Fluorine in PDB 5z9l: Bacterial Gyrb Atpase Domain in Complex with A Chemical Fragment

All present enzymatic activity of Bacterial Gyrb Atpase Domain in Complex with A Chemical Fragment:
5.99.1.3;

The structure of Bacterial Gyrb Atpase Domain in Complex with A Chemical Fragment, PDB code: 5z9l was solved by X.Huang, H.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.21 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.070, 69.065, 102.121, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 24.2

The binding sites of Fluorine atom in the Bacterial Gyrb Atpase Domain in Complex with A Chemical Fragment (pdb code 5z9l). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Bacterial Gyrb Atpase Domain in Complex with A Chemical Fragment, PDB code: 5z9l:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Bacterial Gyrb Atpase Domain in Complex with A Chemical Fragment


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Bacterial Gyrb Atpase Domain in Complex with A Chemical Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:24.7 occ:1.00 FAG A:8H8303 0.0 24.7 1.0 CAF A:8H8303 1.3 23.7 1.0 CAB A:8H8303 2.3 24.2 1.0 CAI A:8H8303 2.3 23.1 1.0 CAC A:8H8303 2.7 25.5 1.0 CG2 A:ILE78 3.4 26.4 1.0 CG A:GLU50 3.4 26.3 1.0 NAD A:8H8303 3.5 26.5 1.0 CAA A:8H8303 3.6 23.6 1.0 CAH A:8H8303 3.6 22.6 1.0 CB A:ASN46 3.7 20.5 1.0 O A:ASN46 3.8 17.4 1.0 C A:ASN46 4.0 17.8 1.0 CAE A:8H8303 4.1 23.6 1.0 CG2 A:THR165 4.3 18.0 1.0 N A:ALA47 4.3 16.6 1.0 CD A:GLU50 4.4 27.2 1.0 CA A:ASN46 4.5 18.9 1.0 CB A:GLU50 4.5 25.1 1.0 CB A:THR165 4.5 18.1 1.0 OD2 A:ASP73 4.6 22.2 1.0 CA A:ALA47 4.6 16.1 1.0 ND2 A:ASN46 4.6 23.8 1.0 OG1 A:THR165 4.7 18.6 1.0 CG A:ASN46 4.7 22.2 1.0 OAJ A:8H8303 4.7 23.4 1.0 CB A:ILE78 4.9 26.2 1.0 OE1 A:GLU50 4.9 30.7 1.0

Fluorine binding site 2 out of 2 in the Bacterial Gyrb Atpase Domain in Complex with A Chemical Fragment


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Bacterial Gyrb Atpase Domain in Complex with A Chemical Fragment within 5.0Å range: probe atom residue distance (Å) B Occ B:F303 b:34.4 occ:1.00 FAG B:8H8303 0.0 34.4 1.0 CAF B:8H8303 1.4 32.8 1.0 CAB B:8H8303 2.3 33.5 1.0 CAI B:8H8303 2.3 31.7 1.0 CAC B:8H8303 2.7 35.3 1.0 O B:HOH483 3.3 48.6 1.0 CG B:GLU50 3.4 31.0 1.0 NAD B:8H8303 3.4 38.5 1.0 CAA B:8H8303 3.6 32.8 1.0 CAH B:8H8303 3.6 31.6 1.0 CD1 B:ILE78 3.8 23.5 1.0 CG1 B:ILE78 3.9 22.9 1.0 O B:ASN46 3.9 21.3 1.0 CB B:ASN46 3.9 22.1 1.0 C B:ASN46 4.1 20.2 1.0 CAE B:8H8303 4.1 32.7 1.0 O B:HOH465 4.1 42.6 1.0 CD B:GLU50 4.2 32.4 1.0 CG2 B:THR165 4.3 17.2 1.0 N B:ALA47 4.4 18.8 1.0 OE2 B:GLU50 4.5 33.8 1.0 CB B:GLU50 4.6 30.3 1.0 OD2 B:ASP73 4.6 23.0 1.0 CA B:ASN46 4.6 20.6 1.0 CB B:THR165 4.6 17.1 1.0 CA B:ALA47 4.7 18.0 1.0 OAJ B:8H8303 4.7 30.4 1.0 OG1 B:THR165 4.8 17.9 1.0 OE1 B:GLU50 5.0 31.8 1.0 CG B:ASN46 5.0 24.1 1.0

X.Huang, J.Guo, Q.Liu, Q.Gu, J.Xu, H.Zhou. Identification of An Auxiliary Druggable Pocket in the Dna Gyrase Atpase Domain Using Fragment Probes Medchemcomm V. 9 1619 2018.
ISSN: ESSN 2040-2511
PubMed: 30429968
DOI: 10.1039/C8MD00148K