Fluorine in PDB 3rad: Quinolone(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae

The structure of Quinolone(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae, PDB code: 3rad was solved by I.Laponogov, X.-S.Pan, D.A.Veselkov, K.E.Mcauley, 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)	41.67 / 3.35
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	157.128, 157.128, 211.091, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 22.8

The structure of Quinolone(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae also contains other interesting chemical elements:

Magnesium	(Mg)	6 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Fluorine atom in the Quinolone(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae (pdb code 3rad). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Quinolone(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae, PDB code: 3rad:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Quinolone(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Quinolone(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ F:F101 b:0.7 occ:1.00 F F:NFX101 0.0 0.7 1.0 C15 F:NFX101 1.3 0.3 1.0 C17 F:NFX101 2.3 0.3 1.0 C11 F:NFX101 2.4 0.3 1.0 H03 F:NFX101 2.5 0.2 1.0 H17 F:NFX101 2.5 0.9 1.0 H03A F:NFX101 2.5 0.2 1.0 C03 F:NFX101 2.7 0.5 1.0 N01 F:NFX101 2.8 0.8 1.0 C2 F:DC4 3.0 0.2 1.0 N3 F:DC4 3.0 0.8 1.0 N1 F:DC4 3.2 0.1 1.0 N7 F:DA5 3.2 98.6 1.0 C4 F:DC4 3.2 0.6 1.0 C6 F:DC4 3.3 0.7 1.0 C5 F:DC4 3.4 0.6 1.0 C8 F:DA5 3.4 0.3 1.0 C5 F:DA5 3.5 0.9 1.0 C14 F:NFX101 3.6 0.9 1.0 C13 F:NFX101 3.6 0.4 1.0 O2 F:DC4 3.6 0.5 1.0 N9 F:DA5 3.8 0.8 1.0 C4 F:DA5 3.9 1.0 1.0 N4 F:DC4 4.0 98.0 1.0 C1' F:DC4 4.0 0.7 1.0 C2' F:DC4 4.1 0.7 1.0 N2 H:DG1 4.1 0.8 1.0 C6 F:DA5 4.1 0.5 1.0 C12 F:NFX101 4.2 1.0 1.0 C04 F:NFX101 4.2 0.1 1.0 C01 F:NFX101 4.2 0.5 1.0 H04 F:NFX101 4.5 0.2 1.0 N6 F:DA5 4.5 0.9 1.0 O4' F:DA5 4.5 0.4 1.0 N1 H:DG1 4.6 0.9 1.0 C2 H:DG1 4.6 0.3 1.0 H01 F:NFX101 4.7 0.5 1.0 N3 F:DA5 4.8 0.4 1.0 C1' F:DA5 4.8 0.8 1.0 C02 F:NFX101 4.8 0.2 1.0 H02A F:NFX101 4.8 0.2 1.0 H04A F:NFX101 4.8 0.2 1.0 C19 F:NFX101 4.8 0.9 1.0 N1 F:DA5 4.9 0.6 1.0 H05 F:NFX101 4.9 1.0 1.0

Fluorine binding site 2 out of 2 in the Quinolone(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Quinolone(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ H:F101 b:0.6 occ:1.00 F H:NFX101 0.0 0.6 1.0 C15 H:NFX101 1.3 0.5 1.0 H04 H:NFX101 2.3 0.4 1.0 C17 H:NFX101 2.3 0.6 1.0 C11 H:NFX101 2.4 0.6 1.0 H17 H:NFX101 2.5 0.2 1.0 H04A H:NFX101 2.5 0.4 1.0 C04 H:NFX101 2.6 0.9 1.0 N01 H:NFX101 2.8 0.9 1.0 N7 H:DA5 2.9 86.2 1.0 N3 H:DT4 3.0 0.1 1.0 C2 H:DT4 3.0 0.2 1.0 C5 H:DA5 3.2 1.0 1.0 C8 H:DA5 3.3 0.5 1.0 C4 H:DT4 3.4 1.0 1.0 N1 H:DT4 3.4 0.6 1.0 O2 H:DT4 3.5 0.5 1.0 C14 H:NFX101 3.6 0.1 1.0 C13 H:NFX101 3.6 0.7 1.0 C6 H:DT4 3.7 0.3 1.0 C5 H:DT4 3.7 0.9 1.0 C4 H:DA5 3.8 0.6 1.0 N9 H:DA5 3.8 0.3 1.0 C6 H:DA5 3.8 94.8 1.0 O4 H:DT4 4.0 0.1 1.0 C2' H:DT4 4.1 0.5 1.0 N6 H:DA5 4.1 93.8 1.0 C02 H:NFX101 4.1 1.0 1.0 C12 H:NFX101 4.1 0.3 1.0 C1' H:DT4 4.2 0.5 1.0 C03 H:NFX101 4.3 0.1 1.0 H02A H:NFX101 4.5 0.6 1.0 H02 H:NFX101 4.6 0.6 1.0 O4' H:DA5 4.6 0.9 1.0 N1 F:DA1 4.7 0.8 1.0 N1 H:DA5 4.7 0.1 1.0 N3 H:DA5 4.7 0.1 1.0 H03A H:NFX101 4.7 0.8 1.0 H03 H:NFX101 4.7 0.8 1.0 C7 H:DT4 4.8 0.8 1.0 C01 H:NFX101 4.8 0.4 1.0 H01 H:NFX101 4.8 0.3 1.0 C19 H:NFX101 4.8 0.8 1.0 C1' H:DA5 4.8 0.6 1.0 C2 H:DA5 5.0 0.1 1.0

I.Laponogov, X.S.Pan, D.A.Veselkov, R.T.Cirz, A.Wagman, H.E.Moser, L.M.Fisher, M.R.Sanderson. Exploring the Active Site of the Streptococcus Pneumoniae Topoisomerase IV-Dna Cleavage Complex with Novel 7,8-Bridged Fluoroquinolones. Open Biol V. 6 2016.
ISSN: ESSN 2046-2441
PubMed: 27655731
DOI: 10.1098/RSOB.160157