binding site 5 out of 6 in 8qmc

Go back to Fluorine Binding Sites List in 8qmc
Fluorine binding site 5 out of 6 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and 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-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F101

b:40.1
occ:1.00
F2 H:TE9101 0.0 40.1 1.0
C16 H:TE9101 1.3 39.8 1.0
C17 H:TE9101 2.4 39.2 1.0
C2 H:TE9101 2.4 40.5 1.0
H2' G:DC15 2.5 23.4 1.0
H11 H:TE9101 2.5 38.6 1.0
H3 H:TE9101 2.6 40.8 1.0
H2'' G:DC15 2.9 24.9 1.0
N3 H:TE9101 2.9 41.3 1.0
C3 H:TE9101 3.0 41.4 1.0
C2' G:DC15 3.0 22.9 1.0
N1 G:DC15 3.1 20.3 1.0
C2 G:DC15 3.1 21.6 1.0
C6 G:DC15 3.4 19.2 1.0
N3 G:DC15 3.5 21.5 1.0
O2 G:DC15 3.5 22.9 1.0
C1' G:DC15 3.6 20.6 1.0
N2 H:TE9101 3.6 40.7 1.0
C18 H:TE9101 3.6 39.3 1.0
HA3 B:GLY457 3.6 22.7 1.0
OP1 F:DG1 3.6 57.0 1.0
C5 G:DC15 3.8 19.2 1.0
C4 G:DC15 3.8 20.3 1.0
H6 G:DC15 3.9 18.5 1.0
HA2 B:GLY457 3.9 23.1 1.0
H1' G:DC15 4.0 21.2 1.0
C1 H:TE9101 4.1 40.1 1.0
C15 H:TE9101 4.2 42.4 1.0
CA B:GLY457 4.2 23.3 1.0
O A:HOH1603 4.2 15.2 1.0
C4 H:TE9101 4.3 42.5 1.0
O5' F:DG1 4.3 55.5 1.0
H22 H:DG5 4.4 41.8 1.0
H5 G:DC15 4.4 18.7 1.0
CL1 H:TE9101 4.4 41.8 1.0
C3' G:DC15 4.5 22.0 1.0
P F:DG1 4.6 57.0 1.0
H3' G:DC15 4.6 22.6 1.0
N B:GLY457 4.6 24.0 1.0
H1 H:DG5 4.7 42.7 1.0
N4 G:DC15 4.7 20.6 1.0
F3 H:TE9101 4.7 38.9 1.0
O4' G:DC15 4.8 18.6 1.0
O1 H:TE9101 4.8 41.9 1.0
C14 H:TE9101 4.8 42.7 1.0
H B:GLY457 4.8 24.4 1.0
O4' F:DG1 4.9 53.1 1.0
H41 G:DC15 4.9 21.0 1.0
C5 H:TE9101 4.9 42.6 1.0
HO3' G:DC15 5.0 30.0 0.0

Fluorine binding site 6 out of 6 in 8qmc

Go back to Fluorine Binding Sites List in 8qmc
Fluorine binding site 6 out of 6 in the High Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-Complex with the V-Site 18MER Dsdna and 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-Complex with the V-Site 18MER Dsdna and Novel Fluoroquinolone Delafloxacin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F101

b:38.9
occ:1.00
F3 H:TE9101 0.0 38.9 1.0
C18 H:TE9101 1.4 39.3 1.0
HA2 B:GLY434 2.3 26.3 1.0
C17 H:TE9101 2.4 39.2 1.0
C1 H:TE9101 2.4 40.1 1.0
H B:ASP435 2.5 26.1 1.0
H1 H:TE9101 2.5 39.9 1.0
H11 H:TE9101 2.6 38.6 1.0
HA B:ARG456 2.6 26.4 1.0
N1 H:TE9101 2.8 40.2 1.0
H4' F:DG1 3.1 56.5 1.0
CA B:GLY434 3.1 26.7 1.0
OD2 B:ASP435 3.2 26.6 1.0
H B:GLY457 3.2 24.4 1.0
HA3 B:GLY434 3.3 26.1 1.0
N B:ASP435 3.3 26.7 1.0
O5' F:DG1 3.3 55.5 1.0
H5' F:DG1 3.4 58.6 1.0
CA B:ARG456 3.5 26.4 1.0
N2 H:TE9101 3.6 40.7 1.0
H2 H:TE9101 3.6 40.8 1.0
C16 H:TE9101 3.6 39.8 1.0
O B:LEU455 3.6 27.4 1.0
C5' F:DG1 3.7 56.6 1.0
C B:GLY434 3.7 27.1 1.0
N B:GLY457 3.7 24.0 1.0
C4' F:DG1 3.7 55.4 1.0
HG2 B:ARG456 3.8 28.7 1.0
C B:ARG456 4.0 24.5 1.0
OP2 F:DG1 4.0 59.8 1.0
C2 H:TE9101 4.1 40.5 1.0
CG B:ASP435 4.1 27.2 1.0
P F:DG1 4.1 57.0 1.0
O4' F:DG1 4.2 53.1 1.0
HB3 B:ARG456 4.2 26.7 1.0
N B:GLY434 4.2 27.1 1.0
HB2 B:ASP435 4.3 26.6 1.0
CB B:ARG456 4.3 27.3 1.0
C B:LEU455 4.4 28.2 1.0
OP1 F:DG1 4.4 57.0 1.0
H B:GLY434 4.4 27.4 1.0
N B:ARG456 4.4 27.5 1.0
CA B:ASP435 4.5 27.2 1.0
CB B:ASP435 4.5 27.1 1.0
CG B:ARG456 4.6 28.8 1.0
H5'' F:DG1 4.7 55.8 1.0
H B:SER436 4.7 25.2 1.0
CL1 H:TE9101 4.7 41.8 1.0
F2 H:TE9101 4.7 40.1 1.0
HA2 B:GLY457 4.7 23.1 1.0
CA B:GLY457 4.8 23.3 1.0
O B:ARG456 4.9 23.1 1.0
H1' F:DG1 4.9 51.5 1.0
HA3 B:GLY457 5.0 22.7 1.0
O B:GLY434 5.0 28.0 1.0
HA B:ASP435 5.0 27.8 1.0

Reference:

S.Najmudin, X.S.Pan, B.Wang, N.E.Chayen, 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.
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