Fluorine in PDB 4pu9: E. Coli Gyrb 43-kDa N-Terminal Fragment in Complex with Adp-BEF3

All present enzymatic activity of E. Coli Gyrb 43-kDa N-Terminal Fragment in Complex with Adp-BEF3:
5.99.1.3;

The structure of E. Coli Gyrb 43-kDa N-Terminal Fragment in Complex with Adp-BEF3, PDB code: 4pu9 was solved by F.V.Stanger, T.Schirmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.08 / 2.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	88.083, 143.245, 79.895, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 27.3

The structure of E. Coli Gyrb 43-kDa N-Terminal Fragment in Complex with Adp-BEF3 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Fluorine atom in the E. Coli Gyrb 43-kDa N-Terminal Fragment in Complex with Adp-BEF3 (pdb code 4pu9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the E. Coli Gyrb 43-kDa N-Terminal Fragment in Complex with Adp-BEF3, PDB code: 4pu9:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the E. Coli Gyrb 43-kDa N-Terminal Fragment in Complex with Adp-BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of E. Coli Gyrb 43-kDa N-Terminal Fragment in Complex with Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:28.8 occ:1.00 F1 A:BEF402 0.0 28.8 1.0 BE A:BEF402 1.5 29.8 1.0 F2 A:BEF402 2.4 27.7 1.0 F3 A:BEF402 2.5 29.7 1.0 O3B A:ADP401 2.5 29.8 1.0 N A:GLY119 2.9 30.9 1.0 N A:VAL118 2.9 34.0 1.0 O A:HOH547 3.1 34.1 1.0 N A:GLY117 3.3 35.7 1.0 O A:HOH548 3.3 44.8 1.0 CB A:HIS116 3.4 33.1 1.0 CA A:VAL118 3.5 33.1 1.0 O3A A:ADP401 3.5 26.7 1.0 CB A:VAL118 3.6 35.1 1.0 CG1 A:VAL118 3.6 34.7 1.0 C A:VAL118 3.7 33.6 1.0 C A:HIS116 3.7 32.0 1.0 CA A:GLY119 3.8 31.3 1.0 N A:HIS116 3.8 29.3 1.0 CA A:HIS116 3.8 32.9 1.0 PB A:ADP401 3.8 27.3 1.0 C A:GLY117 3.9 37.6 1.0 CA A:GLY117 4.1 40.2 1.0 CG A:HIS116 4.3 33.9 1.0 MG A:MG403 4.4 28.2 1.0 ND1 A:HIS116 4.4 33.1 1.0 PA A:ADP401 4.5 29.9 1.0 O A:HIS116 4.6 31.6 1.0 O2B A:ADP401 4.6 27.6 1.0 O2A A:ADP401 4.6 30.4 1.0 O1A A:ADP401 4.6 30.6 1.0 NZ A:LYS337 4.7 41.6 1.0 N A:LEU115 4.9 27.5 1.0 O A:VAL118 4.9 34.1 1.0 O1B A:ADP401 4.9 26.7 1.0 O A:HOH507 4.9 28.5 1.0

Fluorine binding site 2 out of 3 in the E. Coli Gyrb 43-kDa N-Terminal Fragment in Complex with Adp-BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of E. Coli Gyrb 43-kDa N-Terminal Fragment in Complex with Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:27.7 occ:1.00 F2 A:BEF402 0.0 27.7 1.0 BE A:BEF402 1.5 29.8 1.0 F1 A:BEF402 2.4 28.8 1.0 F3 A:BEF402 2.4 29.7 1.0 O3B A:ADP401 2.5 29.8 1.0 N A:LEU115 2.7 27.5 1.0 N A:HIS116 2.7 29.3 1.0 NZ A:LYS337 2.9 41.6 1.0 O A:HOH548 3.3 44.8 1.0 CA A:GLY114 3.3 22.6 1.0 C A:GLY114 3.5 24.7 1.0 CB A:HIS116 3.6 33.1 1.0 CA A:HIS116 3.6 32.9 1.0 C A:LEU115 3.6 29.9 1.0 CA A:LEU115 3.7 30.9 1.0 O A:HOH547 3.7 34.1 1.0 PB A:ADP401 3.9 27.3 1.0 N A:GLY117 3.9 35.7 1.0 CG A:HIS116 3.9 33.9 1.0 CE A:LYS337 4.0 41.2 1.0 ND1 A:HIS116 4.0 33.1 1.0 CD2 A:LEU115 4.0 36.4 1.0 C A:HIS116 4.3 32.0 1.0 O2B A:ADP401 4.3 27.6 1.0 O3A A:ADP401 4.5 26.7 1.0 MG A:MG403 4.5 28.2 1.0 N A:GLY114 4.6 24.4 1.0 O A:GLY113 4.6 25.2 1.0 CB A:LEU115 4.6 30.7 1.0 CG A:LEU115 4.6 34.8 1.0 O A:GLY114 4.7 22.7 1.0 CD2 A:HIS116 4.8 35.7 1.0 O A:LEU115 4.8 24.3 1.0 O1B A:ADP401 4.8 26.7 1.0 CE1 A:HIS116 4.9 33.8 1.0 N A:VAL118 5.0 34.0 1.0

Fluorine binding site 3 out of 3 in the E. Coli Gyrb 43-kDa N-Terminal Fragment in Complex with Adp-BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of E. Coli Gyrb 43-kDa N-Terminal Fragment in Complex with Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:29.7 occ:1.00 F3 A:BEF402 0.0 29.7 1.0 BE A:BEF402 1.5 29.8 1.0 MG A:MG403 2.2 28.2 1.0 F2 A:BEF402 2.4 27.7 1.0 F1 A:BEF402 2.5 28.8 1.0 O3B A:ADP401 2.5 29.8 1.0 O A:HOH548 2.6 44.8 1.0 O2B A:ADP401 3.0 27.6 1.0 O A:HOH507 3.0 28.5 1.0 PB A:ADP401 3.1 27.3 1.0 O3A A:ADP401 3.2 26.7 1.0 O1A A:ADP401 3.6 30.6 1.0 CA A:GLY114 3.8 22.6 1.0 N A:GLY119 3.9 30.9 1.0 NZ A:LYS337 4.0 41.6 1.0 PA A:ADP401 4.0 29.9 1.0 CA A:GLY119 4.1 31.3 1.0 OE2 A:GLU42 4.2 27.7 1.0 O A:HOH547 4.3 34.1 1.0 OD1 A:ASN46 4.3 27.2 1.0 N A:LEU115 4.4 27.5 1.0 O1B A:ADP401 4.6 26.7 1.0 C A:GLY114 4.7 24.7 1.0 N A:VAL118 4.7 34.0 1.0 N A:GLY117 4.8 35.7 1.0 N A:GLY114 4.8 24.4 1.0 N A:HIS116 4.8 29.3 1.0 O2A A:ADP401 4.9 30.4 1.0

F.V.Stanger, C.Dehio, T.Schirmer. Structure of the N-Terminal Gyrase B Fragment in Complex with Adppi Reveals Rigid-Body Motion Induced By Atp Hydrolysis Plos One V. 9 07289 2014.
ISSN: ESSN 1932-6203
PubMed: 25202966
DOI: 10.1371/JOURNAL.PONE.0107289