Fluorine in PDB 3raf: Quinazolinedione-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae

The structure of Quinazolinedione-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae, PDB code: 3raf 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)	114.98 / 3.24
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	158.550, 158.550, 210.330, 90.00, 90.00, 120.00
R / Rfree (%)	16.7 / 20.6

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

Magnesium

(Mg)

4 atoms

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

Fluorine binding site 1 out of 2 in the Quinazolinedione-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 Quinazolinedione-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ F:F0 b:34.6 occ:1.00 F7 F:PDQ0 0.0 34.6 1.0 C6 F:PDQ0 1.3 33.7 1.0 H42 F:PDQ0 2.2 46.3 1.0 C4 F:PDQ0 2.3 34.2 1.0 C8 F:PDQ0 2.5 32.4 1.0 H4 F:PDQ0 2.5 41.0 1.0 C42 F:PDQ0 2.7 38.6 1.0 H42A F:PDQ0 2.8 46.3 1.0 N33 F:PDQ0 2.9 32.1 1.0 C2 F:DC4 3.0 41.5 1.0 N1 F:DC4 3.2 41.2 1.0 N3 F:DC4 3.2 39.3 1.0 N7 F:DA5 3.2 45.0 1.0 O2 F:DC4 3.5 42.4 1.0 C5 F:DA5 3.5 47.7 1.0 C6 F:DC4 3.5 37.8 1.0 C4 F:DC4 3.5 38.1 1.0 C8 F:DA5 3.5 44.4 1.0 C5 F:DC4 3.7 34.9 1.0 C10 F:PDQ0 3.7 31.6 1.0 C3 F:PDQ0 3.7 39.2 1.0 C2' F:DC4 3.8 40.1 1.0 C1' F:DC4 3.8 40.5 1.0 C4 F:DA5 4.0 48.1 1.0 N9 F:DA5 4.0 46.4 1.0 C6 F:DA5 4.0 52.0 1.0 C39 F:PDQ0 4.1 41.5 1.0 H37 F:PDQ0 4.2 46.5 1.0 C12 F:PDQ0 4.2 32.1 1.0 C34 F:PDQ0 4.2 36.5 1.0 N4 F:DC4 4.3 42.1 1.0 N6 F:DA5 4.3 56.3 1.0 N2 H:DG1 4.4 61.0 1.0 N1 H:DG1 4.4 51.2 1.0 C37 F:PDQ0 4.5 38.7 1.0 H39A F:PDQ0 4.5 49.9 1.0 O4' F:DA5 4.5 50.0 1.0 H34 F:PDQ0 4.6 43.8 1.0 C2 H:DG1 4.7 56.1 1.0 N3 F:DA5 4.8 50.6 1.0 H39 F:PDQ0 4.8 49.9 1.0 N1 F:DA5 4.8 51.5 1.0 C29 F:PDQ0 4.9 33.7 1.0 C1' F:DA5 4.9 47.4 1.0 H29 F:PDQ0 4.9 40.4 1.0 H34A F:PDQ0 5.0 43.8 1.0 C1 F:PDQ0 5.0 45.7 1.0

Fluorine binding site 2 out of 2 in the Quinazolinedione-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 Quinazolinedione-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ H:F0 b:39.9 occ:1.00 F7 H:PDQ0 0.0 39.9 1.0 C6 H:PDQ0 1.3 31.2 1.0 H42 H:PDQ0 2.3 44.3 1.0 C4 H:PDQ0 2.3 25.5 1.0 C8 H:PDQ0 2.5 29.7 1.0 H4 H:PDQ0 2.5 30.6 1.0 N33 H:PDQ0 2.9 33.4 1.0 C42 H:PDQ0 2.9 36.9 1.0 C2 H:DT4 3.0 52.1 1.0 N7 H:DA5 3.1 40.2 1.0 N1 H:DT4 3.2 50.7 1.0 C8 H:DA5 3.2 42.2 1.0 N3 H:DT4 3.3 49.6 1.0 O2 H:DT4 3.4 54.0 1.0 H42A H:PDQ0 3.4 44.3 1.0 C5 H:DA5 3.4 41.7 1.0 N9 H:DA5 3.6 43.6 1.0 C2' H:DT4 3.6 49.4 1.0 C6 H:DT4 3.7 51.1 1.0 C10 H:PDQ0 3.7 29.6 1.0 C3 H:PDQ0 3.7 35.0 1.0 C4 H:DA5 3.7 41.1 1.0 C1' H:DT4 3.8 52.0 1.0 C4 H:DT4 3.8 47.1 1.0 C5 H:DT4 4.0 52.0 1.0 H37 H:PDQ0 4.0 52.8 1.0 O4' H:DA5 4.1 50.7 1.0 C6 H:DA5 4.2 43.1 1.0 C39 H:PDQ0 4.2 40.3 1.0 C34 H:PDQ0 4.2 37.5 1.0 C12 H:PDQ0 4.2 25.3 1.0 C37 H:PDQ0 4.4 44.0 1.0 H39A H:PDQ0 4.5 48.3 1.0 C1' H:DA5 4.5 47.2 1.0 H34 H:PDQ0 4.5 45.0 1.0 N3 H:DA5 4.6 40.6 1.0 N1 F:DA1 4.6 37.6 1.0 N6 H:DA5 4.6 43.1 1.0 O4 H:DT4 4.6 45.9 1.0 C2 F:DA1 4.9 38.8 1.0 N1 H:DA5 4.9 44.4 1.0 C1 H:PDQ0 5.0 41.0 1.0 C29 H:PDQ0 5.0 30.8 1.0

I.Laponogov, X.-S.Pan, D.A.Veselkov, K.E.Mcauley, L.M.Fisher, M.R.Sanderson. Inhibitor-Stabilised Cleavage Complexes of Topoisomerase Iia: Structural Analysis of Drug-Dependent Inter- and Intramolecular Interactions To Be Published.