Fluorine in PDB 5btc: 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: 5btc 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)	47.70 / 2.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	108.336, 82.976, 129.703, 90.00, 109.06, 90.00
R / Rfree (%)	22.4 / 25

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 5btc). 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: 5btc:
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:54.5 occ:1.00 F1 G:CPF101 0.0 54.5 1.0 C7 G:CPF101 1.3 55.8 1.0 C6 G:CPF101 2.3 53.3 1.0 H141 G:CPF101 2.3 86.8 1.0 C8 G:CPF101 2.4 60.6 1.0 H6 G:CPF101 2.5 64.0 1.0 H142 G:CPF101 2.5 86.8 1.0 C14 G:CPF101 2.7 72.3 1.0 C2 E:DT14 3.0 0.6 0.5 N2 G:CPF101 3.0 69.7 1.0 H22 H:DG11 3.1 61.8 0.5 C2 G:DC14 3.1 30.9 0.5 N7 G:DA15 3.2 28.2 0.5 O2 E:DT14 3.2 0.5 0.5 N3 E:DT14 3.2 0.1 0.5 N1 E:DT14 3.3 0.3 0.5 N7 E:DA15 3.3 90.3 0.5 N1 G:DC14 3.4 31.1 0.5 C5 G:DA15 3.4 24.1 0.5 O2 G:DC14 3.4 30.2 0.5 H2' G:DC14 3.4 36.2 0.5 C5 E:DA15 3.4 86.5 0.5 N3 G:DC14 3.4 31.5 0.5 C8 G:DA15 3.5 30.6 0.5 H2' E:DT14 3.5 0.3 0.5 C8 E:DA15 3.6 90.8 0.5 C5 G:CPF101 3.6 52.3 1.0 C9 G:CPF101 3.7 57.1 1.0 N2 H:DG11 3.7 51.5 0.5 C4 G:DA15 3.8 25.4 0.5 C4 E:DA15 3.8 86.3 0.5 N9 G:DA15 3.8 29.4 0.5 C4 E:DT14 3.8 0.1 0.5 H172 G:CPF101 3.8 92.2 1.0 C6 E:DT14 3.8 0.4 0.5 H8 G:DA15 3.8 36.7 0.5 H1' E:DT14 3.9 0.8 0.5 C6 G:DC14 3.9 32.0 0.5 C4 G:DC14 3.9 32.4 0.5 C6 E:DA15 3.9 83.8 0.5 H1' G:DC14 3.9 36.7 0.5 H2 F:DA11 3.9 0.1 0.5 N9 E:DA15 3.9 89.6 0.5 C1' E:DT14 3.9 0.5 0.5 C1' G:DC14 4.0 30.6 0.5 C2' G:DC14 4.0 30.1 0.5 C6 G:DA15 4.0 21.3 0.5 C17 G:CPF101 4.0 76.8 1.0 C2' E:DT14 4.0 0.7 0.5 H8 E:DA15 4.0 0.0 0.5 N1 H:DG11 4.0 50.9 0.5 H2'' G:DC14 4.1 36.2 0.5 C5 E:DT14 4.1 0.9 0.5 C5 G:DC14 4.1 32.7 0.5 C10 G:CPF101 4.1 54.0 1.0 N1 F:DA11 4.1 0.1 0.5 C15 G:CPF101 4.2 75.6 1.0 H2'' E:DT14 4.2 0.3 0.5 C2 H:DG11 4.2 51.0 0.5 H62 E:DA15 4.2 0.2 0.5 N6 E:DA15 4.3 83.5 0.5 C2 F:DA11 4.3 0.8 0.5 H21 H:DG11 4.3 61.8 0.5 O4' G:DA15 4.4 37.0 0.5 N6 G:DA15 4.4 21.0 0.5 H6 E:DT14 4.4 0.5 0.5 H151 G:CPF101 4.4 90.7 1.0 H6 G:DC14 4.4 38.4 0.5 H9 G:CPF101 4.5 68.6 1.0 O4' E:DA15 4.5 94.8 0.5 N3 E:DA15 4.5 82.9 0.5 H171 G:CPF101 4.6 92.2 1.0 N3 G:DA15 4.6 23.3 0.5 O4 E:DT14 4.6 0.3 0.5 N1 E:DA15 4.6 81.9 0.5 N1 G:DA15 4.7 20.1 0.5 H152 G:CPF101 4.7 90.7 1.0 N4 G:DC14 4.7 33.2 0.5 C1' G:DA15 4.7 33.8 0.5 H5 G:DC14 4.8 39.2 0.5 C2 E:DA15 4.8 81.8 0.5 C4 G:CPF101 4.9 51.8 1.0 C1' E:DA15 4.9 91.9 0.5 H61 E:DA15 4.9 0.2 0.5 C2 G:DA15 4.9 21.1 0.5 H42 G:DC14 4.9 39.8 0.5 N3 G:CPF101 4.9 79.7 1.0 C6 H:DG11 5.0 50.7 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 G:F102 b:73.0 occ:1.00 F1 G:CPF102 0.0 73.0 1.0 C7 G:CPF102 1.3 74.5 1.0 H141 G:CPF102 2.3 0.0 1.0 C6 G:CPF102 2.3 75.0 1.0 C8 G:CPF102 2.4 78.2 1.0 H6 G:CPF102 2.5 90.0 1.0 H142 G:CPF102 2.6 0.0 1.0 C14 G:CPF102 2.7 83.3 1.0 C2 F:DC14 3.0 0.7 0.5 N2 G:CPF102 3.0 80.3 1.0 C2 H:DT14 3.0 50.5 0.5 N7 H:DA15 3.2 32.5 0.5 N7 F:DA15 3.2 90.4 0.5 O2 F:DC14 3.2 0.6 0.5 N3 F:DC14 3.2 0.9 0.5 N3 H:DT14 3.2 50.5 0.5 N1 H:DT14 3.3 51.5 0.5 C5 F:DA15 3.3 84.0 0.5 N1 F:DC14 3.4 0.3 0.5 O2 H:DT14 3.4 50.0 0.5 C5 H:DA15 3.4 30.6 0.5 H2' H:DT14 3.4 63.4 0.5 C8 H:DA15 3.4 33.1 0.5 H3 H:DT14 3.5 60.6 0.5 C8 F:DA15 3.5 90.4 0.5 H2' F:DC14 3.6 0.8 0.5 C5 G:CPF102 3.6 78.1 1.0 C9 G:CPF102 3.7 79.7 1.0 C4 H:DT14 3.7 51.4 0.5 C6 H:DT14 3.7 52.7 0.5 C4 F:DC14 3.7 0.4 0.5 H2 G:DA11 3.7 58.5 0.5 H172 G:CPF102 3.8 96.4 1.0 H8 H:DA15 3.8 39.7 0.5 C4 H:DA15 3.8 32.0 0.5 N9 H:DA15 3.8 33.0 0.5 C4 F:DA15 3.8 86.2 0.5 C6 F:DA15 3.9 83.3 0.5 H8 F:DA15 3.9 0.5 0.5 C6 F:DC14 3.9 0.1 0.5 H1' F:DC14 3.9 0.1 0.5 N9 F:DA15 3.9 88.3 0.5 N1 G:DA11 4.0 47.6 0.5 C5 H:DT14 4.0 52.7 0.5 C6 H:DA15 4.0 30.1 0.5 C1' H:DT14 4.0 52.1 0.5 H1' H:DT14 4.0 62.5 0.5 C17 G:CPF102 4.0 80.3 1.0 C1' F:DC14 4.0 0.6 0.5 C2' H:DT14 4.0 52.9 0.5 N2 E:DG11 4.0 0.8 0.5 H62 F:DA15 4.0 0.2 0.5 C5 F:DC14 4.1 0.6 0.5 C2 G:DA11 4.1 48.8 0.5 C2' F:DC14 4.1 0.0 0.5 C10 G:CPF102 4.1 80.0 1.0 C15 G:CPF102 4.2 88.0 1.0 N6 F:DA15 4.2 85.2 0.5 H62 H:DA15 4.2 36.0 0.5 H2'' H:DT14 4.2 63.4 0.5 H2'' F:DC14 4.3 0.8 0.5 H6 H:DT14 4.3 63.2 0.5 N1 E:DG11 4.3 0.2 0.5 N6 H:DA15 4.3 30.0 0.5 H151 G:CPF102 4.4 0.6 1.0 H21 E:DG11 4.4 0.4 0.5 O4' H:DA15 4.5 35.6 0.5 O4 H:DT14 4.5 51.6 0.5 H9 G:CPF102 4.5 95.7 1.0 C2 E:DG11 4.5 0.3 0.5 H6 F:DC14 4.5 0.3 0.5 H171 G:CPF102 4.5 96.4 1.0 N4 F:DC14 4.6 0.5 0.5 N3 H:DA15 4.6 31.5 0.5 O4' F:DA15 4.6 93.0 0.5 N1 F:DA15 4.6 81.1 0.5 N3 F:DA15 4.7 84.0 0.5 H152 G:CPF102 4.7 0.6 1.0 N1 H:DA15 4.7 29.6 0.5 C1' H:DA15 4.8 34.5 0.5 H5 F:DC14 4.8 0.9 0.5 C4 G:CPF102 4.9 81.1 1.0 N3 G:CPF102 4.9 84.4 1.0 C2 F:DA15 4.9 79.9 0.5 C6 G:DA11 4.9 47.7 0.5 C1' F:DA15 4.9 89.0 0.5 C2 H:DA15 5.0 29.6 0.5 H61 H:DA15 5.0 36.0 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