Fluorine in PDB 5bta: 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: 5bta 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)	49.46 / 2.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	108.340, 83.205, 129.757, 90.00, 108.55, 90.00
R / Rfree (%)	22.3 / 25.1

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 5bta). 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: 5bta:
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 G:F101 b:48.8 occ:1.00 F G:MFX101 0.0 48.8 1.0 C15 G:MFX101 1.3 48.1 1.0 H04 G:MFX101 2.2 55.6 1.0 C17 G:MFX101 2.4 48.7 1.0 C11 G:MFX101 2.4 46.7 1.0 H17 G:MFX101 2.6 58.5 1.0 C04 G:MFX101 3.0 46.4 1.0 C2 G:DC14 3.0 44.7 0.5 N01 G:MFX101 3.0 46.0 1.0 C2 E:DT14 3.0 0.5 0.5 N3 G:DC14 3.0 44.6 0.5 N7 G:DA15 3.1 36.2 0.5 N3 E:DT14 3.1 0.9 0.5 N7 E:DA15 3.2 1.0 0.5 N1 G:DC14 3.2 46.4 0.5 H03A G:MFX101 3.2 0.8 1.0 C5 E:DA15 3.2 0.1 0.5 C5 G:DA15 3.3 35.2 0.5 N1 E:DT14 3.3 0.9 0.5 C4 G:DC14 3.3 45.9 0.5 H22 H:DG11 3.3 63.4 0.5 H3 E:DT14 3.4 0.1 0.5 O2 E:DT14 3.4 0.2 0.5 C6 G:DC14 3.5 47.7 0.5 C8 G:DA15 3.5 36.7 0.5 O2 G:DC14 3.5 43.8 0.5 C4 E:DT14 3.5 0.7 0.5 C5 G:DC14 3.5 47.4 0.5 C8 E:DA15 3.5 0.6 0.5 H2' E:DT14 3.6 0.4 0.5 C6 E:DT14 3.6 0.6 0.5 H04A G:MFX101 3.6 55.6 1.0 C14 G:MFX101 3.7 48.1 1.0 C4 E:DA15 3.7 0.1 0.5 C03 G:MFX101 3.7 0.6 1.0 C13 G:MFX101 3.7 47.2 1.0 H2' G:DC14 3.7 59.7 0.5 C6 E:DA15 3.7 0.6 0.5 C6 G:DA15 3.8 34.3 0.5 H02 G:MFX101 3.8 72.3 1.0 C5 E:DT14 3.8 0.2 0.5 C4 G:DA15 3.8 35.1 0.5 N9 E:DA15 3.8 0.4 0.5 H8 G:DA15 3.9 44.0 0.5 N9 G:DA15 3.9 36.1 0.5 C02 G:MFX101 4.0 60.3 1.0 H8 E:DA15 4.0 1.0 0.5 N2 H:DG11 4.0 52.9 0.5 N1 H:DG11 4.0 51.6 0.5 H62 E:DA15 4.0 0.9 0.5 C1' G:DC14 4.0 48.0 0.5 C1' E:DT14 4.0 0.9 0.5 H6 G:DC14 4.0 57.2 0.5 H1' G:DC14 4.0 57.6 0.5 N6 G:DA15 4.1 34.3 0.5 N4 G:DC14 4.1 46.9 0.5 H1' E:DT14 4.1 0.3 0.5 H2 F:DA11 4.1 0.8 0.5 N6 E:DA15 4.1 0.5 0.5 H5 G:DC14 4.1 56.9 0.5 C2' E:DT14 4.1 0.8 0.5 N1 F:DA11 4.2 1.0 0.5 C12 G:MFX101 4.2 47.8 1.0 H6 E:DT14 4.2 0.3 0.5 C2' G:DC14 4.2 49.7 0.5 O4 E:DT14 4.2 0.3 0.5 C2 H:DG11 4.3 52.4 0.5 H03 G:MFX101 4.3 0.8 1.0 H2'' E:DT14 4.4 0.4 0.5 C2 F:DA11 4.4 0.9 0.5 N1 E:DA15 4.4 99.0 0.5 H2'' G:DC14 4.4 59.7 0.5 N3 E:DA15 4.4 99.7 0.5 N1 G:DA15 4.6 33.5 0.5 O4' E:DA15 4.6 0.0 0.5 C01 G:MFX101 4.6 60.4 1.0 N3 G:DA15 4.6 34.2 0.5 H72 E:DT14 4.6 0.9 0.5 C2 E:DA15 4.7 98.2 0.5 H61 E:DA15 4.7 0.9 0.5 O4' G:DA15 4.7 37.2 0.5 H21 H:DG11 4.7 63.4 0.5 O01 G:MFX101 4.8 48.2 1.0 HN02 G:MFX101 4.8 71.0 1.0 C7 E:DT14 4.8 0.6 0.5 C1' E:DA15 4.8 0.7 0.5 C2 G:DA15 4.9 33.5 0.5 H G:MFX101 4.9 57.9 1.0 C6 H:DG11 4.9 51.3 0.5 C19 G:MFX101 4.9 49.0 1.0 C1' G:DA15 4.9 36.4 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 H:F101 b:53.5 occ:1.00 F H:MFX101 0.0 53.5 1.0 C15 H:MFX101 1.3 52.5 1.0 H04A H:MFX101 2.2 62.7 1.0 C17 H:MFX101 2.3 51.8 1.0 C11 H:MFX101 2.4 51.8 1.0 H17 H:MFX101 2.5 62.1 1.0 N3 H:DT14 2.7 54.1 0.5 C2 H:DT14 2.9 54.5 0.5 C2 F:DC14 3.0 0.7 0.5 C04 H:MFX101 3.0 52.2 1.0 C4 H:DT14 3.0 57.3 0.5 N3 F:DC14 3.1 0.9 0.5 N01 H:MFX101 3.1 51.7 1.0 N1 H:DT14 3.1 64.3 0.5 N7 F:DA15 3.2 0.1 0.5 N7 H:DA15 3.2 41.0 0.5 N1 F:DC14 3.2 1.0 0.5 C5 H:DT14 3.3 59.1 0.5 C6 H:DT14 3.3 57.6 0.5 C5 H:DA15 3.3 39.9 0.5 C5 F:DA15 3.3 0.8 0.5 C4 F:DC14 3.4 0.1 0.5 O2 H:DT14 3.5 53.5 0.5 O2 F:DC14 3.5 0.3 0.5 C6 F:DC14 3.5 0.1 0.5 H04 H:MFX101 3.6 62.7 1.0 C8 F:DA15 3.6 0.3 0.5 C8 H:DA15 3.6 41.4 0.5 C5 F:DC14 3.6 0.2 0.5 C14 H:MFX101 3.6 51.5 1.0 O4 H:DT14 3.7 55.2 0.5 C13 H:MFX101 3.7 51.5 1.0 H2' H:DT14 3.7 71.5 0.5 H2' F:DC14 3.7 1.0 0.5 H22 E:DG11 3.7 0.9 0.5 C6 H:DA15 3.8 39.1 0.5 C6 F:DA15 3.8 0.4 0.5 H2 G:DA11 3.9 52.0 0.5 C4 H:DA15 3.9 38.8 0.5 N1 G:DA11 3.9 43.4 0.5 H02 H:MFX101 3.9 77.1 1.0 C4 F:DA15 3.9 0.7 0.5 N2 E:DG11 3.9 0.9 0.5 H62 F:DA15 3.9 0.9 0.5 H03A H:MFX101 4.0 90.9 1.0 H6 H:DT14 4.0 69.1 0.5 H62 H:DA15 4.0 48.8 0.5 H8 F:DA15 4.0 0.1 0.5 H8 H:DA15 4.0 49.6 0.5 N9 H:DA15 4.0 39.6 0.5 N9 F:DA15 4.0 0.5 0.5 N1 E:DG11 4.0 0.6 0.5 C1' F:DC14 4.0 0.5 0.5 H1' F:DC14 4.0 0.2 0.5 N6 F:DA15 4.1 0.1 0.5 C1' H:DT14 4.1 57.3 0.5 N6 H:DA15 4.1 40.7 0.5 C02 H:MFX101 4.1 64.3 1.0 N4 F:DC14 4.1 0.9 0.5 H21 E:DG11 4.1 0.4 0.5 H6 F:DC14 4.1 0.1 0.5 C2 G:DA11 4.1 43.3 0.5 C03 H:MFX101 4.1 75.8 1.0 C12 H:MFX101 4.2 51.8 1.0 H73 H:DT14 4.2 70.7 0.5 H1' H:DT14 4.2 68.8 0.5 H5 F:DC14 4.2 0.1 0.5 C2' F:DC14 4.2 0.2 0.5 C2 E:DG11 4.3 0.6 0.5 C2' H:DT14 4.3 59.6 0.5 C7 H:DT14 4.3 58.9 0.5 H42 F:DC14 4.4 0.1 0.5 H2'' F:DC14 4.4 1.0 0.5 N1 H:DA15 4.6 38.3 0.5 H2'' H:DT14 4.6 71.5 0.5 N1 F:DA15 4.6 0.4 0.5 H41 F:DC14 4.6 0.1 0.5 H61 F:DA15 4.7 0.9 0.5 N3 H:DA15 4.7 37.8 0.5 H61 H:DA15 4.7 48.8 0.5 H61 G:DA11 4.7 47.4 0.5 N3 F:DA15 4.7 0.1 0.5 HN02 H:MFX101 4.7 77.6 1.0 H71 H:DT14 4.7 70.7 0.5 C6 G:DA11 4.8 43.5 0.5 O4' H:DA15 4.8 38.9 0.5 O4' F:DA15 4.8 0.5 0.5 C19 H:MFX101 4.8 52.9 1.0 O01 H:MFX101 4.9 51.0 1.0 C01 H:MFX101 4.9 63.7 1.0 H03 H:MFX101 4.9 90.9 1.0 C2 H:DA15 4.9 37.7 0.5 C2 F:DA15 4.9 0.4 0.5 C6 E:DG11 4.9 0.3 0.5 O02 H:MFX101 5.0 53.5 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