Fluorine in PDB 3w0y: Crystal Structure Analysis of Vitamin D Receptor

The structure of Crystal Structure Analysis of Vitamin D Receptor, PDB code: 3w0y was solved by S.Itoh, S.Iijima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.87 / 1.98
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.217, 51.124, 132.664, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 21.8

The binding sites of Fluorine atom in the Crystal Structure Analysis of Vitamin D Receptor (pdb code 3w0y). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 7 binding sites of Fluorine where determined in the Crystal Structure Analysis of Vitamin D Receptor, PDB code: 3w0y:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Fluorine binding site 1 out of 7 in the Crystal Structure Analysis of Vitamin D Receptor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure Analysis of Vitamin D Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:28.0 occ:1.00 F5 A:DS4501 0.0 28.0 1.0 C7 A:DS4501 1.5 26.3 1.0 F6 A:DS4501 2.4 26.5 1.0 F4 A:DS4501 2.5 26.7 1.0 C44 A:DS4501 2.6 26.4 1.0 F2 A:DS4501 2.7 27.5 1.0 O47 A:DS4501 2.8 25.9 1.0 C15 A:DS4501 3.2 26.8 1.0 CD1 A:TYR401 3.2 21.2 1.0 CG1 A:VAL418 3.4 19.5 1.0 CE1 A:TYR401 3.5 21.6 1.0 CD1 A:PHE422 3.7 24.3 1.0 F3 A:DS4501 3.8 27.5 1.0 C43 A:DS4501 3.9 25.5 1.0 CE1 A:PHE422 4.0 23.9 1.0 NE2 A:HIS397 4.1 21.3 1.0 CE1 A:HIS397 4.2 21.1 1.0 CG A:PHE422 4.3 22.3 1.0 CG A:TYR401 4.4 19.7 1.0 F1 A:DS4501 4.5 27.1 1.0 CB A:VAL418 4.7 19.8 1.0 CB A:PHE422 4.7 21.6 1.0 CZ A:TYR401 4.7 27.6 1.0 CD2 A:LEU414 4.7 24.7 1.0 CG2 A:VAL418 4.8 19.2 1.0 CZ A:PHE422 4.9 22.6 1.0 CB A:TYR401 4.9 18.4 1.0 CG1 A:VAL234 5.0 21.3 1.0

Fluorine binding site 2 out of 7 in the Crystal Structure Analysis of Vitamin D Receptor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure Analysis of Vitamin D Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:27.5 occ:1.00 F2 A:DS4501 0.0 27.5 1.0 C15 A:DS4501 1.5 26.8 1.0 F1 A:DS4501 2.4 27.1 1.0 F3 A:DS4501 2.4 27.5 1.0 C44 A:DS4501 2.5 26.4 1.0 O47 A:DS4501 2.7 25.9 1.0 F5 A:DS4501 2.7 28.0 1.0 C7 A:DS4501 2.9 26.3 1.0 CD2 A:LEU404 3.3 40.1 1.0 CD1 A:LEU227 3.4 21.1 1.0 F4 A:DS4501 3.4 26.7 1.0 CD2 A:LEU414 3.5 24.7 1.0 C43 A:DS4501 3.9 25.5 1.0 CD1 A:TYR401 4.0 21.2 1.0 CE1 A:TYR401 4.2 21.6 1.0 NE2 A:HIS305 4.3 29.9 1.0 F6 A:DS4501 4.3 26.5 1.0 CG A:LEU404 4.5 35.8 1.0 CG A:LEU227 4.7 21.1 1.0 C8 A:DS4501 4.8 24.1 1.0 CG1 A:VAL418 4.9 19.5 1.0 CG A:LEU414 4.9 23.7 1.0

Fluorine binding site 3 out of 7 in the Crystal Structure Analysis of Vitamin D Receptor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure Analysis of Vitamin D Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:27.5 occ:1.00 F3 A:DS4501 0.0 27.5 1.0 C15 A:DS4501 1.5 26.8 1.0 F2 A:DS4501 2.4 27.5 1.0 F1 A:DS4501 2.5 27.1 1.0 C44 A:DS4501 2.5 26.4 1.0 F4 A:DS4501 2.6 26.7 1.0 C7 A:DS4501 3.0 26.3 1.0 C43 A:DS4501 3.2 25.5 1.0 CA A:ALA231 3.2 17.5 1.0 N A:ALA231 3.3 17.0 1.0 CD1 A:LEU227 3.3 21.1 1.0 CB A:ALA231 3.5 18.3 1.0 O47 A:DS4501 3.6 25.9 1.0 C A:LEU230 3.7 20.8 1.0 F5 A:DS4501 3.8 28.0 1.0 O A:LEU230 4.0 18.9 1.0 C8 A:DS4501 4.1 24.1 1.0 CD2 A:LEU414 4.3 24.7 1.0 O A:LEU227 4.3 18.4 1.0 CB A:LEU230 4.3 20.0 1.0 F6 A:DS4501 4.4 26.5 1.0 CA A:LEU230 4.6 19.3 1.0 CG A:LEU227 4.6 21.1 1.0 C A:ALA231 4.7 20.8 1.0 C29 A:DS4501 4.9 18.5 1.0 C28 A:DS4501 4.9 20.0 1.0

Fluorine binding site 4 out of 7 in the Crystal Structure Analysis of Vitamin D Receptor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure Analysis of Vitamin D Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:27.1 occ:1.00 F1 A:DS4501 0.0 27.1 1.0 C15 A:DS4501 1.5 26.8 1.0 F2 A:DS4501 2.4 27.5 1.0 F3 A:DS4501 2.5 27.5 1.0 C44 A:DS4501 2.5 26.4 1.0 O47 A:DS4501 2.8 25.9 1.0 NE2 A:HIS305 3.0 29.9 1.0 C43 A:DS4501 3.1 25.5 1.0 CD1 A:LEU227 3.2 21.1 1.0 CD2 A:HIS305 3.4 30.4 1.0 C8 A:DS4501 3.4 24.1 1.0 CD2 A:LEU404 3.8 40.1 1.0 C7 A:DS4501 3.9 26.3 1.0 CB A:ALA303 3.9 20.1 1.0 O A:ALA303 4.0 25.6 1.0 CE1 A:HIS305 4.2 29.6 1.0 F4 A:DS4501 4.4 26.7 1.0 F5 A:DS4501 4.5 28.0 1.0 C28 A:DS4501 4.6 20.0 1.0 CG A:HIS305 4.7 28.9 1.0 C A:ALA303 4.7 26.9 1.0 CG A:LEU227 4.7 21.1 1.0 CB A:LEU230 4.8 20.0 1.0 CA A:ALA303 4.9 19.9 1.0

Fluorine binding site 5 out of 7 in the Crystal Structure Analysis of Vitamin D Receptor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure Analysis of Vitamin D Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:26.5 occ:1.00 F6 A:DS4501 0.0 26.5 1.0 C7 A:DS4501 1.5 26.3 1.0 F5 A:DS4501 2.4 28.0 1.0 F4 A:DS4501 2.5 26.7 1.0 C44 A:DS4501 2.5 26.4 1.0 C43 A:DS4501 2.7 25.5 1.0 O47 A:DS4501 2.8 25.9 1.0 NE2 A:HIS397 3.1 21.3 1.0 CE1 A:HIS397 3.3 21.1 1.0 CG1 A:VAL234 3.5 21.3 1.0 CD1 A:ILE268 3.5 28.1 1.0 CE1 A:PHE422 3.5 23.9 1.0 CZ A:PHE422 3.8 22.6 1.0 C8 A:DS4501 3.8 24.1 1.0 C15 A:DS4501 3.9 26.8 1.0 CG2 A:VAL234 3.9 22.7 1.0 CD1 A:PHE422 4.0 24.3 1.0 CB A:VAL234 4.0 21.7 1.0 CD2 A:HIS397 4.3 21.2 1.0 F2 A:DS4501 4.3 27.5 1.0 F3 A:DS4501 4.4 27.5 1.0 CE2 A:PHE422 4.5 25.0 1.0 ND1 A:HIS397 4.5 21.4 1.0 CG A:PHE422 4.7 22.3 1.0 CG1 A:ILE268 4.7 24.4 1.0 C28 A:DS4501 4.7 20.0 1.0 CD2 A:PHE422 4.9 23.1 1.0

Fluorine binding site 6 out of 7 in the Crystal Structure Analysis of Vitamin D Receptor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure Analysis of Vitamin D Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:26.7 occ:1.00 F4 A:DS4501 0.0 26.7 1.0 C7 A:DS4501 1.5 26.3 1.0 F5 A:DS4501 2.5 28.0 1.0 C44 A:DS4501 2.5 26.4 1.0 F6 A:DS4501 2.5 26.5 1.0 F3 A:DS4501 2.6 27.5 1.0 C15 A:DS4501 2.9 26.8 1.0 C43 A:DS4501 3.1 25.5 1.0 CB A:VAL234 3.4 21.7 1.0 CG1 A:VAL234 3.4 21.3 1.0 F2 A:DS4501 3.4 27.5 1.0 O47 A:DS4501 3.6 25.9 1.0 CA A:ALA231 3.8 17.5 1.0 CG2 A:VAL234 3.8 22.7 1.0 CG1 A:VAL418 3.9 19.5 1.0 CG2 A:VAL418 3.9 19.2 1.0 O A:LEU230 4.3 18.9 1.0 F1 A:DS4501 4.4 27.1 1.0 C8 A:DS4501 4.4 24.1 1.0 CB A:ALA231 4.4 18.3 1.0 O A:ALA231 4.4 20.3 1.0 N A:ALA231 4.5 17.0 1.0 CB A:VAL418 4.5 19.8 1.0 C A:ALA231 4.6 20.8 1.0 CE1 A:PHE422 4.7 23.9 1.0 C A:LEU230 4.7 20.8 1.0 CA A:VAL234 4.8 16.7 1.0 CD1 A:PHE422 4.9 24.3 1.0

Fluorine binding site 7 out of 7 in the Crystal Structure Analysis of Vitamin D Receptor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure Analysis of Vitamin D Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:23.1 occ:1.00 F60 A:DS4501 0.0 23.1 1.0 C53 A:DS4501 1.5 22.1 1.0 C52 A:DS4501 2.5 21.2 1.0 C54 A:DS4501 2.5 22.5 1.0 C56 A:DS4501 2.9 22.0 1.0 CD2 A:TYR236 3.0 16.4 1.0 C57 A:DS4501 3.1 22.3 1.0 O59 A:DS4501 3.1 21.9 1.0 CE2 A:TYR236 3.2 17.0 1.0 OG A:SER237 3.5 20.6 1.0 CE1 A:PHE150 3.5 19.7 1.0 C51 A:DS4501 3.8 20.8 1.0 CZ A:PHE150 3.8 17.2 1.0 C55 A:DS4501 3.8 22.2 1.0 O A:HOH617 3.9 21.1 1.0 O58 A:DS4501 4.0 22.2 1.0 O A:LEU233 4.2 19.8 1.0 CG A:TYR236 4.3 16.8 1.0 C50 A:DS4501 4.3 21.6 1.0 CZ A:TYR236 4.4 19.6 1.0 CD1 A:PHE150 4.6 20.1 1.0 CB A:SER237 4.7 17.4 1.0 N A:SER237 4.7 14.7 1.0 CZ A:PHE153 4.8 19.0 1.0 CA A:SER237 4.8 14.2 1.0 CD1 A:LEU233 4.8 30.3 1.0 CB A:TYR236 4.9 16.6 1.0 CE1 A:PHE153 4.9 21.0 1.0

H.Kashiwagi, Y.Ono, S.Itoh, S.Iijima, F.Ichikawa, S.Harada, S.Takeda, N.Sekiguchi, M.Ishigai, T.Takahashi. Crystal Structure Analysis of Vitamin D Receptor To Be Published.