Fluorine in PDB 5btg: 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: 5btg 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)	46.33 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	108.094, 82.989, 129.101, 90.00, 108.76, 90.00
R / Rfree (%)	22.6 / 24.9

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 5btg). 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: 5btg:
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:34.7 occ:1.00 F E:LFX101 0.0 34.7 1.0 C11 E:LFX101 1.4 34.7 1.0 H02A E:LFX101 2.4 52.5 1.0 C13 E:LFX101 2.4 33.5 1.0 C04 E:LFX101 2.5 36.8 1.0 H02 E:LFX101 2.5 52.5 1.0 H13 E:LFX101 2.6 40.2 1.0 C02 E:LFX101 2.7 43.7 1.0 C2 F:DC14 3.0 0.3 0.5 N01 E:LFX101 3.0 41.3 1.0 C2 H:DT14 3.0 34.4 0.5 N7 H:DA15 3.1 17.0 0.5 N3 H:DT14 3.1 34.8 0.5 N7 F:DA15 3.1 96.3 0.5 N3 F:DC14 3.2 0.5 0.5 C5 H:DA15 3.2 15.9 0.5 C5 F:DA15 3.2 93.8 0.5 N1 H:DT14 3.3 34.6 0.5 N1 F:DC14 3.3 0.7 0.5 C8 H:DA15 3.4 17.9 0.5 O2 F:DC14 3.4 0.5 0.5 C4 H:DT14 3.5 36.1 0.5 C8 F:DA15 3.5 97.4 0.5 O2 H:DT14 3.5 34.1 0.5 H2' H:DT14 3.5 40.0 0.5 H01A E:LFX101 3.5 52.1 1.0 C4 F:DC14 3.6 0.9 0.5 C6 H:DT14 3.6 36.5 0.5 C4 H:DA15 3.6 16.5 0.5 H2' F:DC14 3.7 0.3 0.5 C10 E:LFX101 3.7 32.2 1.0 N9 H:DA15 3.7 18.4 0.5 C5 H:DT14 3.7 36.9 0.5 C4 F:DA15 3.7 93.5 0.5 C6 F:DA15 3.7 91.7 0.5 C06 E:LFX101 3.7 34.0 1.0 H8 H:DA15 3.7 21.5 0.5 C6 F:DC14 3.7 0.7 0.5 C6 H:DA15 3.8 14.7 0.5 C01 E:LFX101 3.8 43.5 1.0 N9 F:DA15 3.9 96.8 0.5 N2 E:DG11 3.9 0.3 0.5 C5 F:DC14 3.9 0.4 0.5 H8 F:DA15 3.9 0.8 0.5 H1' F:DC14 4.0 0.3 0.5 H2 G:DA11 4.0 32.3 0.5 C1' F:DC14 4.1 0.9 0.5 C1' H:DT14 4.1 33.8 0.5 N6 F:DA15 4.1 92.2 0.5 N1 G:DA11 4.1 26.3 0.5 H62 H:DA15 4.1 16.8 0.5 C2' H:DT14 4.1 33.3 0.5 H1' H:DT14 4.2 40.6 0.5 H6 H:DT14 4.2 43.8 0.5 O4 H:DT14 4.2 36.5 0.5 C08 E:LFX101 4.2 46.5 1.0 C2' F:DC14 4.2 0.4 0.5 C05 E:LFX101 4.2 32.7 1.0 N6 H:DA15 4.2 14.0 0.5 N1 E:DG11 4.3 0.6 0.5 H2'' H:DT14 4.3 40.0 0.5 H6 F:DC14 4.3 0.5 0.5 N4 F:DC14 4.3 0.8 0.5 C2 G:DA11 4.4 26.9 0.5 H2'' F:DC14 4.4 0.3 0.5 O4' H:DA15 4.4 22.4 0.5 C2 E:DG11 4.4 0.1 0.5 H08 E:LFX101 4.4 55.8 1.0 H01 E:LFX101 4.4 52.1 1.0 N3 H:DA15 4.4 16.1 0.5 N1 F:DA15 4.5 89.7 0.5 H5 F:DC14 4.5 0.1 0.5 N3 F:DA15 4.5 91.3 0.5 N1 H:DA15 4.5 14.4 0.5 H73 H:DT14 4.6 45.9 0.5 O4' F:DA15 4.6 0.8 0.5 H08A E:LFX101 4.6 55.8 1.0 C1' H:DA15 4.7 21.2 0.5 C2 H:DA15 4.7 14.7 0.5 C7 H:DT14 4.8 38.2 0.5 C2 F:DA15 4.8 89.5 0.5 H61 H:DA15 4.8 16.8 0.5 C1' F:DA15 4.9 99.0 0.5 C07 E:LFX101 4.9 45.5 1.0 C15 E:LFX101 4.9 31.0 1.0 O01 E:LFX101 5.0 33.9 1.0 H41 F:DC14 5.0 0.3 0.5 C6 G:DA11 5.0 25.2 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 F:F101 b:34.3 occ:1.00 F F:LFX101 0.0 34.3 1.0 C11 F:LFX101 1.4 32.6 1.0 H02A F:LFX101 2.3 46.0 1.0 C13 F:LFX101 2.4 30.6 1.0 C04 F:LFX101 2.4 34.0 1.0 H13 F:LFX101 2.6 36.7 1.0 H01A F:LFX101 2.8 46.3 1.0 C02 F:LFX101 2.9 38.3 1.0 N01 F:LFX101 3.0 37.2 1.0 C2 E:DT14 3.1 0.7 0.5 H02 F:LFX101 3.2 46.0 1.0 C2 G:DC14 3.2 29.2 0.5 N7 G:DA15 3.2 26.9 0.5 C5 G:DA15 3.2 25.3 0.5 C5 E:DA15 3.3 63.2 0.5 H22 H:DG11 3.3 80.5 0.5 N7 E:DA15 3.3 68.3 0.5 O2 E:DT14 3.3 0.7 0.5 C01 F:LFX101 3.3 38.6 1.0 N3 E:DT14 3.4 0.4 0.5 N3 G:DC14 3.4 26.2 0.5 N1 G:DC14 3.4 26.9 0.5 C8 G:DA15 3.4 27.4 0.5 N1 E:DT14 3.5 0.4 0.5 C4 E:DA15 3.5 63.5 0.5 H2' G:DC14 3.5 37.3 0.5 C8 E:DA15 3.6 69.0 0.5 C4 G:DA15 3.6 25.2 0.5 O2 G:DC14 3.6 26.9 0.5 H2' E:DT14 3.6 1.0 0.5 N9 G:DA15 3.7 26.9 0.5 C4 G:DC14 3.7 28.1 0.5 C10 F:LFX101 3.7 29.9 1.0 N9 E:DA15 3.7 66.0 0.5 C6 G:DC14 3.7 30.7 0.5 C06 F:LFX101 3.7 32.5 1.0 C6 E:DA15 3.8 61.7 0.5 C6 G:DA15 3.8 22.9 0.5 H01 F:LFX101 3.8 46.3 1.0 H8 G:DA15 3.9 32.8 0.5 C5 G:DC14 3.9 28.7 0.5 C4 E:DT14 3.9 0.6 0.5 C6 E:DT14 4.0 0.4 0.5 N2 H:DG11 4.0 67.1 0.5 H1' G:DC14 4.0 36.4 0.5 H2 F:DA11 4.0 0.6 0.5 H8 E:DA15 4.0 82.7 0.5 C1' G:DC14 4.0 30.3 0.5 H1' E:DT14 4.1 0.3 0.5 C1' E:DT14 4.1 0.9 0.5 C2' G:DC14 4.1 31.1 0.5 C2' E:DT14 4.1 0.8 0.5 N1 H:DG11 4.2 58.1 0.5 N3 E:DA15 4.2 60.6 0.5 C05 F:LFX101 4.2 31.3 1.0 H2'' G:DC14 4.2 37.3 0.5 C5 E:DT14 4.2 0.1 0.5 H2'' E:DT14 4.2 1.0 0.5 H6 G:DC14 4.3 36.8 0.5 N6 G:DA15 4.3 22.7 0.5 N6 E:DA15 4.3 62.8 0.5 H62 E:DA15 4.3 75.3 0.5 O4' E:DA15 4.3 69.4 0.5 O4' G:DA15 4.3 29.7 0.5 C08 F:LFX101 4.3 39.4 1.0 N3 G:DA15 4.3 24.1 0.5 N1 F:DA11 4.3 1.0 0.5 N1 E:DA15 4.3 59.4 0.5 C2 H:DG11 4.4 58.9 0.5 C2 F:DA11 4.4 0.8 0.5 H08 F:LFX101 4.5 47.3 1.0 N1 G:DA15 4.5 22.2 0.5 C2 E:DA15 4.5 58.6 0.5 N4 G:DC14 4.5 26.2 0.5 H5 G:DC14 4.5 34.4 0.5 H6 E:DT14 4.6 0.7 0.5 C1' G:DA15 4.6 28.4 0.5 C1' E:DA15 4.6 67.0 0.5 C07 F:LFX101 4.6 39.6 1.0 C2 G:DA15 4.6 22.6 0.5 O4 E:DT14 4.7 0.1 0.5 H21 H:DG11 4.7 80.5 0.5 H07 F:LFX101 4.8 47.5 1.0 H61 E:DA15 4.9 75.3 0.5 H61 G:DA15 4.9 27.3 0.5 H08A F:LFX101 4.9 47.3 1.0 C15 F:LFX101 5.0 29.4 1.0 O01 F:LFX101 5.0 32.4 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