Fluorine in PDB 3k9f: Detailed Structural Insight Into the Quinolone-Dna Cleavage Complex of Type Iia Topoisomerases

The structure of Detailed Structural Insight Into the Quinolone-Dna Cleavage Complex of Type Iia Topoisomerases, PDB code: 3k9f was solved by I.Laponogov, X.-S.Pan, D.A.Veselkov, 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)	26.73 / 2.90
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	122.407, 122.407, 178.287, 90.00, 90.00, 120.00
R / Rfree (%)	18.3 / 21.8

The structure of Detailed Structural Insight Into the Quinolone-Dna Cleavage Complex of Type Iia Topoisomerases also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Fluorine atom in the Detailed Structural Insight Into the Quinolone-Dna Cleavage Complex of Type Iia Topoisomerases (pdb code 3k9f). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Detailed Structural Insight Into the Quinolone-Dna Cleavage Complex of Type Iia Topoisomerases, PDB code: 3k9f:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Detailed Structural Insight Into the Quinolone-Dna Cleavage Complex of Type Iia Topoisomerases


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Detailed Structural Insight Into the Quinolone-Dna Cleavage Complex of Type Iia Topoisomerases within 5.0Å range: probe atom residue distance (Å) B Occ F:F0 b:0.8 occ:1.00 F F:LFX0 0.0 0.8 1.0 C11 F:LFX0 1.3 93.9 1.0 C13 F:LFX0 2.3 95.0 1.0 C04 F:LFX0 2.3 0.0 1.0 H13 F:LFX0 2.5 0.7 1.0 H01A F:LFX0 2.6 0.6 1.0 N01 F:LFX0 2.8 0.8 1.0 C01 F:LFX0 2.9 0.8 1.0 H01 F:LFX0 2.9 0.6 1.0 N7 F:DA5 3.2 64.0 1.0 N1 F:DC4 3.2 76.3 1.0 C2 F:DC4 3.3 87.2 1.0 C6 F:DC4 3.5 91.5 1.0 C5 F:DA5 3.5 68.6 1.0 C8 F:DA5 3.5 81.9 1.0 N3 F:DC4 3.5 60.1 1.0 C10 F:LFX0 3.6 96.9 1.0 C06 F:LFX0 3.6 0.3 1.0 C5 F:DC4 3.7 73.8 1.0 C4 F:DC4 3.7 65.0 1.0 C2' F:DC4 3.8 85.4 1.0 O2 F:DC4 3.8 95.3 1.0 C1' F:DC4 3.9 71.6 1.0 H02 F:LFX0 3.9 0.3 1.0 C4 F:DA5 4.0 80.6 1.0 C02 F:LFX0 4.0 99.8 1.0 N9 F:DA5 4.0 81.3 1.0 C6 F:DA5 4.0 65.0 1.0 C05 F:LFX0 4.1 0.6 1.0 N6 F:DA5 4.4 68.0 1.0 N1 H:DG1 4.4 75.1 1.0 C07 F:LFX0 4.5 0.2 1.0 N4 F:DC4 4.6 59.0 1.0 O4' F:DA5 4.6 76.5 1.0 O01 F:LFX0 4.6 0.5 1.0 H08 F:LFX0 4.7 81.3 1.0 H02A F:LFX0 4.7 0.3 1.0 N2 H:DG1 4.8 0.4 1.0 C15 F:LFX0 4.8 91.5 1.0 N3 F:DA5 4.8 90.6 1.0 H07A F:LFX0 4.8 0.0 1.0 N1 F:DA5 4.9 65.6 1.0 C08 F:LFX0 4.9 68.1 1.0 C2 H:DG1 4.9 0.0 1.0 C1' F:DA5 4.9 81.2 1.0 H07 F:LFX0 4.9 0.0 1.0 O02 F:LFX0 5.0 0.9 1.0

Fluorine binding site 2 out of 2 in the Detailed Structural Insight Into the Quinolone-Dna Cleavage Complex of Type Iia Topoisomerases


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Detailed Structural Insight Into the Quinolone-Dna Cleavage Complex of Type Iia Topoisomerases within 5.0Å range: probe atom residue distance (Å) B Occ H:F0 b:91.0 occ:1.00 F H:LFX0 0.0 91.0 1.0 C11 H:LFX0 1.3 95.5 1.0 C13 H:LFX0 2.3 99.6 1.0 C04 H:LFX0 2.3 0.5 1.0 H13 H:LFX0 2.5 0.2 1.0 H01A H:LFX0 2.6 0.7 1.0 N01 H:LFX0 2.8 0.4 1.0 H01 H:LFX0 2.8 0.7 1.0 C01 H:LFX0 2.9 0.6 1.0 C2 H:DT4 3.2 81.0 1.0 N7 H:DA5 3.4 59.4 1.0 N1 H:DT4 3.4 76.8 1.0 N3 H:DT4 3.4 64.5 1.0 C5 H:DA5 3.6 73.5 1.0 C10 H:LFX0 3.6 97.8 1.0 C8 H:DA5 3.6 78.0 1.0 C06 H:LFX0 3.6 0.7 1.0 O2 H:DT4 3.6 87.3 1.0 C6 H:DT4 3.7 97.3 1.0 H02 H:LFX0 3.8 0.9 1.0 C4 H:DT4 3.8 68.9 1.0 C02 H:LFX0 3.9 0.8 1.0 C5 H:DT4 3.9 98.7 1.0 C4 H:DA5 4.0 95.7 1.0 C2' H:DT4 4.0 86.9 1.0 N9 H:DA5 4.0 91.7 1.0 C1' H:DT4 4.0 80.9 1.0 C05 H:LFX0 4.1 0.5 1.0 C6 H:DA5 4.2 70.3 1.0 O4' H:DA5 4.4 76.0 1.0 C07 H:LFX0 4.5 0.0 1.0 O4 H:DT4 4.5 58.6 1.0 N1 F:DA1 4.5 71.7 1.0 N6 H:DA5 4.5 61.2 1.0 H02A H:LFX0 4.6 0.9 1.0 H08 H:LFX0 4.6 0.7 1.0 O01 H:LFX0 4.7 0.1 1.0 N3 H:DA5 4.8 0.5 1.0 C15 H:LFX0 4.8 94.7 1.0 C08 H:LFX0 4.8 91.8 1.0 C1' H:DA5 4.9 81.8 1.0 H07A H:LFX0 4.9 0.2 1.0 N1 H:DA5 4.9 77.6 1.0 H07 H:LFX0 4.9 0.2 1.0 C7 H:DT4 4.9 0.8 1.0 O02 H:LFX0 5.0 0.1 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