Fluorine in PDB 4kpf: Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate

The structure of Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate, PDB code: 4kpf was solved by I.Laponogov, X.-S.Pan, D.A.Vesekov, R.T.Cirz, A.S.Wagman, H.E.Moser, 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 / 3.24
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	157.860, 157.860, 210.780, 90.00, 90.00, 120.00
R / Rfree (%)	16.2 / 18.4

The structure of Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Fluorine atom in the Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate (pdb code 4kpf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate, PDB code: 4kpf:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate within 5.0Å range: probe atom residue distance (Å) B Occ H:F101 b:0.2 occ:1.00 F26 H:1UV101 0.0 0.2 1.0 C25 H:1UV101 1.3 0.9 1.0 C24 H:1UV101 2.3 0.8 1.0 C27 H:1UV101 2.3 0.2 1.0 H201 H:1UV101 2.5 0.4 1.0 H271 H:1UV101 2.5 0.0 1.0 N19 H:1UV101 2.7 0.3 1.0 C2 H:DT4 3.0 0.9 1.0 N1 H:DT4 3.0 99.3 1.0 C20 H:1UV101 3.0 0.8 1.0 N3 H:DT4 3.1 99.9 1.0 C6 H:DT4 3.1 95.0 1.0 N7 H:DA5 3.2 93.0 1.0 C4 H:DT4 3.2 91.9 1.0 C5 H:DT4 3.3 93.5 1.0 C5 H:DA5 3.5 91.2 1.0 C14 H:1UV101 3.6 0.3 1.0 O2 H:DT4 3.6 0.8 1.0 C12 H:1UV101 3.6 0.8 1.0 C8 H:DA5 3.7 98.0 1.0 H212 H:1UV101 3.7 0.1 1.0 H202 H:1UV101 3.8 0.4 1.0 C1' H:DT4 3.8 0.9 1.0 C2' H:DT4 3.9 0.9 1.0 C21 H:1UV101 3.9 0.1 1.0 C6 H:DA5 4.0 90.5 1.0 O4 H:DT4 4.0 86.1 1.0 C18 H:1UV101 4.0 0.2 1.0 N6 H:DA5 4.1 88.8 1.0 N1 F:DA1 4.1 0.3 1.0 C13 H:1UV101 4.2 0.2 1.0 C4 H:DA5 4.2 93.7 1.0 H181 H:1UV101 4.2 0.1 1.0 N9 H:DA5 4.3 97.6 1.0 C7 H:DT4 4.3 94.6 1.0 H221 H:1UV101 4.5 0.6 1.0 C22 H:1UV101 4.5 0.3 1.0 C2 F:DA1 4.6 0.1 1.0 H211 H:1UV101 4.7 0.1 1.0 C15 H:1UV101 4.8 0.2 1.0 C10 H:1UV101 4.8 0.0 1.0 C6 F:DA1 4.8 0.5 1.0 N1 H:DA5 4.9 92.5 1.0 N6 F:DA1 4.9 0.4 1.0 O16 H:1UV101 4.9 0.9 1.0 O4' H:DA5 5.0 93.1 1.0

Fluorine binding site 2 out of 2 in the Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate within 5.0Å range: probe atom residue distance (Å) B Occ H:F102 b:0.2 occ:1.00 F26 H:1UV102 0.0 0.2 1.0 C25 H:1UV102 1.3 0.3 1.0 C24 H:1UV102 2.3 0.6 1.0 C27 H:1UV102 2.4 1.0 1.0 H201 H:1UV102 2.5 0.1 1.0 H271 H:1UV102 2.5 0.4 1.0 N19 H:1UV102 2.7 0.3 1.0 C20 H:1UV102 3.0 0.6 1.0 N1 F:DC4 3.0 99.5 1.0 C2 F:DC4 3.1 0.2 1.0 C6 F:DC4 3.1 97.1 1.0 N3 F:DC4 3.1 0.4 1.0 C4 F:DC4 3.2 86.2 1.0 C5 F:DC4 3.2 86.4 1.0 N7 F:DA5 3.3 0.2 1.0 C5 F:DA5 3.5 99.9 1.0 C14 H:1UV102 3.6 0.1 1.0 C12 H:1UV102 3.6 0.7 1.0 O2 F:DC4 3.7 0.5 1.0 H202 H:1UV102 3.7 0.1 1.0 C8 F:DA5 3.8 0.0 1.0 H212 H:1UV102 3.9 0.7 1.0 C1' F:DC4 3.9 0.0 1.0 C6 F:DA5 3.9 98.7 1.0 N1 H:DG1 3.9 0.4 1.0 C21 H:1UV102 4.0 0.4 1.0 N6 F:DA5 4.0 98.3 1.0 N4 F:DC4 4.0 84.8 1.0 C2' F:DC4 4.0 96.0 1.0 C18 H:1UV102 4.0 0.2 1.0 C4 F:DA5 4.2 98.6 1.0 C13 H:1UV102 4.2 1.0 1.0 H181 H:1UV102 4.2 0.9 1.0 N9 F:DA5 4.3 98.2 1.0 N2 H:DG1 4.4 0.6 1.0 C2 H:DG1 4.5 0.0 1.0 H221 H:1UV102 4.5 0.1 1.0 C22 H:1UV102 4.5 0.4 1.0 C6 H:DG1 4.6 0.2 1.0 O6 H:DG1 4.6 0.9 1.0 N1 F:DA5 4.7 96.9 1.0 C15 H:1UV102 4.8 0.7 1.0 C10 H:1UV102 4.8 0.0 1.0 H211 H:1UV102 4.8 0.7 1.0 O16 H:1UV102 4.9 1.0 1.0 O11 H:1UV102 5.0 0.7 1.0 N3 F:DA5 5.0 97.1 1.0

I.Laponogov, X.-S.Pan, D.A.Vesekov, R.T.Cirz, A.S.Wagman, H.E.Moser, L.M.Fisher, M.R.Sanderson. Novel Fluoroquinolones in Complex with Topoisomerase IV From S. Pneumoniae and E-Site G-Gate To Be Published.