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

The structure of Quinolone(Levofloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae, PDB code: 3rae 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)	41.83 / 2.90
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	157.831, 157.831, 211.147, 90.00, 90.00, 120.00
R / Rfree (%)	18.6 / 22.6

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

Magnesium

(Mg)

6 atoms

The binding sites of Fluorine atom in the Quinolone(Levofloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae (pdb code 3rae). 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(Levofloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae, PDB code: 3rae:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Quinolone(Levofloxacin)-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(Levofloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ F:F101 b:96.2 occ:1.00 F F:LFX101 0.0 96.2 1.0 C11 F:LFX101 1.4 88.9 1.0 H01 F:LFX101 2.2 94.5 1.0 C04 F:LFX101 2.3 90.4 1.0 C13 F:LFX101 2.3 84.5 1.0 H13 F:LFX101 2.5 0.5 1.0 H01A F:LFX101 2.5 94.5 1.0 C01 F:LFX101 2.6 78.7 1.0 N01 F:LFX101 2.8 83.5 1.0 C2 F:DC4 3.0 99.4 1.0 N1 F:DC4 3.1 95.9 1.0 N3 F:DC4 3.2 94.5 1.0 N7 F:DA5 3.2 89.3 1.0 C6 F:DC4 3.3 90.7 1.0 C5 F:DA5 3.3 90.6 1.0 C4 F:DC4 3.4 83.5 1.0 C5 F:DC4 3.5 82.1 1.0 C8 F:DA5 3.5 95.9 1.0 C06 F:LFX101 3.6 95.9 1.0 O2 F:DC4 3.6 0.3 1.0 C10 F:LFX101 3.6 91.4 1.0 C4 F:DA5 3.7 97.2 1.0 N9 F:DA5 3.8 0.9 1.0 H02A F:LFX101 3.8 96.9 1.0 C6 F:DA5 3.9 86.4 1.0 C1' F:DC4 3.9 97.2 1.0 C02 F:LFX101 3.9 80.8 1.0 C2' F:DC4 3.9 92.9 1.0 C05 F:LFX101 4.1 94.8 1.0 C07 F:LFX101 4.1 78.2 1.0 N4 F:DC4 4.2 80.3 1.0 N6 F:DA5 4.2 78.8 1.0 N1 H:DG1 4.3 97.3 1.0 H07A F:LFX101 4.4 93.8 1.0 N2 H:DG1 4.4 0.3 1.0 H02 F:LFX101 4.4 96.9 1.0 N3 F:DA5 4.5 94.3 1.0 O4' F:DA5 4.6 0.0 1.0 N1 F:DA5 4.6 90.4 1.0 O01 F:LFX101 4.6 92.7 1.0 H07 F:LFX101 4.7 93.8 1.0 C2 H:DG1 4.7 0.4 1.0 N F:LFX101 4.8 89.2 1.0 C1' F:DA5 4.8 0.5 1.0 C2 F:DA5 4.8 91.0 1.0 C15 F:LFX101 4.9 99.6 1.0 C08 F:LFX101 4.9 89.3 1.0

Fluorine binding site 2 out of 2 in the Quinolone(Levofloxacin)-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(Levofloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ H:F101 b:91.0 occ:1.00 F H:LFX101 0.0 91.0 1.0 C11 H:LFX101 1.4 92.8 1.0 H01 H:LFX101 2.3 0.8 1.0 C04 H:LFX101 2.3 93.9 1.0 C13 H:LFX101 2.4 97.7 1.0 H01A H:LFX101 2.5 0.8 1.0 H13 H:LFX101 2.5 0.2 1.0 C01 H:LFX101 2.6 89.8 1.0 N01 H:LFX101 2.7 91.6 1.0 C2 H:DT4 2.9 99.8 1.0 N3 H:DT4 3.0 92.4 1.0 N7 H:DA5 3.0 69.7 1.0 N1 H:DT4 3.2 0.7 1.0 O2 H:DT4 3.3 0.1 1.0 C8 H:DA5 3.3 75.2 1.0 C5 H:DA5 3.3 79.9 1.0 C4 H:DT4 3.5 88.3 1.0 C06 H:LFX101 3.6 0.6 1.0 C6 H:DT4 3.6 98.2 1.0 C10 H:LFX101 3.6 0.9 1.0 C4 H:DA5 3.7 87.9 1.0 N9 H:DA5 3.7 90.2 1.0 H02A H:LFX101 3.8 0.8 1.0 C2' H:DT4 3.8 96.0 1.0 C5 H:DT4 3.8 93.2 1.0 C02 H:LFX101 3.9 85.7 1.0 C6 H:DA5 3.9 81.9 1.0 C1' H:DT4 4.0 0.4 1.0 C05 H:LFX101 4.1 0.9 1.0 C07 H:LFX101 4.1 89.3 1.0 O4 H:DT4 4.2 89.0 1.0 O4' H:DA5 4.4 96.5 1.0 N6 H:DA5 4.4 79.9 1.0 H02 H:LFX101 4.4 0.8 1.0 H07A H:LFX101 4.4 0.2 1.0 N1 F:DA1 4.5 98.1 1.0 N3 H:DA5 4.6 86.2 1.0 H07 H:LFX101 4.6 0.2 1.0 O01 H:LFX101 4.6 88.0 1.0 C1' H:DA5 4.7 96.1 1.0 N1 H:DA5 4.7 86.8 1.0 N H:LFX101 4.9 91.2 1.0 C15 H:LFX101 4.9 0.9 1.0 C7 H:DT4 4.9 98.5 1.0 C2 H:DA5 4.9 83.5 1.0 C08 H:LFX101 4.9 94.8 1.0

D.A.Veselkov, I.Laponogov, X.S.Pan, J.Selvarajah, G.B.Skamrova, A.Branstrom, J.Narasimhan, J.V.Prasad, L.M.Fisher, M.R.Sanderson. Structure of A Quinolone-Stabilized Cleavage Complex of Topoisomerase IV From Klebsiella Pneumoniae and Comparison with A Related Streptococcus Pneumoniae Complex. Acta Crystallogr.,Sect.D V. 72 488 2016.
ISSN: ISSN 0907-4449
PubMed: 27050128
DOI: 10.1107/S2059798316001212