Fluorine in PDB 3ltn: Inhibitor-Stabilized Topoisomerase IV-Dna Cleavage Complex (S. Pneumoniae)

The structure of Inhibitor-Stabilized Topoisomerase IV-Dna Cleavage Complex (S. Pneumoniae), PDB code: 3ltn 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)	34.13 / 3.10
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	122.507, 122.507, 178.303, 90.00, 90.00, 120.00
R / Rfree (%)	18.6 / 22.8

The structure of Inhibitor-Stabilized Topoisomerase IV-Dna Cleavage Complex (S. Pneumoniae) also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

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

Fluorine binding site 1 out of 2 in the Inhibitor-Stabilized Topoisomerase IV-Dna Cleavage Complex (S. Pneumoniae)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Inhibitor-Stabilized Topoisomerase IV-Dna Cleavage Complex (S. Pneumoniae) within 5.0Å range: probe atom residue distance (Å) B Occ F:F0 b:0.6 occ:1.00 F7 F:PDQ0 0.0 0.6 1.0 C6 F:PDQ0 1.4 1.0 1.0 C4 F:PDQ0 2.4 96.2 1.0 C8 F:PDQ0 2.5 0.3 1.0 H4 F:PDQ0 2.7 0.4 1.0 N33 F:PDQ0 2.9 0.8 1.0 N1 F:DC4 3.0 0.8 1.0 C2 F:DC4 3.0 0.6 1.0 H34A F:PDQ0 3.1 0.5 1.0 C2' F:DC4 3.2 0.2 1.0 C1' F:DC4 3.3 0.8 1.0 O2 F:DC4 3.4 0.4 1.0 H42A F:PDQ0 3.4 0.5 1.0 C6 F:DC4 3.4 0.6 1.0 C34 F:PDQ0 3.5 0.9 1.0 N7 F:DA5 3.6 0.4 1.0 N3 F:DC4 3.6 0.4 1.0 C8 F:DA5 3.6 0.2 1.0 C5 F:DA5 3.7 0.6 1.0 C42 F:PDQ0 3.7 0.1 1.0 N9 F:DA5 3.8 0.5 1.0 C10 F:PDQ0 3.8 88.5 1.0 C4 F:DA5 3.8 0.9 1.0 C3 F:PDQ0 3.9 98.8 1.0 C5 F:DC4 3.9 86.8 1.0 C4 F:DC4 4.0 90.5 1.0 O4' F:DA5 4.0 0.6 1.0 H39A F:PDQ0 4.1 0.1 1.0 H34 F:PDQ0 4.3 0.5 1.0 C39 F:PDQ0 4.3 0.2 1.0 C6 F:DA5 4.4 1.0 1.0 C12 F:PDQ0 4.4 88.8 1.0 C37 F:PDQ0 4.5 0.9 1.0 C1' F:DA5 4.5 0.2 1.0 N3 F:DA5 4.5 0.4 1.0 H42 F:PDQ0 4.6 0.5 1.0 C3' F:DC4 4.7 93.8 1.0 H37 F:PDQ0 4.7 0.3 1.0 O4' F:DC4 4.7 1.0 1.0 N1 H:DG1 4.9 0.0 1.0 O5' F:DA5 4.9 0.2 1.0 N6 F:DA5 4.9 0.5 1.0 N1 F:DA5 4.9 83.9 1.0 N4 F:DC4 5.0 82.1 1.0 H29 F:PDQ0 5.0 0.6 1.0 C2 F:DA5 5.0 95.3 1.0

Fluorine binding site 2 out of 2 in the Inhibitor-Stabilized Topoisomerase IV-Dna Cleavage Complex (S. Pneumoniae)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Inhibitor-Stabilized Topoisomerase IV-Dna Cleavage Complex (S. Pneumoniae) within 5.0Å range: probe atom residue distance (Å) B Occ H:F0 b:0.0 occ:1.00 F7 H:PDQ0 0.0 0.0 1.0 C6 H:PDQ0 1.4 0.2 1.0 C4 H:PDQ0 2.4 99.9 1.0 C8 H:PDQ0 2.5 0.1 1.0 H4 H:PDQ0 2.6 0.9 1.0 H34A H:PDQ0 2.7 0.9 1.0 N33 H:PDQ0 2.9 0.6 1.0 C2 H:DT4 3.1 0.7 1.0 N1 H:DT4 3.1 0.3 1.0 C34 H:PDQ0 3.3 0.9 1.0 O2 H:DT4 3.3 0.4 1.0 C2' H:DT4 3.3 0.3 1.0 C1' H:DT4 3.4 0.4 1.0 N3 H:DT4 3.6 0.6 1.0 C6 H:DT4 3.7 0.6 1.0 N7 H:DA5 3.7 0.6 1.0 C5 H:DA5 3.7 98.3 1.0 C8 H:DA5 3.7 0.3 1.0 H42A H:PDQ0 3.7 0.8 1.0 C10 H:PDQ0 3.8 0.3 1.0 C4 H:DA5 3.8 0.5 1.0 N9 H:DA5 3.8 0.2 1.0 C3 H:PDQ0 3.9 0.0 1.0 C42 H:PDQ0 3.9 0.1 1.0 H34 H:PDQ0 3.9 0.9 1.0 O4' H:DA5 4.0 0.1 1.0 C5 H:DT4 4.2 91.2 1.0 C4 H:DT4 4.2 99.4 1.0 C6 H:DA5 4.3 95.7 1.0 H39A H:PDQ0 4.3 0.6 1.0 C37 H:PDQ0 4.4 0.3 1.0 C12 H:PDQ0 4.4 87.2 1.0 C39 H:PDQ0 4.5 0.8 1.0 N3 H:DA5 4.5 0.6 1.0 H37 H:PDQ0 4.6 0.6 1.0 C1' H:DA5 4.6 0.9 1.0 H42 H:PDQ0 4.8 0.8 1.0 C3' H:DT4 4.8 1.0 1.0 N1 H:DA5 4.8 88.8 1.0 O4' H:DT4 4.9 0.9 1.0 C2 H:DA5 4.9 99.1 1.0 N6 H:DA5 4.9 89.1 1.0 N1 F:DA1 4.9 0.8 1.0 H29 H:PDQ0 5.0 1.0 1.0

I.Laponogov, X.-S.Pan, D.A.Veselkov, K.E.Mcauley, L.M.Fisher, M.R.Sanderson. Structural Basis of Gate-Dna Breakage and Resealing By Type II Topoisomerases Plos One V. 5 E1133 2010.
ISSN: ESSN 1932-6203
PubMed: 20596531
DOI: 10.1371/JOURNAL.PONE.0011338