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Fluorine in PDB 3w0c: Crystal Structure Analysis of Vitamin D Receptor

Protein crystallography data

The structure of Crystal Structure Analysis of Vitamin D Receptor, PDB code: 3w0c 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) 21.19 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 44.370, 51.917, 132.087, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 23.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure Analysis of Vitamin D Receptor (pdb code 3w0c). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure Analysis of Vitamin D Receptor, PDB code: 3w0c:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3w0c

Go back to Fluorine Binding Sites List in 3w0c
Fluorine binding site 1 out of 6 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:23.2
occ:1.00
 F2 A:6DS501 0.0 23.2 1.0
C8 A:6DS501 1.4 23.2 1.0
F1 A:6DS501 2.2 22.6 1.0
F3 A:6DS501 2.2 25.1 1.0
C44 A:6DS501 2.4 21.6 1.0
O47 A:6DS501 2.7 19.8 1.0
C43 A:6DS501 2.9 21.1 1.0
NE2 A:HIS397 3.1 16.5 1.0
CE1 A:HIS397 3.4 16.1 1.0
C7 A:6DS501 3.4 20.6 1.0
CE1 A:PHE422 3.4 19.4 1.0
CG1 A:VAL234 3.6 14.9 1.0
CD1 A:ILE268 3.7 19.5 1.0
C48 A:6DS501 3.8 22.9 1.0
CD1 A:PHE422 3.9 18.6 1.0
CZ A:PHE422 3.9 20.0 1.0
F6 A:6DS501 4.1 23.3 1.0
CG2 A:VAL234 4.1 14.2 1.0
F4 A:6DS501 4.2 23.2 1.0
CB A:VAL234 4.2 14.8 1.0
CD2 A:HIS397 4.3 16.4 1.0
C28 A:6DS501 4.4 18.6 1.0
ND1 A:HIS397 4.6 16.9 1.0
CG A:PHE422 4.6 16.9 1.0
CE2 A:PHE422 4.7 21.6 1.0
F5 A:6DS501 4.7 23.8 1.0
CG1 A:VAL418 4.9 17.3 1.0
CG1 A:ILE268 4.9 18.6 1.0

Fluorine binding site 2 out of 6 in 3w0c

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Fluorine binding site 2 out of 6 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:22.6
occ:1.00
 F1 A:6DS501 0.0 22.6 1.0
C8 A:6DS501 1.4 23.2 1.0
F2 A:6DS501 2.2 23.2 1.0
F3 A:6DS501 2.3 25.1 1.0
C44 A:6DS501 2.4 21.6 1.0
F6 A:6DS501 2.6 23.3 1.0
C43 A:6DS501 2.9 21.1 1.0
C48 A:6DS501 2.9 22.9 1.0
F4 A:6DS501 3.4 23.2 1.0
CG1 A:VAL234 3.5 14.9 1.0
CB A:VAL234 3.5 14.8 1.0
O47 A:6DS501 3.5 19.8 1.0
CG1 A:VAL418 3.8 17.3 1.0
CG2 A:VAL234 3.9 14.2 1.0
CG2 A:VAL418 4.0 16.7 1.0
C7 A:6DS501 4.0 20.6 1.0
CA A:ALA231 4.0 12.1 1.0
F5 A:6DS501 4.2 23.8 1.0
CE1 A:PHE422 4.5 19.4 1.0
O A:LEU230 4.5 15.8 1.0
CB A:VAL418 4.5 17.0 1.0
O A:ALA231 4.6 13.2 1.0
CB A:ALA231 4.6 13.2 1.0
CD1 A:PHE422 4.7 18.6 1.0
N A:ALA231 4.8 11.1 1.0
C A:ALA231 4.9 14.9 1.0
CA A:VAL234 4.9 11.7 1.0
C A:LEU230 5.0 15.8 1.0
C28 A:6DS501 5.0 18.6 1.0

Fluorine binding site 3 out of 6 in 3w0c

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Fluorine binding site 3 out of 6 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:25.1
occ:1.00
 F3 A:6DS501 0.0 25.1 1.0
C8 A:6DS501 1.4 23.2 1.0
F2 A:6DS501 2.2 23.2 1.0
F1 A:6DS501 2.3 22.6 1.0
C44 A:6DS501 2.4 21.6 1.0
F4 A:6DS501 2.6 23.2 1.0
O47 A:6DS501 2.6 19.8 1.0
C48 A:6DS501 2.9 22.9 1.0
CD1 A:TYR401 3.4 16.0 1.0
CG1 A:VAL418 3.4 17.3 1.0
F6 A:6DS501 3.4 23.3 1.0
CE1 A:TYR401 3.6 17.9 1.0
CD1 A:PHE422 3.7 18.6 1.0
C43 A:6DS501 3.7 21.1 1.0
CE1 A:PHE422 4.0 19.4 1.0
NE2 A:HIS397 4.0 16.5 1.0
F5 A:6DS501 4.1 23.8 1.0
CE1 A:HIS397 4.2 16.1 1.0
CG A:PHE422 4.3 16.9 1.0
CG A:TYR401 4.6 14.7 1.0
C7 A:6DS501 4.6 20.6 1.0
CB A:VAL418 4.7 17.0 1.0
CB A:PHE422 4.8 16.2 1.0
CZ A:TYR401 4.8 22.1 1.0
CG2 A:VAL418 4.9 16.7 1.0
CD2 A:LEU414 4.9 19.2 1.0
CZ A:PHE422 5.0 20.0 1.0

Fluorine binding site 4 out of 6 in 3w0c

Go back to Fluorine Binding Sites List in 3w0c
Fluorine binding site 4 out of 6 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:23.3
occ:1.00
 F6 A:6DS501 0.0 23.3 1.0
C48 A:6DS501 1.4 22.9 1.0
F4 A:6DS501 2.2 23.2 1.0
F5 A:6DS501 2.3 23.8 1.0
C44 A:6DS501 2.4 21.6 1.0
F1 A:6DS501 2.6 22.6 1.0
C43 A:6DS501 2.7 21.1 1.0
C8 A:6DS501 2.9 23.2 1.0
CD1 A:LEU227 3.3 17.0 1.0
F3 A:6DS501 3.4 25.1 1.0
CA A:ALA231 3.5 12.1 1.0
O47 A:6DS501 3.6 19.8 1.0
N A:ALA231 3.6 11.1 1.0
CB A:ALA231 3.7 13.2 1.0
C7 A:6DS501 4.0 20.6 1.0
C A:LEU230 4.0 15.8 1.0
F2 A:6DS501 4.1 23.2 1.0
CD2 A:LEU414 4.2 19.2 1.0
O A:LEU230 4.3 15.8 1.0
O A:LEU227 4.5 12.7 1.0
CG A:LEU227 4.6 17.8 1.0
CB A:LEU230 4.6 14.1 1.0
C A:ALA231 4.9 14.9 1.0
CA A:LEU230 5.0 13.8 1.0
C29 A:6DS501 5.0 17.4 1.0
NE2 A:HIS305 5.0 24.0 1.0
C28 A:6DS501 5.0 18.6 1.0

Fluorine binding site 5 out of 6 in 3w0c

Go back to Fluorine Binding Sites List in 3w0c
Fluorine binding site 5 out of 6 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:23.8
occ:1.00
 F5 A:6DS501 0.0 23.8 1.0
C48 A:6DS501 1.4 22.9 1.0
F4 A:6DS501 2.2 23.2 1.0
F6 A:6DS501 2.3 23.3 1.0
C44 A:6DS501 2.3 21.6 1.0
O47 A:6DS501 2.8 19.8 1.0
C43 A:6DS501 2.8 21.1 1.0
NE2 A:HIS305 2.9 24.0 1.0
CD1 A:LEU227 3.2 17.0 1.0
CD2 A:HIS305 3.4 23.9 1.0
C7 A:6DS501 3.5 20.6 1.0
C8 A:6DS501 3.7 23.2 1.0
CD2 A:LEU404 3.8 28.0 1.0
O A:ALA303 4.0 21.8 1.0
CB A:ALA303 4.1 17.5 1.0
F3 A:6DS501 4.1 25.1 1.0
CE1 A:HIS305 4.2 23.9 1.0
F1 A:6DS501 4.2 22.6 1.0
CG A:HIS305 4.7 22.5 1.0
C28 A:6DS501 4.7 18.6 1.0
CG A:LEU227 4.7 17.8 1.0
F2 A:6DS501 4.7 23.2 1.0
C A:ALA303 4.8 21.0 1.0

Fluorine binding site 6 out of 6 in 3w0c

Go back to Fluorine Binding Sites List in 3w0c
Fluorine binding site 6 out of 6 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:23.2
occ:1.00
 F4 A:6DS501 0.0 23.2 1.0
C48 A:6DS501 1.4 22.9 1.0
F6 A:6DS501 2.2 23.3 1.0
F5 A:6DS501 2.2 23.8 1.0
C44 A:6DS501 2.4 21.6 1.0
F3 A:6DS501 2.6 25.1 1.0
O47 A:6DS501 2.8 19.8 1.0
C8 A:6DS501 2.9 23.2 1.0
F1 A:6DS501 3.4 22.6 1.0
CD2 A:LEU404 3.4 28.0 1.0
CD1 A:LEU227 3.5 17.0 1.0
CD2 A:LEU414 3.5 19.2 1.0
C43 A:6DS501 3.7 21.1 1.0
CD1 A:TYR401 4.1 16.0 1.0
F2 A:6DS501 4.2 23.2 1.0
CE1 A:TYR401 4.2 17.9 1.0
NE2 A:HIS305 4.3 24.0 1.0
CG1 A:VAL418 4.7 17.3 1.0
CG A:LEU227 4.7 17.8 1.0
C7 A:6DS501 4.7 20.6 1.0
CG A:LEU404 4.8 27.6 1.0
CG A:LEU414 4.9 21.3 1.0

Reference:

H.Kashiwagi, M.Ohta, Y.Ono, S.Itoh, S.Iijima, H.Sato, T.Takahashi. Structure Analysis of Vitamin D Receptor To Be Published.
Page generated: Mon Jul 14 19:58:31 2025

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