Fluorine in PDB 5iwi: 1.98A Structure of GSK945237 with S.Aureus Dna Gyrase and Singly Nicked Dna

All present enzymatic activity of 1.98A Structure of GSK945237 with S.Aureus Dna Gyrase and Singly Nicked Dna:
5.99.1.3;

The structure of 1.98A Structure of GSK945237 with S.Aureus Dna Gyrase and Singly Nicked Dna, PDB code: 5iwi was solved by B.D.Bax, T.J.Miles, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.00 / 1.98
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	92.897, 92.897, 410.784, 90.00, 90.00, 120.00
R / Rfree (%)	16.6 / 20.2

The structure of 1.98A Structure of GSK945237 with S.Aureus Dna Gyrase and Singly Nicked Dna also contains other interesting chemical elements:

Manganese	(Mn)	5 atoms
Chlorine	(Cl)	1 atom

The binding sites of Fluorine atom in the 1.98A Structure of GSK945237 with S.Aureus Dna Gyrase and Singly Nicked Dna (pdb code 5iwi). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the 1.98A Structure of GSK945237 with S.Aureus Dna Gyrase and Singly Nicked Dna, PDB code: 5iwi:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the 1.98A Structure of GSK945237 with S.Aureus Dna Gyrase and Singly Nicked Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of 1.98A Structure of GSK945237 with S.Aureus Dna Gyrase and Singly Nicked Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:F101 b:39.5 occ:0.65 F1 E:6EJ101 0.0 39.5 0.7 C8 E:6EJ101 1.1 31.4 0.3 O9 E:6EJ101 1.2 30.0 0.3 C2 E:6EJ101 1.3 36.8 0.7 N10 E:6EJ101 1.4 31.3 0.3 C11 E:6EJ101 1.9 31.4 0.3 C33 E:6EJ101 2.3 35.3 0.7 C3 E:6EJ101 2.3 35.0 0.7 C7 E:6EJ101 2.5 30.9 0.3 C34 E:6EJ101 2.7 30.8 0.3 C12 E:6EJ101 3.1 36.6 0.7 N1 G:DT2010 3.1 35.7 0.6 C6 G:DT2010 3.2 35.0 0.6 C2 G:DT2010 3.3 35.1 0.6 C14 E:6EJ101 3.3 39.2 0.7 C2' G:DT2010 3.3 38.7 0.6 C12 E:6EJ101 3.3 32.0 0.3 N3 G:DT2010 3.4 33.1 0.6 C5 G:DT2010 3.4 32.9 0.6 C6 E:6EJ101 3.4 30.2 0.3 C4 G:DT2010 3.5 32.7 0.6 C5 E:6EJ101 3.6 31.3 0.3 C34 E:6EJ101 3.6 36.2 0.7 C33 E:6EJ101 3.6 32.2 0.3 N7 E:DA11 3.6 33.4 0.5 C4 E:6EJ101 3.6 33.8 0.7 N7 G:DA2011 3.7 40.6 0.6 C5 G:DA2011 3.8 37.5 0.6 C1' G:DT2010 3.8 40.3 0.6 O G:HOH2109 3.8 66.6 1.0 N3 E:DT10 3.9 30.1 0.5 C8 E:DA11 3.9 35.0 0.5 O2 G:DT2010 3.9 38.9 0.6 C6 G:DA2011 3.9 36.8 0.6 C4 E:DT10 4.0 31.2 0.5 N6 G:DA2011 4.0 40.6 0.6 C2 E:DT10 4.0 32.2 0.5 C5 E:6EJ101 4.1 34.8 0.7 C14 E:6EJ101 4.1 34.3 0.3 C5 E:DA11 4.2 33.0 0.5 C5 E:DT10 4.3 30.8 0.5 N1 E:DT10 4.3 33.0 0.5 O4 G:DT2010 4.3 30.5 0.6 C7 G:DT2010 4.3 33.9 0.6 C8 G:DA2011 4.3 39.0 0.6 C6 E:DT10 4.4 31.0 0.5 O4 E:DT10 4.4 31.8 0.5 C16 E:6EJ101 4.4 44.4 0.7 N15 E:6EJ101 4.4 46.0 0.7 C11 E:6EJ101 4.4 34.8 0.7 C4 G:DA2011 4.5 36.5 0.6 C3' G:DT2010 4.5 38.1 0.6 O2 E:DT10 4.5 30.7 0.5 N1 G:DA2011 4.6 30.0 0.5 N9 E:DA11 4.6 33.1 0.5 N10 E:6EJ101 4.6 33.7 0.7 N1 G:DA2011 4.7 36.3 0.6 C2' E:DT10 4.7 35.7 0.5 N9 G:DA2011 4.8 37.6 0.6 O4' G:DT2010 4.8 44.9 0.6 N6 G:DA2011 4.8 30.9 0.5 C4 E:DA11 4.8 33.2 0.5 C6 E:DA11 4.8 32.3 0.5 C2 E:6EJ101 4.8 29.9 0.3 C4 E:6EJ101 4.9 29.7 0.3 C6 G:DA2011 4.9 31.2 0.5 N15 E:6EJ101 4.9 34.7 0.3 N1 E:DA11 4.9 32.3 0.6 N6 E:DA11 5.0 30.0 0.5

Fluorine binding site 2 out of 2 in the 1.98A Structure of GSK945237 with S.Aureus Dna Gyrase and Singly Nicked Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of 1.98A Structure of GSK945237 with S.Aureus Dna Gyrase and Singly Nicked Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:F101 b:31.3 occ:0.35 F1 E:6EJ101 0.0 31.3 0.3 C2 E:6EJ101 1.3 29.9 0.3 O9 E:6EJ101 1.5 33.0 0.7 C8 E:6EJ101 1.5 36.5 0.7 N10 E:6EJ101 1.5 33.7 0.7 C11 E:6EJ101 1.7 34.8 0.7 C33 E:6EJ101 2.3 32.2 0.3 C3 E:6EJ101 2.3 29.9 0.3 C34 E:6EJ101 2.9 36.2 0.7 C7 E:6EJ101 2.9 34.8 0.7 C12 E:6EJ101 3.0 32.0 0.3 C14 E:6EJ101 3.1 34.3 0.3 C12 E:6EJ101 3.2 36.6 0.7 O E:HOH236 3.3 34.2 0.5 C34 E:6EJ101 3.5 30.8 0.3 C33 E:6EJ101 3.6 35.3 0.7 C4 E:6EJ101 3.6 29.7 0.3 N7 G:DA2011 3.6 31.6 0.5 N7 E:DA11 3.7 33.6 0.6 O E:HOH236 3.7 33.7 0.5 C5 E:DT10 3.7 41.6 0.6 C6 E:DT10 3.7 43.3 0.6 N6 E:DA11 3.7 33.8 0.6 C4 E:DT10 3.8 41.4 0.6 C6 E:6EJ101 3.8 35.3 0.7 N3 E:DT10 3.8 41.5 0.6 C5 E:DA11 3.8 34.4 0.6 C5 E:6EJ101 3.8 34.8 0.7 N1 E:DT10 3.8 45.3 0.6 C2 E:DT10 3.8 42.5 0.6 C6 E:DA11 3.9 33.2 0.6 O E:HOH203 3.9 41.2 0.7 C14 E:6EJ101 4.0 39.2 0.7 C8 G:DA2011 4.0 31.2 0.5 C5 E:6EJ101 4.1 31.3 0.3 C5 G:DA2011 4.2 30.6 0.5 C2' E:DT10 4.2 45.2 0.6 C2' G:DT2010 4.2 36.1 0.5 N15 E:6EJ101 4.2 34.7 0.3 C16 E:6EJ101 4.3 33.8 0.3 C2 G:DT2010 4.3 38.8 0.5 N3 G:DT2010 4.3 39.6 0.5 N1 G:DT2010 4.3 37.6 0.5 O4 E:DT10 4.3 42.0 0.6 C6 G:DT2010 4.4 37.3 0.5 C11 E:6EJ101 4.4 31.4 0.3 C8 E:DA11 4.4 34.8 0.6 C4 G:DT2010 4.4 37.8 0.5 C7 E:DT10 4.5 42.0 0.6 C5 G:DT2010 4.5 37.1 0.5 O2 E:DT10 4.5 39.9 0.6 C1' E:DT10 4.6 43.8 0.6 N15 E:6EJ101 4.6 46.0 0.7 N10 E:6EJ101 4.6 31.3 0.3 C4 E:DA11 4.6 35.3 0.6 C20 E:6EJ101 4.7 35.5 0.3 C6 G:DA2011 4.7 31.2 0.5 N1 E:DA11 4.7 32.3 0.6 N6 G:DA2011 4.8 30.9 0.5 N9 G:DA2011 4.8 30.7 0.5 O2 G:DT2010 4.8 37.2 0.5 C4 G:DA2011 4.8 30.8 0.5 C2 E:6EJ101 4.9 36.8 0.7 C1' G:DT2010 4.9 37.8 0.5 N9 E:DA11 5.0 34.7 0.6

T.J.Miles, A.J.Hennessy, B.Bax, G.Brooks, B.S.Brown, P.Brown, N.Cailleau, D.Chen, S.Dabbs, D.T.Davies, J.M.Esken, I.Giordano, J.L.Hoover, G.E.Jones, S.K.Kusalakumari Sukmar, R.E.Markwell, E.A.Minthorn, S.Rittenhouse, M.N.Gwynn, N.D.Pearson. Novel Tricyclics (E.G., GSK945237) As Potent Inhibitors of Bacterial Type Iia Topoisomerases. Bioorg.Med.Chem.Lett. V. 26 2464 2016.
ISSN: ESSN 1464-3405
PubMed: 27055939
DOI: 10.1016/J.BMCL.2016.03.106