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Fluorine in PDB 3w0a: Crystal Structure Analysis of Vitamin D Receptor

Protein crystallography data

The structure of Crystal Structure Analysis of Vitamin D Receptor, PDB code: 3w0a 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) 11.10 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 44.619, 51.803, 132.513, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 23.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure Analysis of Vitamin D Receptor (pdb code 3w0a). 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: 3w0a:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3w0a

Go back to Fluorine Binding Sites List in 3w0a
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:23.5
occ:1.00
 F1 A:DS5501 0.0 23.5 1.0
C16 A:DS5501 1.3 25.6 1.0
F2 A:DS5501 2.1 24.6 1.0
F3 A:DS5501 2.2 25.7 1.0
C15 A:DS5501 2.4 23.7 1.0
C14 A:DS5501 2.8 23.7 1.0
O1 A:DS5501 2.9 21.8 1.0
CD1 A:LEU227 3.1 20.1 1.0
NE2 A:HIS305 3.4 29.8 1.0
C13 A:DS5501 3.6 22.2 1.0
CD2 A:HIS305 3.7 29.7 1.0
C17 A:DS5501 3.7 26.5 1.0
CD2 A:LEU404 3.8 31.7 1.0
O A:ALA303 4.0 27.9 1.0
F5 A:DS5501 4.1 25.4 1.0
F4 A:DS5501 4.2 30.2 1.0
CB A:ALA303 4.2 22.0 1.0
CE1 A:HIS305 4.6 29.8 1.0
CG A:LEU227 4.6 19.3 1.0
C12 A:DS5501 4.7 17.4 1.0
F6 A:DS5501 4.8 25.4 1.0
C A:ALA303 4.8 26.1 1.0
CG A:HIS305 5.0 28.0 1.0

Fluorine binding site 2 out of 6 in 3w0a

Go back to Fluorine Binding Sites List in 3w0a
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:24.6
occ:1.00
 F2 A:DS5501 0.0 24.6 1.0
C16 A:DS5501 1.3 25.6 1.0
F1 A:DS5501 2.1 23.5 1.0
F3 A:DS5501 2.2 25.7 1.0
C15 A:DS5501 2.4 23.7 1.0
F5 A:DS5501 2.5 25.4 1.0
C17 A:DS5501 2.9 26.5 1.0
C14 A:DS5501 2.9 23.7 1.0
CD1 A:LEU227 3.3 20.1 1.0
F4 A:DS5501 3.4 30.2 1.0
CA A:ALA231 3.6 14.1 1.0
O1 A:DS5501 3.6 21.8 1.0
N A:ALA231 3.7 13.6 1.0
C13 A:DS5501 3.7 22.2 1.0
CB A:ALA231 3.8 14.6 1.0
C A:LEU230 4.1 16.9 1.0
F6 A:DS5501 4.1 25.4 1.0
CD2 A:LEU414 4.2 21.1 1.0
O A:LEU230 4.3 14.9 1.0
O A:LEU227 4.6 15.1 1.0
CB A:LEU230 4.7 15.0 1.0
CG A:LEU227 4.7 19.3 1.0
C12 A:DS5501 4.9 17.4 1.0
C A:ALA231 5.0 16.3 1.0
CA A:LEU230 5.0 15.1 1.0

Fluorine binding site 3 out of 6 in 3w0a

Go back to Fluorine Binding Sites List in 3w0a
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:25.7
occ:1.00
 F3 A:DS5501 0.0 25.7 1.0
C16 A:DS5501 1.3 25.6 1.0
F1 A:DS5501 2.2 23.5 1.0
F2 A:DS5501 2.2 24.6 1.0
C15 A:DS5501 2.4 23.7 1.0
F4 A:DS5501 2.7 30.2 1.0
O1 A:DS5501 2.8 21.8 1.0
C17 A:DS5501 3.0 26.5 1.0
CD2 A:LEU404 3.4 31.7 1.0
F5 A:DS5501 3.4 25.4 1.0
CD1 A:LEU227 3.4 20.1 1.0
CD2 A:LEU414 3.4 21.1 1.0
C14 A:DS5501 3.6 23.7 1.0
CD1 A:TYR401 4.0 19.2 1.0
CE1 A:TYR401 4.1 20.8 1.0
F6 A:DS5501 4.2 25.4 1.0
NE2 A:HIS305 4.5 29.8 1.0
C13 A:DS5501 4.7 22.2 1.0
CG1 A:VAL418 4.7 17.9 1.0
CG A:LEU227 4.7 19.3 1.0
CG A:LEU404 4.8 29.7 1.0
CG A:LEU414 4.8 22.6 1.0

Fluorine binding site 4 out of 6 in 3w0a

Go back to Fluorine Binding Sites List in 3w0a
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:30.2
occ:1.00
 F4 A:DS5501 0.0 30.2 1.0
C17 A:DS5501 1.3 26.5 1.0
F5 A:DS5501 2.2 25.4 1.0
F6 A:DS5501 2.2 25.4 1.0
C15 A:DS5501 2.4 23.7 1.0
F3 A:DS5501 2.7 25.7 1.0
O1 A:DS5501 2.7 21.8 1.0
C16 A:DS5501 2.9 25.6 1.0
F2 A:DS5501 3.4 24.6 1.0
CG1 A:VAL418 3.4 17.9 1.0
CD1 A:TYR401 3.5 19.2 1.0
C14 A:DS5501 3.6 23.7 1.0
CE1 A:TYR401 3.6 20.8 1.0
CD1 A:PHE422 3.6 21.1 1.0
CE1 A:PHE422 3.9 21.6 1.0
NE2 A:HIS397 4.1 20.1 1.0
F1 A:DS5501 4.2 23.5 1.0
CE1 A:HIS397 4.3 19.9 1.0
CG A:PHE422 4.3 19.6 1.0
CB A:VAL418 4.6 18.8 1.0
CG2 A:VAL418 4.6 17.9 1.0
C13 A:DS5501 4.7 22.2 1.0
CG A:TYR401 4.7 17.6 1.0
CZ A:PHE422 4.7 21.4 1.0
CB A:PHE422 4.8 18.2 1.0
CD2 A:LEU414 4.8 21.1 1.0
CZ A:TYR401 4.9 24.8 1.0
CG1 A:VAL234 4.9 17.5 1.0

Fluorine binding site 5 out of 6 in 3w0a

Go back to Fluorine Binding Sites List in 3w0a
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:25.4
occ:1.00
 F5 A:DS5501 0.0 25.4 1.0
C17 A:DS5501 1.3 26.5 1.0
F4 A:DS5501 2.2 30.2 1.0
F6 A:DS5501 2.2 25.4 1.0
C15 A:DS5501 2.4 23.7 1.0
F2 A:DS5501 2.5 24.6 1.0
C16 A:DS5501 2.9 25.6 1.0
C14 A:DS5501 2.9 23.7 1.0
F3 A:DS5501 3.4 25.7 1.0
CG1 A:VAL234 3.4 17.5 1.0
CB A:VAL234 3.5 17.3 1.0
O1 A:DS5501 3.6 21.8 1.0
C13 A:DS5501 3.7 22.2 1.0
CG2 A:VAL234 3.7 17.7 1.0
CG1 A:VAL418 4.0 17.9 1.0
CG2 A:VAL418 4.0 17.9 1.0
F1 A:DS5501 4.1 23.5 1.0
CA A:ALA231 4.1 14.1 1.0
O A:LEU230 4.4 14.9 1.0
CE1 A:PHE422 4.5 21.6 1.0
CB A:VAL418 4.7 18.8 1.0
CB A:ALA231 4.7 14.6 1.0
O A:ALA231 4.8 15.2 1.0
CD1 A:PHE422 4.8 21.1 1.0
N A:ALA231 4.8 13.6 1.0
C12 A:DS5501 4.8 17.4 1.0
C A:LEU230 4.9 16.9 1.0
CA A:VAL234 4.9 14.6 1.0
C A:ALA231 5.0 16.3 1.0

Fluorine binding site 6 out of 6 in 3w0a

Go back to Fluorine Binding Sites List in 3w0a
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:25.4
occ:1.00
 F6 A:DS5501 0.0 25.4 1.0
C17 A:DS5501 1.3 26.5 1.0
F5 A:DS5501 2.2 25.4 1.0
F4 A:DS5501 2.2 30.2 1.0
C15 A:DS5501 2.4 23.7 1.0
C14 A:DS5501 2.8 23.7 1.0
O1 A:DS5501 2.9 21.8 1.0
NE2 A:HIS397 3.1 20.1 1.0
CE1 A:PHE422 3.4 21.6 1.0
C13 A:DS5501 3.5 22.2 1.0
CE1 A:HIS397 3.5 19.9 1.0
CG1 A:VAL234 3.6 17.5 1.0
C16 A:DS5501 3.8 25.6 1.0
CZ A:PHE422 3.8 21.4 1.0
CD1 A:PHE422 3.9 21.1 1.0
CD1 A:ILE268 3.9 19.6 1.0
CG2 A:VAL234 4.1 17.7 1.0
F2 A:DS5501 4.1 24.6 1.0
CB A:VAL234 4.2 17.3 1.0
F3 A:DS5501 4.2 25.7 1.0
CD2 A:HIS397 4.3 19.9 1.0
CE2 A:PHE422 4.6 24.4 1.0
C12 A:DS5501 4.6 17.4 1.0
CG A:PHE422 4.7 19.6 1.0
ND1 A:HIS397 4.7 20.7 1.0
F1 A:DS5501 4.8 23.5 1.0
CG1 A:ILE268 4.9 20.3 1.0
CD2 A:PHE422 5.0 22.2 1.0
CG1 A:VAL418 5.0 17.9 1.0

Reference:

H.Kashiwagi, M.Ohta, Y.Ono, S.Itoh, S.Iijima, H.Sato, T.Takahashi. Structure Analysis of Vitamin D3 Receptor To Be Published.
Page generated: Wed Jul 31 23:25:01 2024

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