Fluorine in PDB 5btf: Crystal Structure of A Topoisomerase II Complex

All present enzymatic activity of Crystal Structure of A Topoisomerase II Complex:
5.99.1.3;

The structure of Crystal Structure of A Topoisomerase II Complex, PDB code: 5btf was solved by T.R.Blower, B.H.Williamson, R.J.Kerns, J.M.Berger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.78 / 2.61
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	108.955, 84.019, 130.590, 90.00, 108.87, 90.00
R / Rfree (%)	23 / 26.1

The structure of Crystal Structure of A Topoisomerase II Complex also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Fluorine atom in the Crystal Structure of A Topoisomerase II Complex (pdb code 5btf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of A Topoisomerase II Complex, PDB code: 5btf:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of A Topoisomerase II Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of A Topoisomerase II Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:F101 b:51.3 occ:1.00 F27 F:GFN101 0.0 51.3 1.0 C09 F:GFN101 1.3 49.7 1.0 C08 F:GFN101 2.4 52.1 1.0 C10 F:GFN101 2.4 48.2 1.0 H101 F:GFN101 2.6 57.8 1.0 N04 F:GFN101 2.7 53.4 1.0 H052 F:GFN101 2.8 68.2 1.0 C2 H:DT14 3.0 62.7 0.5 N7 F:DA15 3.1 0.8 0.5 N3 H:DT14 3.1 62.7 0.5 C2 F:DC14 3.2 0.8 0.5 C5 F:DA15 3.2 0.2 0.5 N7 H:DA15 3.2 37.2 0.5 C05 F:GFN101 3.2 56.9 1.0 N1 H:DT14 3.3 63.1 0.5 C5 H:DA15 3.3 35.1 0.5 N3 F:DC14 3.4 0.9 0.5 O2 H:DT14 3.4 62.4 0.5 N1 F:DC14 3.4 0.8 0.5 C8 F:DA15 3.4 1.0 0.5 C8 H:DA15 3.5 37.8 0.5 H2' H:DT14 3.5 76.8 0.5 O2 F:DC14 3.5 0.4 0.5 C4 H:DT14 3.6 63.0 0.5 H2' F:DC14 3.6 0.1 0.5 C4 H:DA15 3.6 34.5 0.5 C4 F:DA15 3.6 0.4 0.5 C6 H:DT14 3.6 63.4 0.5 C13 F:GFN101 3.6 48.9 1.0 C11 F:GFN101 3.7 47.8 1.0 C6 F:DA15 3.7 0.7 0.5 N9 H:DA15 3.8 36.2 0.5 C4 F:DC14 3.8 0.9 0.5 N9 F:DA15 3.8 0.9 0.5 C6 H:DA15 3.8 33.8 0.5 C6 F:DC14 3.8 0.4 0.5 C5 H:DT14 3.8 63.4 0.5 H061 F:GFN101 3.9 67.1 1.0 H8 F:DA15 3.9 0.4 0.5 H8 H:DA15 3.9 45.3 0.5 C03 F:GFN101 4.0 52.9 1.0 C5 F:DC14 4.0 0.2 0.5 C1' H:DT14 4.0 63.1 0.5 H051 F:GFN101 4.0 68.2 1.0 H1' H:DT14 4.0 75.7 0.5 N2 E:DG11 4.0 0.3 0.5 H031 F:GFN101 4.0 63.5 1.0 H1' F:DC14 4.0 0.1 0.5 H2 G:DA11 4.0 60.0 0.5 C1' F:DC14 4.1 0.8 0.5 C2' H:DT14 4.1 64.0 0.5 N6 F:DA15 4.1 0.8 0.5 N1 G:DA11 4.2 49.7 0.5 C06 F:GFN101 4.2 55.9 1.0 C12 F:GFN101 4.2 47.6 1.0 C2' F:DC14 4.2 0.6 0.5 H62 H:DA15 4.2 41.2 0.5 H6 H:DT14 4.2 76.1 0.5 N6 H:DA15 4.2 34.4 0.5 H2'' H:DT14 4.3 76.8 0.5 O4 H:DT14 4.3 63.0 0.5 H2'' F:DC14 4.3 0.1 0.5 C2 G:DA11 4.3 50.0 0.5 H6 F:DC14 4.3 0.5 0.5 N3 H:DA15 4.4 32.9 0.5 H021 F:GFN101 4.4 66.0 1.0 O4' H:DA15 4.4 38.8 0.5 N3 F:DA15 4.4 0.8 0.5 N1 F:DA15 4.5 0.2 0.5 N1 E:DG11 4.5 0.1 0.5 N1 H:DA15 4.5 32.1 0.5 O4' F:DA15 4.5 0.7 0.5 C2 E:DG11 4.5 0.5 0.5 N4 F:DC14 4.5 0.5 0.5 H5 F:DC14 4.6 0.1 0.5 H032 F:GFN101 4.7 63.5 1.0 C2 H:DA15 4.7 31.8 0.5 C02 F:GFN101 4.7 55.0 1.0 C2 F:DA15 4.7 0.4 0.5 C1' H:DA15 4.7 36.6 0.5 H73 H:DT14 4.7 76.6 0.5 C1' F:DA15 4.8 0.9 0.5 O14 F:GFN101 4.8 49.5 1.0 C19 F:GFN101 4.8 47.4 1.0 H61 H:DA15 4.8 41.2 0.5 H062 F:GFN101 4.9 67.1 1.0 C7 H:DT14 4.9 63.8 0.5 O20 F:GFN101 4.9 48.2 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of A Topoisomerase II Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of A Topoisomerase II Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:F101 b:50.5 occ:1.00 F27 G:GFN101 0.0 50.5 1.0 C09 G:GFN101 1.3 49.8 1.0 C08 G:GFN101 2.4 51.4 1.0 C10 G:GFN101 2.4 48.6 1.0 H101 G:GFN101 2.6 58.3 1.0 N04 G:GFN101 2.7 54.9 1.0 H052 G:GFN101 2.9 68.3 1.0 C2 G:DC14 3.1 66.7 0.5 N7 E:DA15 3.1 77.5 0.5 N7 G:DA15 3.2 44.6 0.5 C2 E:DT14 3.2 0.4 0.5 C5 E:DA15 3.2 75.4 0.5 C5 G:DA15 3.3 42.9 0.5 N1 G:DC14 3.3 67.6 0.5 N3 G:DC14 3.3 66.8 0.5 H2' E:DT14 3.3 0.2 0.5 C05 G:GFN101 3.3 57.0 1.0 C8 E:DA15 3.3 77.3 0.5 N1 E:DT14 3.3 0.7 0.5 C8 G:DA15 3.5 44.7 0.5 N3 E:DT14 3.5 0.7 0.5 O2 G:DC14 3.5 66.4 0.5 H2' G:DC14 3.5 84.1 0.5 C4 E:DA15 3.5 74.0 0.5 O2 E:DT14 3.6 0.1 0.5 N9 E:DA15 3.6 75.2 0.5 C4 G:DC14 3.6 67.7 0.5 C6 G:DC14 3.6 68.5 0.5 C13 G:GFN101 3.6 50.2 1.0 C4 G:DA15 3.7 41.9 0.5 C11 G:GFN101 3.7 49.3 1.0 H8 E:DA15 3.7 92.8 0.5 C6 E:DT14 3.7 0.2 0.5 N9 G:DA15 3.8 43.1 0.5 C6 G:DA15 3.8 42.1 0.5 C5 G:DC14 3.8 68.8 0.5 H3 E:DT14 3.8 0.0 0.5 C6 E:DA15 3.9 74.7 0.5 H8 G:DA15 3.9 53.6 0.5 C2' E:DT14 3.9 0.7 0.5 C4 E:DT14 3.9 0.1 0.5 C1' E:DT14 3.9 0.9 0.5 C03 G:GFN101 3.9 57.0 1.0 H1' G:DC14 3.9 80.4 0.5 C1' G:DC14 4.0 67.0 0.5 H1' E:DT14 4.0 0.2 0.5 C5 E:DT14 4.0 0.4 0.5 H051 G:GFN101 4.0 68.3 1.0 H2'' E:DT14 4.0 0.2 0.5 H031 G:GFN101 4.0 68.4 1.0 C2' G:DC14 4.1 70.1 0.5 H071 G:GFN101 4.1 70.1 1.0 O4' E:DA15 4.2 76.7 0.5 N2 H:DG11 4.2 57.6 0.5 C12 G:GFN101 4.2 49.8 1.0 H6 G:DC14 4.2 82.3 0.5 H22 H:DG11 4.2 69.1 0.5 H21 H:DG11 4.2 69.1 0.5 N6 G:DA15 4.2 43.0 0.5 H2'' G:DC14 4.2 84.1 0.5 H6 E:DT14 4.2 0.7 0.5 C06 G:GFN101 4.2 58.1 1.0 H2 F:DA11 4.3 0.2 0.5 N1 H:DG11 4.3 57.3 0.5 H061 G:GFN101 4.3 69.7 1.0 H62 E:DA15 4.3 91.5 0.5 N3 E:DA15 4.3 72.0 0.5 N6 E:DA15 4.4 76.2 0.5 H5 G:DC14 4.4 82.5 0.5 N4 G:DC14 4.4 67.2 0.5 N3 G:DA15 4.4 40.3 0.5 O4' G:DA15 4.5 43.5 0.5 C1' E:DA15 4.5 74.8 0.5 N1 F:DA11 4.5 0.8 0.5 N07 G:GFN101 4.5 58.4 1.0 N1 G:DA15 4.5 40.5 0.5 C2 H:DG11 4.5 57.5 0.5 N1 E:DA15 4.6 72.8 0.5 C2 F:DA11 4.6 0.2 0.5 C02 G:GFN101 4.6 58.2 1.0 H032 G:GFN101 4.6 68.4 1.0 O4 E:DT14 4.7 0.5 0.5 C2 E:DA15 4.7 71.6 0.5 C2 G:DA15 4.7 39.7 0.5 H021 G:GFN101 4.7 69.9 1.0 C1' G:DA15 4.7 42.9 0.5 O14 G:GFN101 4.8 50.2 1.0 C19 G:GFN101 4.8 52.2 1.0 H72 E:DT14 4.8 0.6 0.5 O20 G:GFN101 4.9 55.4 1.0 H1' E:DA15 5.0 89.8 0.5 H61 E:DA15 5.0 91.5 0.5

T.R.Blower, B.H.Williamson, R.J.Kerns, J.M.Berger. Crystal Structure and Stability of Gyrase-Fluoroquinolone Cleaved Complexes From Mycobacterium Tuberculosis. Proc.Natl.Acad.Sci.Usa V. 113 1706 2016.
ISSN: ESSN 1091-6490
PubMed: 26792525
DOI: 10.1073/PNAS.1525047113