Fluorine in PDB 4gvh: Crystal Structure of Salmonella Typhimurium Family 3 Glycoside Hydrolase (Nagz) Covalently Bound to 5-Fluoro-Glcnac.

All present enzymatic activity of Crystal Structure of Salmonella Typhimurium Family 3 Glycoside Hydrolase (Nagz) Covalently Bound to 5-Fluoro-Glcnac.:
3.2.1.52;

The structure of Crystal Structure of Salmonella Typhimurium Family 3 Glycoside Hydrolase (Nagz) Covalently Bound to 5-Fluoro-Glcnac., PDB code: 4gvh was solved by J.P.Bacik, B.L.Mark, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.62 / 1.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.260, 65.923, 94.724, 90.00, 99.28, 90.00
R / Rfree (%)	16.5 / 19.5

The binding sites of Fluorine atom in the Crystal Structure of Salmonella Typhimurium Family 3 Glycoside Hydrolase (Nagz) Covalently Bound to 5-Fluoro-Glcnac. (pdb code 4gvh). 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 Salmonella Typhimurium Family 3 Glycoside Hydrolase (Nagz) Covalently Bound to 5-Fluoro-Glcnac., PDB code: 4gvh:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Salmonella Typhimurium Family 3 Glycoside Hydrolase (Nagz) Covalently Bound to 5-Fluoro-Glcnac.


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 Salmonella Typhimurium Family 3 Glycoside Hydrolase (Nagz) Covalently Bound to 5-Fluoro-Glcnac. within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:12.1 occ:1.00 F A:0XY401 0.0 12.1 1.0 C5 A:0XY401 1.4 11.2 1.0 C6 A:0XY401 2.3 9.3 1.0 O5 A:0XY401 2.4 12.3 1.0 C4 A:0XY401 2.4 9.5 1.0 OD2 A:ASP248 2.6 14.7 1.0 O4 A:0XY401 2.7 8.2 1.0 C1 A:0XY401 2.9 11.5 1.0 C3 A:0XY401 2.9 8.7 1.0 CG A:ASP248 3.0 21.7 1.0 SD A:MET210 3.1 12.6 1.0 CE A:MET210 3.4 13.8 1.0 OD1 A:ASP248 3.5 15.5 1.0 C2 A:0XY401 3.5 11.1 1.0 CD2 A:LEU277 3.5 17.0 1.0 O6 A:0XY401 3.6 10.0 1.0 CB A:ASP248 3.9 25.1 1.0 O3 A:0XY401 4.3 7.4 1.0 CA A:ASP248 4.4 17.4 1.0 N2 A:0XY401 4.6 9.4 1.0 CG A:MET210 4.7 11.8 1.0 CD2 A:PHE117 4.8 6.0 1.0 OD1 A:ASP62 4.8 8.6 1.0 CE2 A:PHE117 4.9 9.1 1.0 CG A:LEU277 4.9 10.9 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Salmonella Typhimurium Family 3 Glycoside Hydrolase (Nagz) Covalently Bound to 5-Fluoro-Glcnac.


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 Salmonella Typhimurium Family 3 Glycoside Hydrolase (Nagz) Covalently Bound to 5-Fluoro-Glcnac. within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:12.6 occ:1.00 F B:0XY401 0.0 12.6 1.0 C5 B:0XY401 1.4 13.0 1.0 C6 B:0XY401 2.3 10.3 1.0 O5 B:0XY401 2.4 10.7 1.0 C4 B:0XY401 2.4 10.4 1.0 OD2 B:ASP248 2.6 11.7 1.0 O4 B:0XY401 2.7 8.5 1.0 C1 B:0XY401 2.9 13.3 1.0 C3 B:0XY401 2.9 8.6 1.0 CG B:ASP248 3.0 18.9 1.0 SD B:MET210 3.1 9.7 0.7 CE B:MET210 3.2 6.0 0.3 OD1 B:ASP248 3.5 14.1 1.0 CD2 B:LEU277 3.5 14.2 1.0 C2 B:0XY401 3.5 8.9 1.0 O6 B:0XY401 3.6 11.0 1.0 CE B:MET210 3.6 9.6 0.7 SD B:MET210 3.7 14.4 0.3 CB B:ASP248 3.9 20.7 1.0 O3 B:0XY401 4.2 7.0 1.0 CA B:ASP248 4.4 17.6 1.0 CG B:MET210 4.5 9.7 0.3 CG B:MET210 4.6 9.4 0.7 N2 B:0XY401 4.6 9.6 1.0 CD2 B:PHE117 4.7 5.9 1.0 OD1 B:ASP62 4.8 8.1 1.0 CE2 B:PHE117 4.9 8.0 1.0 CG B:LEU277 4.9 10.8 1.0 N B:ASP249 5.0 31.7 1.0

J.P.Bacik, G.E.Whitworth, K.A.Stubbs, D.J.Vocadlo, B.L.Mark. Active Site Plasticity Within the Glycoside Hydrolase Nagz Underlies A Dynamic Mechanism of Substrate Distortion. Chem.Biol. V. 19 1471 2012.
ISSN: ISSN 1074-5521
PubMed: 23177201
DOI: 10.1016/J.CHEMBIOL.2012.09.016