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Fluorine in PDB 8qmb: Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER Dna Complex with the Novel Fluoroquinolone Delafloxacin

Enzymatic activity of Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER Dna Complex with the Novel Fluoroquinolone Delafloxacin

All present enzymatic activity of Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER Dna Complex with the Novel Fluoroquinolone Delafloxacin:
5.6.2.2;

Protein crystallography data

The structure of Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER Dna Complex with the Novel Fluoroquinolone Delafloxacin, PDB code: 8qmb 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) 83.63 / 2.00
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.215, 157.215, 211.948, 90, 90, 120
R / Rfree (%) 16.9 / 20.6

Other elements in 8qmb:

The structure of Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER Dna Complex with the 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 Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER Dna Complex with the Novel Fluoroquinolone Delafloxacin (pdb code 8qmb). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER Dna Complex with the Novel Fluoroquinolone Delafloxacin, PDB code: 8qmb:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8qmb

Go back to Fluorine Binding Sites List in 8qmb
Fluorine binding site 1 out of 6 in the Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER 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 Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER Dna Complex with the Novel Fluoroquinolone Delafloxacin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F101

b:41.5
occ:1.00
 F1 F:TE9101 0.0 41.5 1.0
C9 F:TE9101 1.4 39.0 1.0
C10 F:TE9101 2.3 35.0 1.0
C8 F:TE9101 2.5 36.1 1.0
H6 F:TE9101 2.5 36.0 1.0
H5 F:TE9101 2.7 35.8 1.0
C11 F:TE9101 2.7 34.8 1.0
H4 F:TE9101 2.7 35.3 1.0
N4 F:TE9101 2.7 35.3 1.0
C2 F:DT4 2.9 47.4 1.0
H2' F:DT4 3.0 71.3 1.0
N3 F:DT4 3.0 45.5 1.0
C8 F:DA5 3.0 31.9 1.0
H8 F:DA5 3.0 32.7 1.0
N1 F:DT4 3.0 50.8 1.0
N7 F:DA5 3.1 31.2 1.0
C6 F:DT4 3.3 54.9 1.0
C4 F:DT4 3.3 47.2 1.0
H3 F:DT4 3.4 46.4 1.0
C5 F:DT4 3.4 51.9 1.0
O2 F:DT4 3.4 47.0 1.0
C14 F:TE9101 3.6 32.9 1.0
C2' F:DT4 3.6 75.1 1.0
N9 F:DA5 3.7 36.4 1.0
C7 F:TE9101 3.7 29.2 1.0
C5 F:DA5 3.8 28.0 1.0
C1' F:DT4 3.8 63.6 1.0
H6 F:DT4 3.8 53.2 1.0
H2'' F:DT4 3.9 71.2 1.0
H1' F:DT4 3.9 62.8 1.0
O4 F:DT4 4.1 51.7 1.0
C15 F:TE9101 4.2 29.3 1.0
C4 F:DA5 4.2 29.3 1.0
C13 F:TE9101 4.2 32.5 1.0
H73 F:DT4 4.2 33.1 0.0
C12 F:TE9101 4.2 38.3 1.0
N1 H:DA1 4.3 37.1 1.0
H2 H:DA1 4.5 36.4 1.0
O4' F:DA5 4.5 42.0 1.0
C7 F:DT4 4.5 44.8 1.0
C1' F:DA5 4.6 40.7 1.0
H62 F:DA5 4.6 31.3 1.0
C6 F:DA5 4.6 30.4 1.0
C2 H:DA1 4.7 34.6 1.0
H1' F:DA5 4.7 40.5 1.0
H9 F:TE9101 4.7 34.4 1.0
H7 F:TE9101 4.7 37.5 1.0
H61 H:DA1 4.9 34.9 1.0
H10 F:TE9101 4.9 34.3 1.0
C6 F:TE9101 4.9 35.2 1.0
N6 F:DA5 4.9 31.8 1.0
H8 F:TE9101 5.0 33.1 0.0
H71 F:DT4 5.0 33.1 0.0
C3' F:DT4 5.0 71.7 1.0

Fluorine binding site 2 out of 6 in 8qmb

Go back to Fluorine Binding Sites List in 8qmb
Fluorine binding site 2 out of 6 in the Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER 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 Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER Dna Complex with the Novel Fluoroquinolone Delafloxacin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F101

b:44.7
occ:1.00
 F2 F:TE9101 0.0 44.7 1.0
C16 F:TE9101 1.3 34.9 1.0
C2 F:TE9101 2.3 29.7 1.0
C17 F:TE9101 2.4 34.4 1.0
H2'' E:DT15 2.6 31.9 1.0
H11 F:TE9101 2.6 33.1 1.0
H3 F:TE9101 2.7 39.6 1.0
H2' E:DT15 2.8 31.8 1.0
N1 E:DT15 3.0 25.9 1.0
C2 E:DT15 3.0 25.7 1.0
C2' E:DT15 3.0 31.1 1.0
N3 F:TE9101 3.1 34.2 1.0
C3 F:TE9101 3.2 40.6 1.0
N3 E:DT15 3.3 28.3 1.0
C6 E:DT15 3.4 27.2 1.0
O2 E:DT15 3.4 33.0 1.0
HA3 A:GLY457 3.5 36.2 1.0
C1' E:DT15 3.5 29.9 1.0
N2 F:TE9101 3.5 25.4 1.0
C18 F:TE9101 3.6 28.7 1.0
C4 E:DT15 3.7 30.1 1.0
C5 E:DT15 3.7 30.4 1.0
H3 E:DT15 3.8 28.2 1.0
H1' E:DT15 3.8 29.3 1.0
H6 E:DT15 3.8 27.7 1.0
C1 F:TE9101 4.1 27.6 1.0
HA2 A:GLY457 4.1 36.6 1.0
CA A:GLY457 4.2 38.4 1.0
O E:HOH110 4.3 33.2 1.0
CL1 F:TE9101 4.3 44.6 1.0
C15 F:TE9101 4.3 29.3 1.0
OP1 H:DA1 4.4 41.5 1.0
N A:GLY457 4.5 33.7 1.0
C4 F:TE9101 4.5 43.7 1.0
C3' E:DT15 4.5 35.6 1.0
O4 E:DT15 4.6 27.5 1.0
H73 E:DT15 4.6 33.1 0.0
H A:GLY457 4.8 35.0 1.0
O4' E:DT15 4.8 29.4 1.0
N1 F:DA5 4.8 31.5 1.0
H2 F:DA5 4.8 30.2 1.0
O2 F:TE9101 4.8 49.8 1.0
C7 E:DT15 4.8 37.5 1.0
C14 F:TE9101 4.8 32.9 1.0
H3' E:DT15 4.8 34.6 1.0
F3 F:TE9101 4.9 38.1 1.0
C A:ARG456 4.9 33.3 1.0
HO3' E:DT15 4.9 33.1 0.0
O A:ARG456 4.9 34.5 1.0

Fluorine binding site 3 out of 6 in 8qmb

Go back to Fluorine Binding Sites List in 8qmb
Fluorine binding site 3 out of 6 in the Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER 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 Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER Dna Complex with the Novel Fluoroquinolone Delafloxacin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F101

b:38.1
occ:1.00
 F3 F:TE9101 0.0 38.1 1.0
C18 F:TE9101 1.4 28.7 1.0
H2 F:TE9101 2.2 31.9 1.0
H A:ASP435 2.3 37.3 1.0
C1 F:TE9101 2.4 27.6 1.0
C17 F:TE9101 2.5 34.4 1.0
HA A:ARG456 2.5 37.1 1.0
N1 F:TE9101 2.6 34.0 1.0
HA2 A:GLY434 2.6 39.2 1.0
H11 F:TE9101 2.7 33.1 1.0
H4' H:DA1 3.1 42.9 1.0
HG2 A:ARG456 3.2 43.9 1.0
O5' H:DA1 3.2 33.1 1.0
N A:ASP435 3.2 37.7 1.0
OD2 A:ASP435 3.4 44.9 1.0
CA A:ARG456 3.5 38.6 1.0
CA A:GLY434 3.5 41.1 1.0
H1 F:TE9101 3.6 32.0 1.0
N2 F:TE9101 3.7 25.4 1.0
H A:GLY457 3.7 35.0 1.0
HB2 A:ASP435 3.7 38.0 1.0
HB3 A:ARG456 3.7 39.7 1.0
C16 F:TE9101 3.8 34.9 1.0
C4' H:DA1 3.8 41.4 1.0
C A:GLY434 3.8 38.4 1.0
HA3 A:GLY434 3.8 39.4 1.0
O A:LEU455 3.9 41.1 1.0
P H:DA1 3.9 44.1 1.0
CB A:ARG456 3.9 39.1 1.0
CG A:ARG456 3.9 44.7 1.0
C5' H:DA1 4.0 39.8 1.0
O4' H:DA1 4.0 41.4 1.0
O E:HOH110 4.0 33.2 1.0
OP1 H:DA1 4.0 41.5 1.0
CG A:ASP435 4.0 41.7 1.0
C A:ARG456 4.1 33.3 1.0
N A:GLY457 4.1 33.7 1.0
CB A:ASP435 4.1 37.5 1.0
CA A:ASP435 4.2 37.6 1.0
H5' H:DA1 4.2 38.4 1.0
C2 F:TE9101 4.3 29.7 1.0
N A:ARG456 4.4 35.6 1.0
OP2 H:DA1 4.4 49.3 1.0
C A:LEU455 4.5 41.9 1.0
N A:GLY434 4.6 37.9 1.0
H A:GLY434 4.6 39.5 1.0
HD3 A:ARG456 4.6 46.0 1.0
HG3 A:ARG456 4.6 44.3 1.0
H A:SER436 4.7 37.2 1.0
HE A:ARG456 4.7 48.3 1.0
HA A:ASP435 4.8 38.6 1.0
CD A:ARG456 4.8 46.8 1.0
H1' H:DA1 4.8 49.7 1.0
H5'' H:DA1 4.8 38.4 1.0
F2 F:TE9101 4.9 44.7 1.0
HB2 A:ARG456 4.9 40.1 1.0
O A:ARG456 5.0 34.5 1.0
OD1 A:ASP435 5.0 48.9 1.0

Fluorine binding site 4 out of 6 in 8qmb

Go back to Fluorine Binding Sites List in 8qmb
Fluorine binding site 4 out of 6 in the Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER 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 Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER Dna Complex with the Novel Fluoroquinolone Delafloxacin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F101

b:42.8
occ:1.00
 F1 H:TE9101 0.0 42.8 1.0
C9 H:TE9101 1.3 37.4 1.0
C10 H:TE9101 2.3 36.8 1.0
C8 H:TE9101 2.4 36.6 1.0
H6 H:TE9101 2.6 39.1 1.0
H4 H:TE9101 2.6 36.1 1.0
N4 H:TE9101 2.7 37.6 1.0
C11 H:TE9101 2.7 38.0 1.0
H5 H:TE9101 2.7 39.0 1.0
C2 H:DC4 2.9 52.1 1.0
H2' H:DC4 3.0 68.1 1.0
N7 H:DG5 3.0 36.6 1.0
C8 H:DG5 3.1 34.0 1.0
N1 H:DC4 3.1 50.2 1.0
N3 H:DC4 3.1 48.5 1.0
H8 H:DG5 3.2 35.8 1.0
O2 H:DC4 3.3 51.4 1.0
C4 H:DC4 3.5 43.0 1.0
C6 H:DC4 3.5 43.9 1.0
C2' H:DC4 3.6 72.0 1.0
C5 H:DG5 3.6 34.2 1.0
N9 H:DG5 3.6 38.9 1.0
C14 H:TE9101 3.6 34.9 1.0
H2'' H:DC4 3.6 68.1 1.0
C5 H:DC4 3.6 38.9 1.0
C7 H:TE9101 3.7 33.8 1.0
C1' H:DC4 3.7 59.1 1.0
H1' H:DC4 3.8 59.9 1.0
C4 H:DG5 3.9 30.1 1.0
H1 F:DG1 3.9 38.0 1.0
H22 F:DG1 4.0 53.8 1.0
H6 H:DC4 4.0 44.3 1.0
C15 H:TE9101 4.1 31.9 1.0
C13 H:TE9101 4.1 35.1 1.0
C12 H:TE9101 4.2 42.9 1.0
O4' H:DG5 4.3 44.4 1.0
N4 H:DC4 4.3 48.5 1.0
H5 H:DC4 4.3 41.1 1.0
N2 F:DG1 4.4 60.5 1.0
C6 H:DG5 4.4 35.9 1.0
C1' H:DG5 4.4 44.8 1.0
N1 F:DG1 4.5 36.0 1.0
H9 H:TE9101 4.6 37.3 1.0
H1' H:DG5 4.6 44.2 1.0
H41 H:DC4 4.6 46.8 1.0
H7 H:TE9101 4.7 41.4 1.0
C2 F:DG1 4.8 42.7 1.0
H42 H:DC4 4.8 46.7 1.0
H21 F:DG1 4.9 53.5 1.0
O6 H:DG5 4.9 39.3 1.0
C6 H:TE9101 4.9 32.6 1.0
H10 H:TE9101 4.9 37.2 1.0
N3 H:DG5 4.9 27.1 1.0

Fluorine binding site 5 out of 6 in 8qmb

Go back to Fluorine Binding Sites List in 8qmb
Fluorine binding site 5 out of 6 in the Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER 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 Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER Dna Complex with the Novel Fluoroquinolone Delafloxacin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F101

b:44.1
occ:1.00
 F2 H:TE9101 0.0 44.1 1.0
C16 H:TE9101 1.3 39.1 1.0
C2 H:TE9101 2.2 33.5 1.0
C17 H:TE9101 2.5 34.8 1.0
H3 H:TE9101 2.6 34.0 1.0
H11 H:TE9101 2.7 35.1 1.0
H2'' G:DC15 2.7 29.7 1.0
N3 H:TE9101 2.9 33.3 1.0
O F:HOH208 3.0 44.2 1.0
C3 H:TE9101 3.0 33.2 1.0
C2 G:DC15 3.1 29.0 1.0
N1 G:DC15 3.1 27.6 1.0
H2' G:DC15 3.1 29.7 1.0
C2' G:DC15 3.2 29.5 1.0
N3 G:DC15 3.4 28.6 1.0
C6 G:DC15 3.5 30.3 1.0
N2 H:TE9101 3.5 29.8 1.0
O2 G:DC15 3.5 30.3 1.0
HA3 B:GLY457 3.6 46.4 1.0
C1' G:DC15 3.6 27.1 1.0
C4 G:DC15 3.7 26.4 1.0
C18 H:TE9101 3.7 32.2 1.0
C5 G:DC15 3.8 25.9 1.0
H1' G:DC15 3.8 28.8 1.0
H6 G:DC15 3.9 28.6 1.0
HA2 B:GLY457 4.0 46.8 1.0
H22 H:DG5 4.1 43.7 1.0
C1 H:TE9101 4.1 34.2 1.0
C15 H:TE9101 4.2 31.9 1.0
CA B:GLY457 4.2 49.2 1.0
CL1 H:TE9101 4.2 46.5 1.0
C4 H:TE9101 4.3 35.9 1.0
OP1 F:DG1 4.4 48.8 1.0
H5 G:DC15 4.4 27.0 1.0
O F:HOH209 4.4 27.3 1.0
H1 H:DG5 4.4 35.9 1.0
N2 H:DG5 4.5 48.5 1.0
N B:GLY457 4.6 43.6 1.0
N4 G:DC15 4.6 29.6 1.0
O1 H:TE9101 4.6 44.6 1.0
C3' G:DC15 4.7 32.7 1.0
C14 H:TE9101 4.8 34.9 1.0
H B:GLY457 4.9 43.6 1.0
H21 H:DG5 4.9 43.7 1.0
O4' G:DC15 4.9 33.5 1.0
O5' F:DG1 4.9 39.0 1.0
O G:HOH110 4.9 47.1 1.0
F3 H:TE9101 4.9 35.0 1.0
N1 H:DG5 5.0 36.1 1.0
H41 G:DC15 5.0 28.7 1.0
HH11 A:ARG1117 5.0 97.2 1.0
HH12 A:ARG1117 5.0 98.1 1.0
C B:ARG456 5.0 38.4 1.0

Fluorine binding site 6 out of 6 in 8qmb

Go back to Fluorine Binding Sites List in 8qmb
Fluorine binding site 6 out of 6 in the Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER 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 Nucleant-Assisted 2.0 A Resolution Structure of the Streptococcus Pneumoniae Topoisomerase IV-V18MER Dna Complex with the Novel Fluoroquinolone Delafloxacin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F101

b:35.0
occ:1.00
 F3 H:TE9101 0.0 35.0 1.0
C18 H:TE9101 1.4 32.2 1.0
H B:ASP435 2.2 37.4 1.0
H2 H:TE9101 2.4 37.1 1.0
C1 H:TE9101 2.5 34.2 1.0
C17 H:TE9101 2.5 34.8 1.0
HA B:ARG456 2.6 40.6 1.0
HA2 B:GLY434 2.6 39.6 1.0
H11 H:TE9101 2.7 35.1 1.0
N1 H:TE9101 2.8 38.5 1.0
N B:ASP435 3.1 38.0 1.0
H4' F:DG1 3.1 45.2 1.0
O5' F:DG1 3.1 39.0 1.0
HG2 B:ARG456 3.2 51.3 1.0
OD2 B:ASP435 3.3 44.9 1.0
CA B:GLY434 3.5 40.6 1.0
HB2 B:ASP435 3.5 38.7 1.0
CA B:ARG456 3.5 40.3 1.0
N2 H:TE9101 3.7 29.8 1.0
C B:GLY434 3.8 38.4 1.0
H1 H:TE9101 3.8 37.2 1.0
P F:DG1 3.8 43.5 1.0
C4' F:DG1 3.8 45.8 1.0
C16 H:TE9101 3.8 39.1 1.0
HA3 B:GLY434 3.8 39.7 1.0
H B:GLY457 3.8 43.6 1.0
O B:LEU455 3.8 42.2 1.0
C5' F:DG1 3.9 42.1 1.0
HB3 B:ARG456 3.9 45.0 1.0
CG B:ASP435 3.9 45.0 1.0
H5' F:DG1 4.0 42.0 1.0
CB B:ASP435 4.0 37.9 1.0
CG B:ARG456 4.0 53.0 1.0
CB B:ARG456 4.0 44.6 1.0
O4' F:DG1 4.0 46.8 1.0
O F:HOH209 4.1 27.3 1.0
CA B:ASP435 4.1 36.7 1.0
OP1 F:DG1 4.1 48.8 1.0
C B:ARG456 4.2 38.4 1.0
N B:GLY457 4.2 43.6 1.0
OP2 F:DG1 4.3 41.6 1.0
C2 H:TE9101 4.3 33.5 1.0
N B:ARG456 4.4 39.6 1.0
C B:LEU455 4.5 41.2 1.0
N B:GLY434 4.6 40.4 1.0
H B:GLY434 4.6 40.9 1.0
HA B:ASP435 4.6 37.5 1.0
HD3 B:ARG456 4.6 53.0 1.0
HG3 B:ARG456 4.7 51.7 1.0
H B:SER436 4.7 32.7 1.0
HE B:ARG456 4.7 51.0 1.0
H5'' F:DG1 4.8 42.1 1.0
CD B:ARG456 4.8 54.9 1.0
H1' F:DG1 4.9 51.0 1.0
HB3 B:ASP435 4.9 39.4 1.0
F2 H:TE9101 4.9 44.1 1.0
O B:GLY434 5.0 36.8 1.0
OD1 B:ASP435 5.0 48.1 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.
Page generated: Thu Oct 31 19:55:18 2024

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