Fluorine in PDB 5bs8: 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: 5bs8 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)	102.25 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	108.357, 83.070, 129.856, 90.00, 109.33, 90.00
R / Rfree (%)	19.6 / 23.3

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 5bs8). 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: 5bs8:
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:51.6 occ:1.00 F G:MFX101 0.0 51.6 1.0 C15 G:MFX101 1.3 46.0 1.0 H04 G:MFX101 2.3 59.2 1.0 C17 G:MFX101 2.3 44.2 1.0 C11 G:MFX101 2.4 46.1 1.0 H17 G:MFX101 2.5 53.0 1.0 H04A G:MFX101 2.6 59.2 1.0 C04 G:MFX101 2.7 49.4 1.0 C2 G:DC14 2.8 28.6 0.5 C2 E:DT14 2.9 0.2 0.5 N1 G:DC14 3.0 31.6 0.5 N01 G:MFX101 3.0 48.0 1.0 N3 G:DC14 3.0 29.6 0.5 N3 E:DT14 3.1 0.4 0.5 N1 E:DT14 3.2 0.2 0.5 N7 G:DA15 3.2 46.6 0.5 N7 E:DA15 3.3 69.9 0.5 O2 G:DC14 3.3 27.5 0.5 O2 E:DT14 3.3 1.0 0.5 C5 E:DA15 3.3 66.9 0.5 C6 G:DC14 3.4 35.5 0.5 C4 G:DC14 3.4 33.6 0.5 H2' G:DC14 3.4 38.3 0.5 C5 G:DA15 3.4 43.4 0.5 H2' E:DT14 3.4 0.2 0.5 C8 G:DA15 3.5 48.4 0.5 C5 G:DC14 3.6 35.8 0.5 C8 E:DA15 3.6 71.0 0.5 C4 E:DT14 3.6 0.7 0.5 C14 G:MFX101 3.6 43.0 1.0 C6 E:DT14 3.7 0.8 0.5 C13 G:MFX101 3.7 44.8 1.0 C1' G:DC14 3.7 29.2 0.5 H1' G:DC14 3.7 35.1 0.5 C4 E:DA15 3.8 66.6 0.5 C6 E:DA15 3.8 65.1 0.5 N2 H:DG11 3.9 35.5 0.5 C5 E:DT14 3.9 0.1 0.5 C2' G:DC14 3.9 31.9 0.5 H8 G:DA15 3.9 58.0 0.5 C4 G:DA15 3.9 43.2 0.5 H1' E:DT14 3.9 0.0 0.5 C1' E:DT14 3.9 0.2 0.5 H6 G:DC14 3.9 42.6 0.5 N9 E:DA15 3.9 69.2 0.5 N9 G:DA15 4.0 47.9 0.5 C6 G:DA15 4.0 40.8 0.5 H2'' G:DC14 4.0 38.3 0.5 C2' E:DT14 4.0 0.0 0.5 H8 E:DA15 4.0 85.2 0.5 H2 F:DA11 4.0 0.1 0.5 N1 F:DA11 4.1 0.7 0.5 H62 E:DA15 4.1 83.3 0.5 N1 H:DG11 4.1 38.9 0.5 C12 G:MFX101 4.2 44.5 1.0 H03 G:MFX101 4.2 66.0 1.0 N6 E:DA15 4.2 69.4 0.5 H5 G:DC14 4.2 43.0 0.5 H2'' E:DT14 4.2 0.2 0.5 C03 G:MFX101 4.2 55.0 1.0 H6 E:DT14 4.2 0.4 0.5 N4 G:DC14 4.2 35.7 0.5 N6 G:DA15 4.3 41.0 0.5 C02 G:MFX101 4.3 61.5 1.0 C2 H:DG11 4.3 38.7 0.5 C2 F:DA11 4.3 0.5 0.5 O4 E:DT14 4.4 0.0 0.5 H42 G:DC14 4.5 42.8 0.5 N1 E:DA15 4.5 63.4 0.5 N3 E:DA15 4.6 65.8 0.5 O4' G:DA15 4.6 52.1 0.5 O4' E:DA15 4.6 74.3 0.5 H02 G:MFX101 4.6 73.8 1.0 HN02 G:MFX101 4.7 70.3 1.0 N3 G:DA15 4.7 40.9 0.5 H41 G:DC14 4.7 42.8 0.5 N1 G:DA15 4.8 38.3 0.5 H61 E:DA15 4.8 83.3 0.5 C2 E:DA15 4.8 63.4 0.5 O01 G:MFX101 4.8 44.8 1.0 C19 G:MFX101 4.9 42.9 1.0 H72 E:DT14 4.9 0.5 0.5 C01 G:MFX101 4.9 61.2 1.0 H61 G:DA15 4.9 49.2 0.5 C1' E:DA15 4.9 72.9 0.5 C1' G:DA15 4.9 48.1 0.5 C6 F:DA11 4.9 0.8 0.5 N02 G:MFX101 5.0 58.6 1.0 H03A G:MFX101 5.0 66.0 1.0 C7 E:DT14 5.0 0.1 0.5 H61 F:DA11 5.0 0.8 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:49.8 occ:1.00 F H:MFX101 0.0 49.8 1.0 C15 H:MFX101 1.3 47.0 1.0 H04 H:MFX101 2.3 56.9 1.0 C17 H:MFX101 2.3 45.8 1.0 C11 H:MFX101 2.4 47.5 1.0 H04A H:MFX101 2.5 56.9 1.0 H17 H:MFX101 2.5 55.0 1.0 C04 H:MFX101 2.7 47.4 1.0 C2 H:DT14 2.9 41.5 0.5 N3 H:DT14 2.9 43.5 0.5 N01 H:MFX101 3.0 50.7 1.0 C2 F:DC14 3.1 0.6 0.5 N1 H:DT14 3.1 42.9 0.5 N7 F:DA15 3.2 0.0 0.5 N7 H:DA15 3.2 35.1 0.5 N3 F:DC14 3.2 0.9 0.5 H3 H:DT14 3.2 52.2 0.5 N1 F:DC14 3.3 0.7 0.5 C4 H:DT14 3.3 48.3 0.5 C5 H:DA15 3.3 34.1 0.5 O2 H:DT14 3.3 38.7 0.5 C5 F:DA15 3.4 0.2 0.5 H22 E:DG11 3.4 1.0 0.5 C6 H:DT14 3.5 47.8 0.5 O2 F:DC14 3.5 0.3 0.5 C4 F:DC14 3.5 0.1 0.5 C8 H:DA15 3.5 37.6 0.5 C5 H:DT14 3.6 49.2 0.5 H2' H:DT14 3.6 51.5 0.5 C8 F:DA15 3.6 0.0 0.5 C14 H:MFX101 3.6 43.0 1.0 C6 F:DC14 3.7 0.7 0.5 H2' F:DC14 3.7 0.2 0.5 C13 H:MFX101 3.7 47.5 1.0 C5 F:DC14 3.8 0.1 0.5 C6 F:DA15 3.8 0.4 0.5 C6 H:DA15 3.8 33.6 0.5 C4 H:DA15 3.8 33.7 0.5 N2 E:DG11 3.8 0.8 0.5 H2 G:DA11 3.9 34.8 0.5 C4 F:DA15 3.9 0.4 0.5 H8 H:DA15 3.9 45.1 0.5 N9 H:DA15 3.9 36.2 0.5 C1' H:DT14 4.0 42.0 0.5 N1 G:DA11 4.0 29.2 0.5 H8 F:DA15 4.0 0.4 0.5 H1' F:DC14 4.0 0.4 0.5 N1 E:DG11 4.0 0.8 0.5 H1' H:DT14 4.0 50.3 0.5 H62 H:DA15 4.0 40.8 0.5 N9 F:DA15 4.0 0.5 0.5 C1' F:DC14 4.0 0.7 0.5 O4 H:DT14 4.0 50.2 0.5 H6 H:DT14 4.1 57.4 0.5 N6 F:DA15 4.1 0.3 0.5 C2' H:DT14 4.1 42.9 0.5 N6 H:DA15 4.1 34.0 0.5 C12 H:MFX101 4.2 43.4 1.0 C2 G:DA11 4.2 29.0 0.5 H6 F:DC14 4.2 0.3 0.5 C2 E:DG11 4.2 0.9 0.5 C2' F:DC14 4.2 0.3 0.5 H03A H:MFX101 4.3 60.5 1.0 C03 H:MFX101 4.3 50.4 1.0 C02 H:MFX101 4.3 50.9 1.0 N4 F:DC14 4.3 0.7 0.5 H2'' H:DT14 4.3 51.5 0.5 H21 E:DG11 4.3 1.0 0.5 H5 F:DC14 4.4 0.7 0.5 H2'' F:DC14 4.5 0.2 0.5 H73 H:DT14 4.6 62.3 0.5 N1 H:DA15 4.6 32.9 0.5 H02 H:MFX101 4.6 61.1 1.0 N1 F:DA15 4.6 0.2 0.5 N3 H:DA15 4.6 33.4 0.5 C7 H:DT14 4.7 51.9 0.5 O4' H:DA15 4.7 35.9 0.5 HN02 H:MFX101 4.7 61.0 1.0 N3 F:DA15 4.7 0.1 0.5 H61 H:DA15 4.7 40.8 0.5 O4' F:DA15 4.8 0.8 0.5 H41 F:DC14 4.8 0.4 0.5 C19 H:MFX101 4.9 41.8 1.0 O01 H:MFX101 4.9 47.8 1.0 H61 G:DA11 4.9 35.0 0.5 C6 G:DA11 4.9 29.4 0.5 C2 H:DA15 4.9 32.6 0.5 N02 H:MFX101 4.9 50.8 1.0 C01 H:MFX101 4.9 49.2 1.0 C6 E:DG11 4.9 0.1 0.5 C2 F:DA15 4.9 98.9 0.5 C1' H:DA15 5.0 34.5 0.5 H71 H:DT14 5.0 62.3 0.5 H03 H:MFX101 5.0 60.5 1.0 O02 H:MFX101 5.0 42.6 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