Fluorine in PDB 5btl: 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: 5btl 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)	49.60 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	107.938, 83.047, 128.737, 90.00, 108.88, 90.00
R / Rfree (%)	23 / 25.6

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 5btl). 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: 5btl:
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:42.9 occ:1.00 F17 E:8MX101 0.0 42.9 1.0 C06 E:8MX101 1.3 41.7 1.0 C07 E:8MX101 2.3 41.5 1.0 C05 E:8MX101 2.4 41.7 1.0 H051 E:8MX101 2.6 50.0 1.0 N08 E:8MX101 2.7 42.8 1.0 C2 G:DC14 2.9 31.4 0.5 C2 E:DT14 2.9 0.6 0.5 N3 G:DC14 3.0 32.2 0.5 N3 E:DT14 3.0 0.2 0.5 N7 G:DA15 3.0 54.1 0.5 N7 E:DA15 3.0 81.3 0.5 N1 E:DT14 3.1 0.9 0.5 N1 G:DC14 3.1 34.0 0.5 C4 G:DC14 3.1 34.7 0.5 C5 E:DA15 3.2 79.0 0.5 C4 E:DT14 3.2 0.0 0.5 C5 G:DA15 3.3 53.0 0.5 C6 G:DC14 3.3 36.0 0.5 C6 E:DT14 3.3 0.6 0.5 C5 G:DC14 3.3 36.9 0.5 H3 E:DT14 3.3 0.2 0.5 H2' E:DT14 3.3 0.8 0.5 C8 E:DA15 3.4 80.9 0.5 C8 G:DA15 3.4 55.0 0.5 C5 E:DT14 3.4 0.9 0.5 O2 E:DT14 3.5 0.0 0.5 H22 H:DG11 3.5 92.2 0.5 H2' G:DC14 3.5 45.1 0.5 O2 G:DC14 3.5 29.5 0.5 H161 E:8MX101 3.5 66.6 1.0 C02 E:8MX101 3.6 41.5 1.0 H092 E:8MX101 3.7 54.4 1.0 C04 E:8MX101 3.7 41.2 1.0 C16 E:8MX101 3.7 55.5 1.0 H8 G:DA15 3.7 66.0 0.5 H8 E:DA15 3.7 97.1 0.5 C09 E:8MX101 3.7 45.3 1.0 C4 E:DA15 3.7 77.3 0.5 C6 E:DA15 3.8 78.5 0.5 N9 E:DA15 3.8 78.6 0.5 C6 G:DA15 3.8 52.5 0.5 H6 G:DC14 3.9 43.2 0.5 C4 G:DA15 3.9 52.9 0.5 H6 E:DT14 3.9 0.3 0.5 C1' E:DT14 3.9 0.3 0.5 H5 G:DC14 3.9 44.3 0.5 N9 G:DA15 3.9 53.8 0.5 N4 G:DC14 3.9 36.1 0.5 C1' G:DC14 3.9 34.8 0.5 H62 E:DA15 4.0 96.4 0.5 C2' E:DT14 4.0 0.3 0.5 O4 E:DT14 4.0 0.7 0.5 H1' G:DC14 4.0 41.7 0.5 H1' E:DT14 4.0 0.4 0.5 N6 G:DA15 4.1 52.9 0.5 C2' G:DC14 4.1 37.6 0.5 N1 H:DG11 4.1 75.1 0.5 N6 E:DA15 4.1 80.3 0.5 H2 F:DA11 4.2 88.9 0.5 C03 E:8MX101 4.2 41.9 1.0 N2 H:DG11 4.2 76.8 0.5 N1 F:DA11 4.2 75.7 0.5 H091 E:8MX101 4.2 54.4 1.0 H72 E:DT14 4.3 0.1 0.5 H2'' E:DT14 4.3 0.8 0.5 H162 E:8MX101 4.3 66.6 1.0 H2'' G:DC14 4.3 45.1 0.5 C7 E:DT14 4.5 0.2 0.5 C2 F:DA11 4.5 74.1 0.5 C2 H:DG11 4.5 75.2 0.5 C15 E:8MX101 4.5 54.9 1.0 H151 E:8MX101 4.5 65.8 1.0 O4' E:DA15 4.6 79.7 0.5 N1 E:DA15 4.6 76.3 0.5 N3 E:DA15 4.6 75.5 0.5 C10 E:8MX101 4.7 45.9 1.0 N1 G:DA15 4.7 51.9 0.5 O4' G:DA15 4.7 55.7 0.5 H011 E:8MX101 4.7 50.3 1.0 H61 E:DA15 4.7 96.4 0.5 N3 G:DA15 4.8 52.8 0.5 C18 E:8MX101 4.8 41.5 1.0 C01 E:8MX101 4.8 42.0 1.0 C1' E:DA15 4.8 77.9 0.5 H21 H:DG11 4.9 92.2 0.5 C2 E:DA15 4.9 75.0 0.5 O19 E:8MX101 4.9 41.7 1.0 H73 E:DT14 4.9 0.1 0.5 C6 H:DG11 4.9 74.4 0.5 C1' G:DA15 5.0 54.7 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:40.9 occ:1.00 F17 H:8MX101 0.0 40.9 1.0 C06 H:8MX101 1.3 41.0 1.0 H162 H:8MX101 2.3 47.2 1.0 C05 H:8MX101 2.3 41.0 1.0 C07 H:8MX101 2.4 42.1 1.0 H051 H:8MX101 2.5 49.3 1.0 H161 H:8MX101 2.6 47.2 1.0 C16 H:8MX101 2.6 39.3 1.0 C2 H:DT14 2.9 60.6 0.5 N08 H:8MX101 2.9 43.4 1.0 C2 F:DC14 3.0 99.6 0.5 N3 H:DT14 3.0 61.0 0.5 N3 F:DC14 3.0 0.8 0.5 N7 F:DA15 3.1 93.7 0.5 N7 H:DA15 3.2 37.2 0.5 N1 H:DT14 3.2 61.8 0.5 C5 F:DA15 3.3 91.5 0.5 C5 H:DA15 3.3 36.1 0.5 N1 F:DC14 3.3 0.8 0.5 H3 H:DT14 3.3 73.2 0.5 O2 H:DT14 3.4 60.3 0.5 C4 F:DC14 3.4 0.3 0.5 O2 F:DC14 3.4 98.1 0.5 C4 H:DT14 3.4 62.0 0.5 C8 H:DA15 3.5 38.9 0.5 C8 F:DA15 3.5 93.7 0.5 H2' H:DT14 3.5 74.1 0.5 C6 H:DT14 3.5 62.4 0.5 C04 H:8MX101 3.6 41.9 1.0 C6 F:DC14 3.7 0.8 0.5 C5 H:DT14 3.7 62.5 0.5 C02 H:8MX101 3.7 43.0 1.0 N2 E:DG11 3.7 0.6 0.5 C4 H:DA15 3.7 36.5 0.5 C5 F:DC14 3.7 0.1 0.5 C6 F:DA15 3.7 90.9 0.5 H2' F:DC14 3.8 0.5 0.5 N9 H:DA15 3.8 38.3 0.5 C15 H:8MX101 3.8 39.8 1.0 C6 H:DA15 3.8 34.8 0.5 C4 F:DA15 3.9 90.3 0.5 H8 H:DA15 3.9 46.7 0.5 H2 G:DA11 3.9 61.6 0.5 H8 F:DA15 3.9 0.4 0.5 N1 G:DA11 3.9 50.7 0.5 H091 H:8MX101 4.0 52.9 1.0 N6 F:DA15 4.0 92.3 0.5 C1' H:DT14 4.0 61.6 0.5 N9 F:DA15 4.0 92.0 0.5 C09 H:8MX101 4.0 44.1 1.0 H1' H:DT14 4.0 74.0 0.5 N1 E:DG11 4.1 0.3 0.5 C2' H:DT14 4.1 61.7 0.5 C1' F:DC14 4.1 99.7 0.5 H1' F:DC14 4.1 0.6 0.5 H6 H:DT14 4.1 74.8 0.5 H62 H:DA15 4.1 41.4 0.5 O4 H:DT14 4.1 62.5 0.5 N4 F:DC14 4.1 0.8 0.5 C03 H:8MX101 4.2 42.9 1.0 C2 G:DA11 4.2 51.3 0.5 H151 H:8MX101 4.2 47.7 1.0 C2 E:DG11 4.2 0.8 0.5 N6 H:DA15 4.2 34.5 0.5 H6 F:DC14 4.3 0.4 0.5 C2' F:DC14 4.3 98.8 0.5 H2'' H:DT14 4.3 74.1 0.5 H101 H:8MX101 4.3 53.0 1.0 H5 F:DC14 4.4 0.1 0.5 C10 H:8MX101 4.4 44.1 1.0 O4' H:DA15 4.5 41.6 0.5 N3 H:DA15 4.5 36.2 0.5 H2'' F:DC14 4.5 0.5 0.5 N1 H:DA15 4.6 34.3 0.5 H73 H:DT14 4.6 75.2 0.5 N1 F:DA15 4.6 89.3 0.5 N14 H:8MX101 4.7 40.2 1.0 C18 H:8MX101 4.7 44.0 1.0 H141 H:8MX101 4.7 48.2 1.0 N3 F:DA15 4.7 88.7 0.5 C7 H:DT14 4.7 62.7 0.5 C2 H:DA15 4.8 34.8 0.5 C1' H:DA15 4.8 40.1 0.5 C6 G:DA11 4.8 51.3 0.5 H61 H:DA15 4.8 41.4 0.5 O19 H:8MX101 4.8 45.7 1.0 H092 H:8MX101 4.8 52.9 1.0 O4' F:DA15 4.8 92.9 0.5 H011 H:8MX101 4.9 52.3 1.0 C01 H:8MX101 4.9 43.6 1.0 C2 F:DA15 4.9 88.3 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