Fluorine in PDB 6fqs: 3.11A Complex of S.Aureus Gyrase with Imidazopyrazinone T3 and Dna

All present enzymatic activity of 3.11A Complex of S.Aureus Gyrase with Imidazopyrazinone T3 and Dna:
5.99.1.3;

The structure of 3.11A Complex of S.Aureus Gyrase with Imidazopyrazinone T3 and Dna, PDB code: 6fqs was solved by B.D.Bax, T.Germe, E.Basque, A.Maxwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.01 / 3.11
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	94.027, 94.027, 420.470, 90.00, 90.00, 120.00
R / Rfree (%)	17.9 / 21

The structure of 3.11A Complex of S.Aureus Gyrase with Imidazopyrazinone T3 and Dna also contains other interesting chemical elements:

Manganese	(Mn)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Fluorine atom in the 3.11A Complex of S.Aureus Gyrase with Imidazopyrazinone T3 and Dna (pdb code 6fqs). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the 3.11A Complex of S.Aureus Gyrase with Imidazopyrazinone T3 and Dna, PDB code: 6fqs:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the 3.11A Complex of S.Aureus Gyrase with Imidazopyrazinone T3 and Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of 3.11A Complex of S.Aureus Gyrase with Imidazopyrazinone T3 and Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:F102 b:97.4 occ:1.00 F E:E3E102 0.0 97.4 1.0 C E:E3E102 1.3 91.2 1.0 C1 E:E3E102 2.3 96.5 1.0 C5 E:E3E102 2.4 94.1 1.0 C6 E:E3E102 2.8 0.4 1.0 C2 F:DC4 2.8 99.1 1.0 C10 E:E3E102 2.9 0.8 1.0 O2 F:DC4 3.0 87.0 1.0 N7 F:DA5 3.1 76.3 1.0 N1 F:DC4 3.1 0.5 1.0 N3 F:DC4 3.3 0.4 1.0 C8 F:DA5 3.4 82.3 1.0 C5 F:DA5 3.4 71.5 1.0 C1' F:DC4 3.5 0.3 1.0 C4 E:E3E102 3.6 82.0 1.0 C2 E:E3E102 3.6 94.2 1.0 N2 E:DG1 3.7 0.8 1.0 C6 F:DC4 3.7 1.0 1.0 C4 F:DC4 3.9 0.9 1.0 N1 E:DG1 3.9 0.9 1.0 N9 F:DA5 3.9 78.9 1.0 C4 F:DA5 4.0 73.2 1.0 C2 E:DG1 4.0 0.3 1.0 C7 E:E3E102 4.0 0.5 1.0 C6 F:DA5 4.0 74.4 1.0 C9 E:E3E102 4.1 0.0 1.0 C5 F:DC4 4.1 0.8 1.0 C3 E:E3E102 4.1 86.1 1.0 N6 F:DA5 4.3 72.7 1.0 C2' F:DC4 4.5 90.1 1.0 O4' F:DC4 4.6 0.4 1.0 N3 E:E3E102 4.8 0.8 1.0 C6 E:DG1 4.8 0.1 1.0 N4 F:DC4 4.8 0.5 1.0 O4' F:DA5 4.9 75.9 1.0 N3 F:DA5 4.9 72.7 1.0 N1 F:DA5 4.9 80.6 1.0 C8 E:E3E102 4.9 0.4 1.0 C1' F:DA5 4.9 75.6 1.0 N3 E:DG1 4.9 0.2 1.0 N E:E3E102 5.0 0.4 1.0

Fluorine binding site 2 out of 3 in the 3.11A Complex of S.Aureus Gyrase with Imidazopyrazinone T3 and Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of 3.11A Complex of S.Aureus Gyrase with Imidazopyrazinone T3 and Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:F103 b:0.4 occ:0.50 F E:E3E103 0.0 0.4 0.5 F E:E3E103 1.3 0.6 0.5 C E:E3E103 1.3 0.9 0.5 C E:E3E103 1.4 0.2 0.5 C5 E:E3E103 1.5 0.1 0.5 C6 E:E3E103 1.7 0.9 0.5 C10 E:E3E103 1.9 0.9 0.5 C1 E:E3E103 2.3 0.4 0.5 C5 E:E3E103 2.4 0.6 0.5 C10 E:E3E103 2.7 0.1 0.5 C1 E:E3E103 2.7 0.0 0.5 C4 E:E3E103 2.8 0.7 0.5 C6 E:E3E103 2.8 1.0 0.5 C2 E:DC4 3.0 0.5 0.5 C7 E:E3E103 3.0 0.9 0.5 C2 E:DC4 3.1 0.7 0.5 C9 E:E3E103 3.2 0.9 0.5 N3 E:DC4 3.2 0.7 0.5 N3 E:DC4 3.2 0.7 0.5 N1 E:DC4 3.3 0.9 0.5 O2 E:DC4 3.3 0.5 0.5 O2 E:DC4 3.4 0.4 0.5 N7 E:DA5 3.4 0.4 0.5 N1 E:DC4 3.5 0.2 0.5 C8 E:DA5 3.5 0.3 0.5 C2' E:DC4 3.5 0.5 0.5 N7 E:DA5 3.5 0.3 0.5 C5 E:DA5 3.6 0.1 0.5 C2 E:E3E103 3.6 0.2 0.5 C4 E:E3E103 3.6 0.7 0.5 C5 E:DA5 3.6 0.7 0.5 C2 E:E3E103 3.6 0.3 0.5 C4 E:DC4 3.7 0.6 0.5 C8 E:DA5 3.7 1.0 0.5 C3 E:E3E103 3.7 0.2 0.5 C4 E:DC4 3.7 0.7 0.5 C6 E:DC4 3.7 0.7 0.5 N2 F:DG1 3.7 0.6 0.5 C2' E:DC4 3.8 0.6 0.5 N9 E:DA5 3.8 0.7 0.5 C4 E:DA5 3.8 0.7 0.5 C4 E:DA5 3.8 0.8 0.5 N9 E:DA5 3.8 0.8 0.5 C5 E:DC4 3.9 0.2 0.5 C1' E:DC4 3.9 0.0 0.5 N2 F:DG1 3.9 0.8 0.5 C8 E:E3E103 3.9 1.0 0.5 C9 E:E3E103 3.9 1.0 0.5 C6 E:DC4 4.0 0.2 0.5 N E:E3E103 4.0 0.7 0.5 C3 E:E3E103 4.1 0.7 0.5 C5 E:DC4 4.1 0.5 0.5 C1' E:DC4 4.1 0.2 0.5 C7 E:E3E103 4.2 0.5 0.5 C6 E:DA5 4.2 0.7 0.5 C6 E:DA5 4.2 0.6 0.5 O4' E:DA5 4.3 0.3 0.5 C2 F:DG1 4.4 0.9 0.5 O4' E:DA5 4.4 0.2 0.5 N1 F:DG1 4.4 0.2 0.5 N4 E:DC4 4.5 0.1 0.5 N4 E:DC4 4.5 0.9 0.5 C1' E:DA5 4.6 0.1 0.5 N3 E:DA5 4.6 0.1 0.5 C2 F:DG1 4.6 0.6 0.5 N3 E:DA5 4.6 0.1 0.5 N1 F:DG1 4.6 0.7 0.5 C1' E:DA5 4.7 0.3 0.5 C3' E:DC4 4.7 0.2 0.5 N6 E:DA5 4.7 0.9 0.5 N3 E:E3E103 4.7 0.3 0.5 N6 E:DA5 4.8 0.0 0.5 N1 E:DA5 4.8 0.0 0.5 C3' E:DC4 4.9 0.3 0.5 N1 E:DA5 4.9 0.2 0.5 C2 E:DA5 4.9 0.2 0.5 N3 E:E3E103 5.0 0.0 0.5 C2 E:DA5 5.0 0.1 0.5 N E:E3E103 5.0 0.6 0.5

Fluorine binding site 3 out of 3 in the 3.11A Complex of S.Aureus Gyrase with Imidazopyrazinone T3 and Dna


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of 3.11A Complex of S.Aureus Gyrase with Imidazopyrazinone T3 and Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:F103 b:0.6 occ:0.50 F E:E3E103 0.0 0.6 0.5 F E:E3E103 1.3 0.4 0.5 C E:E3E103 1.3 0.2 0.5 C10 E:E3E103 1.6 0.1 0.5 C6 E:E3E103 1.8 1.0 0.5 C E:E3E103 1.9 0.9 0.5 C5 E:E3E103 2.0 0.6 0.5 C1 E:E3E103 2.3 0.0 0.5 C5 E:E3E103 2.4 0.1 0.5 C10 E:E3E103 2.7 0.9 0.5 C9 E:E3E103 2.8 1.0 0.5 C6 E:E3E103 2.9 0.9 0.5 C7 E:E3E103 3.0 0.5 0.5 N9 E:DA5 3.1 0.7 0.5 N9 E:DA5 3.1 0.8 0.5 C1 E:E3E103 3.2 0.4 0.5 C4 E:DA5 3.2 0.8 0.5 C4 E:DA5 3.2 0.7 0.5 C8 E:DA5 3.3 0.3 0.5 O4' E:DA5 3.3 0.3 0.5 C4 E:E3E103 3.3 0.7 0.5 C8 E:DA5 3.4 1.0 0.5 C5 E:DA5 3.4 0.1 0.5 C5 E:DA5 3.5 0.7 0.5 O4' E:DA5 3.5 0.2 0.5 N7 E:DA5 3.5 0.4 0.5 C1' E:DA5 3.6 0.1 0.5 C2 E:E3E103 3.6 0.3 0.5 C4 E:E3E103 3.6 0.7 0.5 N7 E:DA5 3.6 0.3 0.5 C1' E:DA5 3.7 0.3 0.5 N3 E:DA5 3.7 0.1 0.5 N E:E3E103 3.7 0.6 0.5 C8 E:E3E103 3.8 0.2 0.5 N3 E:DA5 3.8 0.1 0.5 O2 E:DC4 3.8 0.4 0.5 C2' E:DC4 3.8 0.5 0.5 O2 E:DC4 3.8 0.5 0.5 C2 E:DC4 3.9 0.5 0.5 C2 E:DC4 3.9 0.7 0.5 C9 E:E3E103 4.0 0.9 0.5 N2 F:DG1 4.0 0.6 0.5 C2' E:DC4 4.0 0.6 0.5 C3 E:E3E103 4.1 0.2 0.5 N2 F:DG1 4.1 0.8 0.5 C6 E:DA5 4.2 0.7 0.5 C2 E:E3E103 4.2 0.2 0.5 N1 E:DC4 4.2 0.9 0.5 C6 E:DA5 4.2 0.6 0.5 C7 E:E3E103 4.3 0.9 0.5 C3 E:E3E103 4.3 0.7 0.5 N3 E:DC4 4.3 0.7 0.5 C2 E:DA5 4.3 0.2 0.5 N3 E:DC4 4.3 0.7 0.5 C2 E:DA5 4.3 0.1 0.5 N1 E:DC4 4.4 0.2 0.5 C1' E:DC4 4.5 0.0 0.5 N1 E:DA5 4.5 0.0 0.5 N1 E:DA5 4.6 0.2 0.5 C4' E:DA5 4.7 0.1 0.5 C1' E:DC4 4.7 0.2 0.5 N3 E:E3E103 4.8 0.0 0.5 C2 F:DG1 4.8 0.9 0.5 C4' E:DA5 4.9 0.2 0.5 C6 E:DC4 4.9 0.7 0.5 C4 E:DC4 4.9 0.6 0.5 C2 F:DG1 4.9 0.6 0.5 C4 E:DC4 4.9 0.7 0.5 N6 E:DA5 5.0 0.9 0.5

T.Germe, J.Voros, F.Jeannot, T.Taillier, R.A.Stavenger, E.Bacque, A.Maxwell, B.D.Bax. A New Class of Antibacterials, the Imidazopyrazinones, Reveal Structural Transitions Involved in Dna Gyrase Poisoning and Mechanisms of Resistance. Nucleic Acids Res. V. 46 4114 2018.
ISSN: ESSN 1362-4962
PubMed: 29538767
DOI: 10.1093/NAR/GKY181