Fluorine in PDB 5btn: 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: 5btn 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)	49.65 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	108.337, 82.914, 129.078, 90.00, 108.78, 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 5btn). 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: 5btn:
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:62.6 occ:1.00 F17 G:8MX101 0.0 62.6 1.0 C06 G:8MX101 1.3 63.4 1.0 C05 G:8MX101 2.4 62.5 1.0 C07 G:8MX101 2.4 66.2 1.0 H051 G:8MX101 2.6 75.0 1.0 N08 G:8MX101 2.7 71.4 1.0 C2 G:DC14 2.9 60.5 0.5 N7 E:DA15 3.0 70.0 0.5 N7 G:DA15 3.0 43.6 0.5 N3 G:DC14 3.0 57.8 0.5 N1 G:DC14 3.1 59.7 0.5 C2 E:DT14 3.1 94.5 0.5 N3 E:DT14 3.1 95.1 0.5 C5 E:DA15 3.1 66.5 0.5 C5 G:DA15 3.2 43.1 0.5 N1 E:DT14 3.3 94.9 0.5 C4 G:DC14 3.3 57.7 0.5 C8 G:DA15 3.3 44.1 0.5 C6 G:DC14 3.4 58.9 0.5 C8 E:DA15 3.4 69.8 0.5 O2 G:DC14 3.4 57.6 0.5 H2' G:DC14 3.4 78.6 0.5 H3 E:DT14 3.4 0.1 0.5 H22 H:DG11 3.4 0.8 0.5 C4 E:DT14 3.4 96.0 0.5 H091 G:8MX101 3.5 91.9 1.0 C5 G:DC14 3.5 58.4 0.5 H2' E:DT14 3.5 0.5 0.5 O2 E:DT14 3.5 94.2 0.5 C6 E:DT14 3.6 95.8 0.5 C4 E:DA15 3.6 65.7 0.5 C09 G:8MX101 3.6 76.6 1.0 C04 G:8MX101 3.6 61.4 1.0 C02 G:8MX101 3.6 64.3 1.0 C5 E:DT14 3.7 96.4 0.5 C6 E:DA15 3.7 68.2 0.5 H8 G:DA15 3.7 53.0 0.5 C4 G:DA15 3.7 43.6 0.5 N9 E:DA15 3.7 68.0 0.5 N9 G:DA15 3.8 43.9 0.5 H8 E:DA15 3.8 83.8 0.5 C6 G:DA15 3.8 42.6 0.5 C1' G:DC14 3.8 62.8 0.5 C16 G:8MX101 3.9 94.6 1.0 H1' G:DC14 3.9 75.4 0.5 H6 G:DC14 3.9 70.7 0.5 H162 G:8MX101 3.9 0.6 1.0 H62 E:DA15 4.0 80.3 0.5 C2' G:DC14 4.0 65.5 0.5 H092 G:8MX101 4.0 91.9 1.0 N6 E:DA15 4.1 66.9 0.5 C1' E:DT14 4.1 94.7 0.5 H5 G:DC14 4.1 70.1 0.5 C2' E:DT14 4.1 95.4 0.5 H6 E:DT14 4.1 0.9 0.5 N4 G:DC14 4.1 57.1 0.5 O4 E:DT14 4.2 96.7 0.5 C03 G:8MX101 4.2 62.6 1.0 H1' E:DT14 4.2 0.6 0.5 H2'' G:DC14 4.2 78.6 0.5 N2 H:DG11 4.2 84.9 0.5 H2 F:DA11 4.2 76.1 0.5 N6 G:DA15 4.2 43.0 0.5 N1 H:DG11 4.2 79.2 0.5 H161 G:8MX101 4.2 0.6 1.0 N1 F:DA11 4.3 63.3 0.5 H2'' E:DT14 4.4 0.5 0.5 H42 G:DC14 4.4 68.5 0.5 N3 E:DA15 4.4 63.7 0.5 N1 E:DA15 4.4 64.2 0.5 O4' G:DA15 4.5 46.3 0.5 O4' E:DA15 4.5 72.4 0.5 H72 E:DT14 4.5 0.4 0.5 C2 F:DA11 4.5 63.4 0.5 C2 H:DG11 4.6 81.1 0.5 N3 G:DA15 4.6 43.0 0.5 H41 G:DC14 4.6 68.5 0.5 C10 G:8MX101 4.6 78.9 1.0 N1 G:DA15 4.6 41.9 0.5 H112 G:8MX101 4.6 0.3 1.0 H61 E:DA15 4.7 80.3 0.5 C2 E:DA15 4.7 62.3 0.5 C7 E:DT14 4.7 97.8 0.5 C18 G:8MX101 4.7 60.0 1.0 C1' E:DA15 4.7 68.7 0.5 C1' G:DA15 4.8 45.4 0.5 H011 G:8MX101 4.8 78.1 1.0 H61 G:DA15 4.8 51.6 0.5 C15 G:8MX101 4.8 94.6 1.0 O19 G:8MX101 4.8 60.5 1.0 C01 G:8MX101 4.9 65.1 1.0 C2 G:DA15 4.9 42.5 0.5 H21 H:DG11 4.9 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:47.5 occ:1.00 F17 H:8MX101 0.0 47.5 1.0 C06 H:8MX101 1.3 49.4 1.0 H161 H:8MX101 2.3 83.3 1.0 C05 H:8MX101 2.3 49.3 1.0 C07 H:8MX101 2.4 52.6 1.0 H051 H:8MX101 2.5 59.2 1.0 C16 H:8MX101 2.7 69.4 1.0 H162 H:8MX101 2.7 83.3 1.0 C2 H:DT14 2.9 69.9 0.5 N08 H:8MX101 2.9 56.2 1.0 C2 F:DC14 3.0 93.1 0.5 N3 H:DT14 3.0 63.4 0.5 N7 F:DA15 3.1 91.6 0.5 N3 F:DC14 3.1 87.2 0.5 N7 H:DA15 3.1 28.2 0.5 N1 H:DT14 3.2 65.6 0.5 C5 F:DA15 3.2 87.0 0.5 C5 H:DA15 3.3 27.0 0.5 N1 F:DC14 3.3 83.0 0.5 H3 H:DT14 3.3 76.0 0.5 O2 H:DT14 3.4 64.6 0.5 C8 H:DA15 3.4 29.1 0.5 C4 H:DT14 3.4 66.8 0.5 C4 F:DC14 3.4 92.5 0.5 C8 F:DA15 3.4 91.1 0.5 H2' H:DT14 3.5 90.9 0.5 O2 F:DC14 3.5 86.0 0.5 C6 H:DT14 3.5 69.8 0.5 C6 F:DC14 3.6 90.6 0.5 C04 H:8MX101 3.6 50.2 1.0 H2' F:DC14 3.6 0.1 0.5 C5 H:DT14 3.6 65.0 0.5 C4 H:DA15 3.7 27.1 0.5 C02 H:8MX101 3.7 52.9 1.0 C5 F:DC14 3.7 88.1 0.5 N9 H:DA15 3.7 27.5 0.5 C6 F:DA15 3.8 87.0 0.5 N2 E:DG11 3.8 0.6 0.5 C4 F:DA15 3.8 85.6 0.5 H8 H:DA15 3.8 34.9 0.5 H092 H:8MX101 3.8 71.5 1.0 C15 H:8MX101 3.8 69.2 1.0 H8 F:DA15 3.8 0.4 0.5 C6 H:DA15 3.8 26.6 0.5 N9 F:DA15 3.9 86.1 0.5 C09 H:8MX101 3.9 59.5 1.0 C1' H:DT14 4.0 78.6 0.5 H1' H:DT14 4.0 94.4 0.5 C1' F:DC14 4.0 94.6 0.5 C2' H:DT14 4.1 75.8 0.5 H1' F:DC14 4.1 0.5 0.5 N6 F:DA15 4.1 86.3 0.5 H2 G:DA11 4.1 60.4 0.5 H6 H:DT14 4.1 83.8 0.5 N1 G:DA11 4.1 50.0 0.5 O4 H:DT14 4.1 65.3 0.5 H62 H:DA15 4.2 32.0 0.5 C03 H:8MX101 4.2 52.2 1.0 H6 F:DC14 4.2 0.8 0.5 H151 H:8MX101 4.2 83.1 1.0 C2' F:DC14 4.2 93.5 0.5 N4 F:DC14 4.2 91.4 0.5 N1 E:DG11 4.2 0.9 0.5 N6 H:DA15 4.3 26.7 0.5 H2'' H:DT14 4.3 90.9 0.5 H101 H:8MX101 4.3 72.8 1.0 H5 F:DC14 4.3 0.7 0.5 C2 E:DG11 4.3 0.9 0.5 C10 H:8MX101 4.3 60.7 1.0 C2 G:DA11 4.4 50.3 0.5 H2'' F:DC14 4.4 0.1 0.5 O4' H:DA15 4.4 30.7 0.5 N3 H:DA15 4.5 26.9 0.5 H73 H:DT14 4.5 79.8 0.5 N1 F:DA15 4.6 86.8 0.5 N1 H:DA15 4.6 26.1 0.5 N3 F:DA15 4.6 85.7 0.5 O4' F:DA15 4.7 87.8 0.5 C1' H:DA15 4.7 28.9 0.5 C18 H:8MX101 4.7 50.1 1.0 C7 H:DT14 4.7 66.5 0.5 H141 H:8MX101 4.7 82.7 1.0 N14 H:8MX101 4.8 68.9 1.0 H091 H:8MX101 4.8 71.5 1.0 C2 H:DA15 4.8 27.2 0.5 H41 F:DC14 4.8 0.7 0.5 O19 H:8MX101 4.8 50.7 1.0 C2 F:DA15 4.9 86.9 0.5 H013 H:8MX101 4.9 65.2 1.0 H61 H:DA15 4.9 32.0 0.5 C01 H:8MX101 4.9 54.4 1.0 C1' F:DA15 4.9 86.2 0.5 C6 G:DA11 5.0 50.1 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