Fluorine in PDB 4bc5: Crystal Structure of Human D-Xylulokinase in Complex with Inhibitor 5-Deoxy-5-Fluoro-D-Xylulose

All present enzymatic activity of Crystal Structure of Human D-Xylulokinase in Complex with Inhibitor 5-Deoxy-5-Fluoro-D-Xylulose:
2.7.1.17;

The structure of Crystal Structure of Human D-Xylulokinase in Complex with Inhibitor 5-Deoxy-5-Fluoro-D-Xylulose, PDB code: 4bc5 was solved by R.D.Bunker, K.M.Loomes, E.N.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.98 / 1.98
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	102.109, 102.109, 159.101, 90.00, 90.00, 120.00
R / Rfree (%)	17.16 / 19.24

The binding sites of Fluorine atom in the Crystal Structure of Human D-Xylulokinase in Complex with Inhibitor 5-Deoxy-5-Fluoro-D-Xylulose (pdb code 4bc5). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Human D-Xylulokinase in Complex with Inhibitor 5-Deoxy-5-Fluoro-D-Xylulose, PDB code: 4bc5:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Human D-Xylulokinase in Complex with Inhibitor 5-Deoxy-5-Fluoro-D-Xylulose


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 Human D-Xylulokinase in Complex with Inhibitor 5-Deoxy-5-Fluoro-D-Xylulose within 5.0Å range: probe atom residue distance (Å) B Occ A:F1531 b:37.4 occ:1.00 F A:5FX1531 0.0 37.4 1.0 C5 A:5FX1531 1.4 35.9 1.0 H52C A:5FX1531 2.1 35.9 1.0 H51C A:5FX1531 2.1 34.4 1.0 C4 A:5FX1531 2.4 36.4 1.0 HB2 A:GLN97 2.4 35.7 1.0 H4 A:5FX1531 2.6 35.5 1.0 HA A:GLN97 2.8 35.6 1.0 O4 A:5FX1531 2.8 34.5 1.0 O A:HOH2009 2.9 52.0 1.0 CB A:GLN97 3.1 35.6 1.0 HB3 A:GLN97 3.1 35.3 1.0 H A:GLN98 3.1 32.9 1.0 OD2 A:ASP280 3.2 50.4 1.0 HB A:5FX1531 3.2 34.0 1.0 CA A:GLN97 3.3 35.4 1.0 CD1 A:TRP137 3.3 38.9 1.0 HD1 A:TRP137 3.4 39.5 1.0 NE1 A:TRP137 3.5 37.5 1.0 HE1 A:TRP137 3.7 38.6 1.0 HG1 A:THR17 3.7 37.3 1.0 OG1 A:THR17 3.7 37.1 1.0 C3 A:5FX1531 3.7 32.8 1.0 N A:GLN98 3.8 34.1 1.0 CG A:TRP137 3.9 36.4 1.0 H3 A:5FX1531 3.9 33.3 1.0 CG A:ASP280 4.0 49.6 1.0 C A:GLN97 4.0 38.5 1.0 O A:HOH2005 4.1 52.2 1.0 OD1 A:ASP280 4.1 54.0 1.0 CE2 A:TRP137 4.1 39.3 1.0 HB3 A:TRP137 4.2 35.1 1.0 O3 A:5FX1531 4.3 32.2 1.0 CD2 A:TRP137 4.3 36.5 1.0 HA A:5FX1531 4.4 32.9 1.0 H A:THR17 4.5 35.7 1.0 CG A:GLN97 4.5 33.1 1.0 CB A:TRP137 4.6 35.1 1.0 OE1 A:GLN97 4.7 34.0 1.0 N A:GLN97 4.7 36.9 1.0 HA A:SER16 4.9 36.2 1.0 HG3 A:GLN97 4.9 35.6 1.0 O A:HOH2058 4.9 33.5 1.0 HB2 A:TRP137 4.9 35.9 1.0 C2 A:5FX1531 4.9 34.0 1.0 CD A:GLN97 4.9 39.7 1.0 O A:GLN98 5.0 39.1 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Human D-Xylulokinase in Complex with Inhibitor 5-Deoxy-5-Fluoro-D-Xylulose


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 Human D-Xylulokinase in Complex with Inhibitor 5-Deoxy-5-Fluoro-D-Xylulose within 5.0Å range: probe atom residue distance (Å) B Occ B:F1532 b:37.0 occ:1.00 F B:5FX1532 0.0 37.0 1.0 C5 B:5FX1532 1.4 37.5 1.0 H52C B:5FX1532 2.0 37.9 1.0 H51C B:5FX1532 2.0 36.6 1.0 C4 B:5FX1532 2.4 34.8 1.0 HB2 B:GLN97 2.5 33.9 1.0 H4 B:5FX1532 2.6 35.6 1.0 HA B:GLN97 2.8 31.9 1.0 O4 B:5FX1532 2.9 38.9 1.0 CB B:GLN97 3.1 34.0 1.0 HB3 B:GLN97 3.1 35.3 1.0 OD2 B:ASP280 3.2 49.9 1.0 H B:GLN98 3.2 32.3 1.0 CD1 B:TRP137 3.3 38.7 1.0 HD1 B:TRP137 3.4 38.9 1.0 CA B:GLN97 3.4 32.4 1.0 NE1 B:TRP137 3.5 40.1 1.0 HE1 B:TRP137 3.6 40.3 1.0 C3 B:5FX1532 3.7 33.0 1.0 HB B:5FX1532 3.8 38.4 1.0 HG1 B:THR17 3.8 43.5 1.0 OG1 B:THR17 3.8 43.9 1.0 CG B:TRP137 3.9 35.5 1.0 N B:GLN98 3.9 31.8 1.0 H3 B:5FX1532 3.9 33.7 1.0 CG B:ASP280 4.0 41.2 1.0 C B:GLN97 4.0 34.3 1.0 CE2 B:TRP137 4.1 40.8 1.0 O B:HOH2002 4.1 52.8 1.0 OD1 B:ASP280 4.2 44.4 1.0 HB3 B:TRP137 4.2 36.8 1.0 HA B:5FX1532 4.2 34.4 1.0 CD2 B:TRP137 4.3 35.9 1.0 O3 B:5FX1532 4.3 33.6 1.0 H B:THR17 4.4 36.8 1.0 CG B:GLN97 4.5 36.7 1.0 CB B:TRP137 4.6 36.2 1.0 O B:HOH2253 4.6 69.9 1.0 OE1 B:GLN97 4.7 33.0 1.0 N B:GLN97 4.7 33.8 1.0 HA B:SER16 4.8 33.1 1.0 CZ2 B:TRP137 4.9 40.2 1.0 HB2 B:TRP137 4.9 37.7 1.0 HG3 B:GLN97 4.9 36.8 1.0 CD B:GLN97 4.9 37.7 1.0 C2 B:5FX1532 4.9 38.6 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Human D-Xylulokinase in Complex with Inhibitor 5-Deoxy-5-Fluoro-D-Xylulose


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human D-Xylulokinase in Complex with Inhibitor 5-Deoxy-5-Fluoro-D-Xylulose within 5.0Å range: probe atom residue distance (Å) B Occ C:F1532 b:36.6 occ:1.00 F C:5FX1532 0.0 36.6 1.0 C5 C:5FX1532 1.4 35.9 1.0 H51C C:5FX1532 2.0 36.5 1.0 H52C C:5FX1532 2.0 33.9 1.0 C4 C:5FX1532 2.4 39.3 1.0 HB2 C:GLN97 2.5 35.6 1.0 H4 C:5FX1532 2.5 37.3 1.0 HA C:GLN97 2.9 34.9 1.0 O4 C:5FX1532 2.9 38.4 1.0 O C:HOH2007 3.0 50.6 1.0 H C:GLN98 3.1 32.3 1.0 CB C:GLN97 3.2 36.7 1.0 HB3 C:GLN97 3.2 36.9 1.0 OD2 C:ASP280 3.2 47.3 1.0 CD1 C:TRP137 3.2 40.3 1.0 HB C:5FX1532 3.3 38.4 1.0 HD1 C:TRP137 3.3 40.0 1.0 NE1 C:TRP137 3.4 39.5 1.0 CA C:GLN97 3.4 35.4 1.0 HE1 C:TRP137 3.6 40.8 1.0 OG1 C:THR17 3.7 41.8 1.0 C3 C:5FX1532 3.7 36.7 1.0 CG C:TRP137 3.8 37.4 1.0 HG1 C:THR17 3.8 41.1 1.0 N C:GLN98 3.8 33.4 1.0 H3 C:5FX1532 3.9 38.1 1.0 CE2 C:TRP137 4.0 40.7 1.0 CG C:ASP280 4.0 38.6 1.0 C C:GLN97 4.0 36.2 1.0 HB3 C:TRP137 4.1 40.2 1.0 OD1 C:ASP280 4.1 38.0 1.0 HA C:5FX1532 4.1 40.8 1.0 CD2 C:TRP137 4.2 37.8 1.0 O3 C:5FX1532 4.3 38.9 1.0 CB C:TRP137 4.5 37.7 1.0 H C:THR17 4.5 36.1 1.0 CG C:GLN97 4.6 37.2 1.0 O C:HOH2002 4.6 48.9 1.0 OE1 C:GLN97 4.7 43.0 1.0 N C:GLN97 4.8 36.6 1.0 HB2 C:TRP137 4.8 36.4 1.0 CZ2 C:TRP137 4.8 40.4 1.0 C2 C:5FX1532 4.8 39.8 1.0 HG3 C:GLN97 4.9 36.0 1.0 O C:GLN98 4.9 35.0 1.0 HB2 C:GLN98 5.0 31.1 1.0 CD C:GLN97 5.0 51.6 1.0 HG3 C:GLN98 5.0 31.0 1.0 O C:HOH2058 5.0 32.5 1.0

R.D.Bunker, E.M.M.Bulloch, J.M.J.Dickson, K.M.Loomes, E.N.Baker. Structure and Function of Human Xylulokinase, An Enzyme with Important Roles in Carbohydrate Metabolism J.Biol.Chem. V. 288 1643 2013.
ISSN: ISSN 0021-9258
PubMed: 23179721
DOI: 10.1074/JBC.M112.427997