Fluorine in PDB 5bti: 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: 5bti 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)	49.43 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	108.390, 83.280, 129.701, 90.00, 108.73, 90.00
R / Rfree (%)	21.5 / 24

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 5bti). 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: 5bti:
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:39.0 occ:1.00 F E:LFX101 0.0 39.0 1.0 C11 E:LFX101 1.4 39.1 1.0 C04 E:LFX101 2.4 41.6 1.0 C13 E:LFX101 2.4 37.6 1.0 H13 E:LFX101 2.6 45.2 1.0 N01 E:LFX101 2.8 44.7 1.0 N7 F:DA15 3.0 80.7 0.5 N7 H:DA15 3.0 29.0 0.5 C2 H:DT14 3.0 46.0 0.5 N3 H:DT14 3.1 45.9 0.5 C2 F:DC14 3.2 96.2 0.5 C5 H:DA15 3.2 28.1 0.5 C5 F:DA15 3.2 80.4 0.5 N1 H:DT14 3.2 47.9 0.5 C8 H:DA15 3.3 29.2 0.5 C8 F:DA15 3.3 80.7 0.5 H02A E:LFX101 3.3 56.3 1.0 N1 F:DC14 3.3 98.5 0.5 N3 F:DC14 3.3 97.8 0.5 C4 H:DT14 3.4 47.6 0.5 H2' H:DT14 3.4 60.5 0.5 H2' F:DC14 3.5 0.6 0.5 O2 H:DT14 3.5 44.9 0.5 C6 H:DT14 3.5 49.7 0.5 C4 H:DA15 3.6 27.9 0.5 O2 F:DC14 3.6 96.5 0.5 C4 F:DA15 3.6 79.5 0.5 N9 H:DA15 3.6 28.6 0.5 C02 E:LFX101 3.6 47.0 1.0 C4 F:DC14 3.6 99.0 0.5 C5 H:DT14 3.6 49.7 0.5 N9 F:DA15 3.6 80.9 0.5 C6 F:DC14 3.6 97.2 0.5 H8 F:DA15 3.6 96.8 0.5 H8 H:DA15 3.6 35.1 0.5 C10 E:LFX101 3.7 37.8 1.0 C06 E:LFX101 3.7 41.4 1.0 C6 F:DA15 3.8 78.6 0.5 C6 H:DA15 3.8 27.5 0.5 C5 F:DC14 3.8 98.2 0.5 H01A E:LFX101 3.9 55.3 1.0 C01 E:LFX101 3.9 46.1 1.0 C1' F:DC14 4.0 98.4 0.5 C1' H:DT14 4.0 49.2 0.5 H62 F:DA15 4.0 95.9 0.5 H1' F:DC14 4.1 0.1 0.5 C2' H:DT14 4.1 50.5 0.5 C2' F:DC14 4.1 97.2 0.5 H6 H:DT14 4.1 59.6 0.5 H62 H:DA15 4.1 33.2 0.5 H1' H:DT14 4.1 59.0 0.5 O4 H:DT14 4.1 47.7 0.5 N2 E:DG11 4.2 0.3 0.5 N6 F:DA15 4.2 79.9 0.5 H6 F:DC14 4.2 0.7 0.5 N6 H:DA15 4.2 27.7 0.5 H2 G:DA11 4.2 40.5 0.5 C05 E:LFX101 4.2 39.6 1.0 N1 G:DA11 4.2 32.5 0.5 H2'' F:DC14 4.2 0.6 0.5 H08 E:LFX101 4.3 58.4 1.0 H2'' H:DT14 4.3 60.5 0.5 H02 E:LFX101 4.3 56.3 1.0 O4' H:DA15 4.3 29.6 0.5 O4' F:DA15 4.4 83.4 0.5 N3 H:DA15 4.4 27.2 0.5 H5 F:DC14 4.4 0.8 0.5 N4 F:DC14 4.4 98.1 0.5 N3 F:DA15 4.4 80.8 0.5 N1 E:DG11 4.5 0.1 0.5 H73 H:DT14 4.5 62.9 0.5 C2 G:DA11 4.5 33.8 0.5 N1 H:DA15 4.5 26.9 0.5 N1 F:DA15 4.5 79.8 0.5 C08 E:LFX101 4.5 48.7 1.0 C1' H:DA15 4.6 28.7 0.5 H07 E:LFX101 4.6 57.1 1.0 H01 E:LFX101 4.6 55.3 1.0 C1' F:DA15 4.6 82.0 0.5 C2 E:DG11 4.6 0.1 0.5 C7 H:DT14 4.7 52.4 0.5 H42 F:DC14 4.7 0.7 0.5 C2 H:DA15 4.7 26.8 0.5 C2 F:DA15 4.8 79.8 0.5 H61 F:DA15 4.8 79.9 0.5 C07 E:LFX101 4.8 47.6 1.0 H61 H:DA15 4.8 33.2 0.5 H41 F:DC14 4.9 0.7 0.5 O01 E:LFX101 5.0 42.7 1.0 C15 E:LFX101 5.0 36.8 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 F:F101 b:38.1 occ:1.00 F F:LFX101 0.0 38.1 1.0 C11 F:LFX101 1.4 38.6 1.0 C13 F:LFX101 2.4 37.0 1.0 C04 F:LFX101 2.4 42.4 1.0 H02A F:LFX101 2.5 61.3 1.0 H13 F:LFX101 2.6 44.4 1.0 H02 F:LFX101 2.6 61.3 1.0 C02 F:LFX101 2.8 51.1 1.0 N01 F:LFX101 3.0 48.5 1.0 C2 E:DT14 3.0 0.5 0.5 C2 G:DC14 3.2 30.6 0.5 N7 G:DA15 3.2 49.3 0.5 N7 E:DA15 3.2 59.0 0.5 C5 E:DA15 3.2 57.5 0.5 C5 G:DA15 3.3 47.3 0.5 N1 G:DC14 3.3 35.4 0.5 N3 E:DT14 3.3 0.6 0.5 N1 E:DT14 3.3 0.5 0.5 O2 E:DT14 3.3 0.8 0.5 N3 G:DC14 3.4 31.4 0.5 C8 G:DA15 3.4 49.9 0.5 H22 H:DG11 3.4 47.6 0.5 H2' E:DT14 3.4 0.0 0.5 H2' G:DC14 3.4 44.2 0.5 C8 E:DA15 3.4 58.9 0.5 C4 E:DA15 3.5 56.5 0.5 C4 G:DA15 3.6 47.4 0.5 C6 G:DC14 3.6 34.2 0.5 O2 G:DC14 3.6 31.2 0.5 N9 G:DA15 3.6 48.9 0.5 N9 E:DA15 3.6 57.5 0.5 C4 G:DC14 3.6 31.8 0.5 C10 F:LFX101 3.7 36.9 1.0 C06 F:LFX101 3.7 40.7 1.0 H01A F:LFX101 3.7 62.1 1.0 C5 G:DC14 3.8 34.4 0.5 C6 E:DT14 3.8 0.4 0.5 H8 G:DA15 3.8 59.9 0.5 C4 E:DT14 3.8 0.5 0.5 C6 E:DA15 3.8 57.0 0.5 C6 G:DA15 3.9 45.9 0.5 H8 E:DA15 3.9 70.7 0.5 C01 F:LFX101 3.9 51.8 1.0 C1' E:DT14 3.9 0.7 0.5 C1' G:DC14 4.0 34.9 0.5 H1' E:DT14 4.0 0.6 0.5 C2' E:DT14 4.0 0.9 0.5 C2' G:DC14 4.0 36.8 0.5 H1' G:DC14 4.0 41.9 0.5 C5 E:DT14 4.0 0.5 0.5 H6 G:DC14 4.1 41.1 0.5 H2'' E:DT14 4.1 0.0 0.5 H2'' G:DC14 4.1 44.2 0.5 N2 H:DG11 4.1 39.6 0.5 O4' E:DA15 4.2 58.5 0.5 C05 F:LFX101 4.2 38.8 1.0 N1 H:DG11 4.2 36.4 0.5 O4' G:DA15 4.2 52.6 0.5 N3 E:DA15 4.2 55.3 0.5 H2 F:DA11 4.3 99.1 0.5 H62 E:DA15 4.3 69.6 0.5 C08 F:LFX101 4.3 53.6 1.0 N6 E:DA15 4.3 58.0 0.5 N3 G:DA15 4.3 46.2 0.5 H6 E:DT14 4.3 0.5 0.5 N6 G:DA15 4.3 46.2 0.5 H5 G:DC14 4.4 41.3 0.5 H01 F:LFX101 4.4 62.1 1.0 N1 E:DA15 4.4 55.9 0.5 N4 G:DC14 4.5 31.8 0.5 N1 F:DA11 4.5 83.6 0.5 C2 H:DG11 4.5 37.7 0.5 N1 G:DA15 4.5 44.7 0.5 C1' E:DA15 4.5 57.3 0.5 C1' G:DA15 4.6 49.9 0.5 O4 E:DT14 4.6 0.7 0.5 C2 E:DA15 4.6 55.1 0.5 H08 F:LFX101 4.6 64.3 1.0 C2 F:DA11 4.6 82.6 0.5 C2 G:DA15 4.7 45.0 0.5 H42 G:DC14 4.7 38.2 0.5 H08A F:LFX101 4.8 64.3 1.0 H21 H:DG11 4.8 47.6 0.5 H16B F:LFX101 4.9 67.7 1.0 H61 E:DA15 4.9 69.6 0.5 C15 F:LFX101 5.0 35.9 1.0 O01 F:LFX101 5.0 41.0 1.0 H72 E:DT14 5.0 0.1 0.5 H1' E:DA15 5.0 68.8 0.5 H61 G:DA15 5.0 55.4 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