Fluorine in PDB 5btd: 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: 5btd 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)	47.39 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	107.907, 83.158, 129.203, 90.00, 108.65, 90.00
R / Rfree (%)	21.5 / 24.6

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 5btd). 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: 5btd:
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 E:F101 b:43.9 occ:1.00 F27 E:GFN101 0.0 43.9 1.0 C09 E:GFN101 1.3 42.1 1.0 C08 E:GFN101 2.4 42.4 1.0 C10 E:GFN101 2.4 41.5 1.0 H101 E:GFN101 2.6 49.8 1.0 H052 E:GFN101 2.7 54.6 1.0 N04 E:GFN101 2.7 43.7 1.0 C2 H:DT14 3.0 52.1 0.5 N7 F:DA15 3.1 0.7 0.5 C2 F:DC14 3.1 88.2 0.5 N3 H:DT14 3.1 52.5 0.5 N7 H:DA15 3.1 26.1 0.5 C5 F:DA15 3.2 0.1 0.5 C05 E:GFN101 3.2 45.5 1.0 C5 H:DA15 3.2 25.5 0.5 N3 F:DC14 3.2 89.3 0.5 N1 H:DT14 3.2 54.6 0.5 C8 H:DA15 3.4 26.4 0.5 O2 H:DT14 3.4 50.2 0.5 H3 H:DT14 3.4 63.1 0.5 N1 F:DC14 3.4 89.9 0.5 C8 F:DA15 3.4 0.2 0.5 O2 F:DC14 3.4 88.1 0.5 H2' H:DT14 3.5 73.2 0.5 C4 H:DT14 3.5 54.8 0.5 C4 H:DA15 3.6 25.5 0.5 C6 H:DT14 3.6 56.4 0.5 C4 F:DA15 3.6 99.9 0.5 C13 E:GFN101 3.6 43.2 1.0 C6 F:DA15 3.7 98.4 0.5 C4 F:DC14 3.7 89.6 0.5 C11 E:GFN101 3.7 40.2 1.0 N9 H:DA15 3.7 26.6 0.5 N2 E:DG11 3.7 0.7 0.5 H8 H:DA15 3.7 31.7 0.5 H2' F:DC14 3.8 0.3 0.5 N9 F:DA15 3.8 0.4 0.5 H061 E:GFN101 3.8 55.5 1.0 C5 H:DT14 3.8 57.1 0.5 C6 H:DA15 3.8 25.0 0.5 C6 F:DC14 3.8 89.2 0.5 H8 F:DA15 3.9 0.0 0.5 H62 F:DA15 3.9 99.0 0.5 H051 E:GFN101 4.0 54.6 1.0 C5 F:DC14 4.0 90.0 0.5 C03 E:GFN101 4.0 45.4 1.0 H2 G:DA11 4.0 41.7 0.5 C1' H:DT14 4.0 57.5 0.5 H1' H:DT14 4.0 69.0 0.5 N6 F:DA15 4.0 99.0 0.5 H031 E:GFN101 4.1 54.5 1.0 N1 G:DA11 4.1 33.9 0.5 H1' F:DC14 4.1 0.4 0.5 C2' H:DT14 4.1 61.0 0.5 C06 E:GFN101 4.1 46.2 1.0 C1' F:DC14 4.1 90.3 0.5 C12 E:GFN101 4.2 41.7 1.0 H62 H:DA15 4.2 30.0 0.5 N1 E:DG11 4.2 0.1 0.5 H6 H:DT14 4.2 67.7 0.5 C2 E:DG11 4.3 0.9 0.5 N6 H:DA15 4.3 25.0 0.5 C2 G:DA11 4.3 34.7 0.5 O4 H:DT14 4.3 55.4 0.5 H2'' H:DT14 4.3 73.2 0.5 C2' F:DC14 4.3 90.2 0.5 O4' H:DA15 4.4 32.5 0.5 H021 E:GFN101 4.4 57.8 1.0 N1 F:DA15 4.4 96.3 0.5 N3 H:DA15 4.4 25.1 0.5 H6 F:DC14 4.4 0.1 0.5 N4 F:DC14 4.4 90.9 0.5 H2'' F:DC14 4.4 0.3 0.5 N3 F:DA15 4.4 97.8 0.5 N1 H:DA15 4.6 24.6 0.5 O4' F:DA15 4.6 0.0 0.5 H5 F:DC14 4.6 1.0 0.5 C1' H:DA15 4.6 30.7 0.5 H032 E:GFN101 4.7 54.5 1.0 C02 E:GFN101 4.7 48.2 1.0 C2 F:DA15 4.7 96.5 0.5 H73 H:DT14 4.7 72.8 0.5 C2 H:DA15 4.7 24.7 0.5 C19 E:GFN101 4.8 39.3 1.0 H062 E:GFN101 4.8 55.5 1.0 O14 E:GFN101 4.8 45.5 1.0 C1' F:DA15 4.8 0.2 0.5 C7 H:DT14 4.9 60.6 0.5 H61 H:DA15 4.9 30.0 0.5 O20 E:GFN101 4.9 40.0 1.0 C6 G:DA11 4.9 33.1 0.5

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:46.5 occ:1.00 F27 G:GFN101 0.0 46.5 1.0 C09 G:GFN101 1.3 43.2 1.0 C08 G:GFN101 2.4 45.2 1.0 C10 G:GFN101 2.4 41.0 1.0 H101 G:GFN101 2.6 49.2 1.0 H052 G:GFN101 2.7 58.5 1.0 N04 G:GFN101 2.7 49.7 1.0 C2 G:DC14 3.0 34.7 0.5 C2 E:DT14 3.1 1.0 0.5 N7 G:DA15 3.1 37.4 0.5 C5 E:DA15 3.2 74.6 0.5 N3 E:DT14 3.2 0.1 0.5 C05 G:GFN101 3.2 48.7 1.0 N7 E:DA15 3.2 78.2 0.5 N3 G:DC14 3.2 35.1 0.5 H22 H:DG11 3.2 67.9 0.5 C5 G:DA15 3.3 36.9 0.5 N1 G:DC14 3.3 36.6 0.5 O2 E:DT14 3.4 0.3 0.5 H3 E:DT14 3.4 0.1 0.5 O2 G:DC14 3.4 33.1 0.5 N1 E:DT14 3.4 0.4 0.5 C8 G:DA15 3.4 37.7 0.5 C8 E:DA15 3.5 78.2 0.5 C4 E:DA15 3.6 72.6 0.5 C4 G:DC14 3.6 36.4 0.5 H2' G:DC14 3.6 49.3 0.5 C13 G:GFN101 3.6 44.2 1.0 C6 E:DA15 3.6 73.3 0.5 C4 G:DA15 3.7 37.0 0.5 C11 G:GFN101 3.7 40.6 1.0 C6 G:DC14 3.7 38.3 0.5 C4 E:DT14 3.7 0.3 0.5 H2' E:DT14 3.7 0.6 0.5 H061 G:GFN101 3.7 59.5 1.0 N9 G:DA15 3.8 37.5 0.5 N9 E:DA15 3.8 75.3 0.5 C6 G:DA15 3.8 36.5 0.5 C5 G:DC14 3.8 38.3 0.5 H8 G:DA15 3.8 45.3 0.5 C6 E:DT14 3.9 0.7 0.5 N2 H:DG11 3.9 56.6 0.5 C03 G:GFN101 3.9 52.4 1.0 H2 F:DA11 3.9 81.3 0.5 H1' G:DC14 3.9 45.0 0.5 H051 G:GFN101 3.9 58.5 1.0 C1' G:DC14 4.0 37.5 0.5 H8 E:DA15 4.0 93.8 0.5 H031 G:GFN101 4.0 62.8 1.0 C5 E:DT14 4.0 0.2 0.5 N1 H:DG11 4.0 53.5 0.5 H62 E:DA15 4.0 91.3 0.5 C06 G:GFN101 4.1 49.6 1.0 N6 E:DA15 4.1 76.1 0.5 C2' G:DC14 4.1 41.1 0.5 N1 F:DA11 4.1 70.9 0.5 H1' E:DT14 4.2 0.0 0.5 C12 G:GFN101 4.2 43.3 1.0 C1' E:DT14 4.2 0.2 0.5 N6 G:DA15 4.2 36.4 0.5 H6 G:DC14 4.2 46.0 0.5 C2 H:DG11 4.3 55.6 0.5 H2'' G:DC14 4.3 49.3 0.5 C2 F:DA11 4.3 67.8 0.5 C2' E:DT14 4.3 0.3 0.5 N3 E:DA15 4.3 69.4 0.5 N1 E:DA15 4.3 70.2 0.5 H021 G:GFN101 4.3 62.9 1.0 O4 E:DT14 4.4 0.4 0.5 N4 G:DC14 4.4 36.8 0.5 H2'' E:DT14 4.4 0.6 0.5 O4' G:DA15 4.4 38.2 0.5 N3 G:DA15 4.4 36.6 0.5 H5 G:DC14 4.5 45.9 0.5 H6 E:DT14 4.5 0.2 0.5 O4' E:DA15 4.5 78.4 0.5 N1 G:DA15 4.5 36.1 0.5 C2 E:DA15 4.5 69.4 0.5 H21 H:DG11 4.6 67.9 0.5 H42 G:DC14 4.6 44.2 0.5 H032 G:GFN101 4.6 62.8 1.0 C02 G:GFN101 4.6 52.5 1.0 C1' G:DA15 4.7 37.8 0.5 C2 G:DA15 4.7 36.2 0.5 H062 G:GFN101 4.7 59.5 1.0 C1' E:DA15 4.8 75.0 0.5 O14 G:GFN101 4.8 45.6 1.0 C19 G:GFN101 4.8 40.1 1.0 H41 G:DC14 4.9 44.2 0.5 H61 G:DA15 4.9 43.6 0.5 C6 H:DG11 4.9 52.6 0.5 O20 G:GFN101 4.9 41.7 1.0 H72 E:DT14 5.0 0.2 0.5 N07 G:GFN101 5.0 52.0 1.0

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