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Fluorine in PDB 3dr1: Side-Chain Fluorine Atoms of Non-Steroidal Vitamin D3 Analogs Stabilize Helix 12 of Vitamin D Receptor

Enzymatic activity of Side-Chain Fluorine Atoms of Non-Steroidal Vitamin D3 Analogs Stabilize Helix 12 of Vitamin D Receptor

All present enzymatic activity of Side-Chain Fluorine Atoms of Non-Steroidal Vitamin D3 Analogs Stabilize Helix 12 of Vitamin D Receptor:
2.3.1.48;

Protein crystallography data

The structure of Side-Chain Fluorine Atoms of Non-Steroidal Vitamin D3 Analogs Stabilize Helix 12 of Vitamin D Receptor, PDB code: 3dr1 was solved by Y.Sato, N.Rochel, D.Moras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.70
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 66.100, 66.100, 265.600, 90.00, 90.00, 120.00
R / Rfree (%) 22.6 / 28.6

Other elements in 3dr1:

The structure of Side-Chain Fluorine Atoms of Non-Steroidal Vitamin D3 Analogs Stabilize Helix 12 of Vitamin D Receptor also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Side-Chain Fluorine Atoms of Non-Steroidal Vitamin D3 Analogs Stabilize Helix 12 of Vitamin D Receptor (pdb code 3dr1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Side-Chain Fluorine Atoms of Non-Steroidal Vitamin D3 Analogs Stabilize Helix 12 of Vitamin D Receptor, PDB code: 3dr1:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3dr1

Go back to Fluorine Binding Sites List in 3dr1
Fluorine binding site 1 out of 6 in the Side-Chain Fluorine Atoms of Non-Steroidal Vitamin D3 Analogs Stabilize Helix 12 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 Side-Chain Fluorine Atoms of Non-Steroidal Vitamin D3 Analogs Stabilize Helix 12 of Vitamin D Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F500

b:45.7
occ:1.00
 F11 A:C5D500 0.0 45.7 1.0
C27 A:C5D500 1.3 44.5 1.0
F19 A:C5D500 2.2 44.8 1.0
F21 A:C5D500 2.2 44.7 1.0
C25 A:C5D500 2.4 44.1 1.0
F28 A:C5D500 2.7 41.3 1.0
O3 A:C5D500 2.8 45.8 1.0
C26 A:C5D500 3.0 43.5 1.0
CE1 A:TYR427 3.3 31.5 1.0
CD1 A:TYR427 3.4 33.8 1.0
CG1 A:VAL444 3.5 28.2 1.0
F29 A:C5D500 3.5 46.7 1.0
C24 A:C5D500 3.6 43.0 1.0
CD1 A:PHE448 4.1 36.3 1.0
F30 A:C5D500 4.2 40.8 1.0
CE1 A:PHE448 4.2 37.6 1.0
CD2 A:LEU440 4.3 24.9 1.0
CZ A:TYR427 4.5 31.6 1.0
NE2 A:HIS423 4.5 37.0 1.0
CG A:TYR427 4.7 35.1 1.0
C23 A:C5D500 4.8 40.9 1.0
CB A:VAL444 4.8 30.1 1.0
CG1 A:VAL262 4.8 24.5 1.0
CG2 A:VAL444 4.8 27.0 1.0
CE1 A:HIS423 4.9 38.6 1.0
OH A:TYR427 5.0 33.5 1.0

Fluorine binding site 2 out of 6 in 3dr1

Go back to Fluorine Binding Sites List in 3dr1
Fluorine binding site 2 out of 6 in the Side-Chain Fluorine Atoms of Non-Steroidal Vitamin D3 Analogs Stabilize Helix 12 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 Side-Chain Fluorine Atoms of Non-Steroidal Vitamin D3 Analogs Stabilize Helix 12 of Vitamin D Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F500

b:44.8
occ:1.00
 F19 A:C5D500 0.0 44.8 1.0
C27 A:C5D500 1.3 44.5 1.0
F11 A:C5D500 2.2 45.7 1.0
F21 A:C5D500 2.2 44.7 1.0
C25 A:C5D500 2.4 44.1 1.0
O3 A:C5D500 2.8 45.8 1.0
C24 A:C5D500 2.8 43.0 1.0
NE2 A:HIS423 3.1 37.0 1.0
CE1 A:PHE448 3.5 37.6 1.0
C23 A:C5D500 3.6 40.9 1.0
CE1 A:HIS423 3.6 38.6 1.0
CG1 A:VAL262 3.7 24.5 1.0
C26 A:C5D500 3.8 43.5 1.0
CD1 A:PHE448 4.0 36.3 1.0
CZ A:PHE448 4.1 38.4 1.0
CG2 A:VAL262 4.2 23.4 1.0
F28 A:C5D500 4.2 41.3 1.0
F29 A:C5D500 4.2 46.7 1.0
CD2 A:HIS423 4.3 38.3 1.0
CB A:VAL262 4.4 28.2 1.0
CD1 A:TYR427 4.4 33.8 1.0
F30 A:C5D500 4.7 40.8 1.0
CE1 A:TYR427 4.8 31.5 1.0
C22 A:C5D500 4.8 39.7 1.0
ND1 A:HIS423 4.9 39.9 1.0
CG1 A:VAL444 4.9 28.2 1.0
CG A:PHE448 4.9 35.1 1.0
CE2 A:PHE448 5.0 37.9 1.0

Fluorine binding site 3 out of 6 in 3dr1

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Fluorine binding site 3 out of 6 in the Side-Chain Fluorine Atoms of Non-Steroidal Vitamin D3 Analogs Stabilize Helix 12 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 Side-Chain Fluorine Atoms of Non-Steroidal Vitamin D3 Analogs Stabilize Helix 12 of Vitamin D Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F500

b:44.7
occ:1.00
 F21 A:C5D500 0.0 44.7 1.0
C27 A:C5D500 1.3 44.5 1.0
F19 A:C5D500 2.2 44.8 1.0
F11 A:C5D500 2.2 45.7 1.0
C25 A:C5D500 2.4 44.1 1.0
F29 A:C5D500 2.7 46.7 1.0
C24 A:C5D500 2.9 43.0 1.0
C26 A:C5D500 3.0 43.5 1.0
CG2 A:VAL262 3.2 23.4 1.0
CB A:VAL262 3.2 28.2 1.0
CG1 A:VAL262 3.3 24.5 1.0
F28 A:C5D500 3.4 41.3 1.0
O3 A:C5D500 3.6 45.8 1.0
C23 A:C5D500 3.7 40.9 1.0
CA A:ALA259 4.2 30.6 1.0
F30 A:C5D500 4.2 40.8 1.0
O A:LEU258 4.4 31.1 1.0
CG1 A:VAL444 4.4 28.2 1.0
CG2 A:VAL444 4.5 27.0 1.0
CE1 A:PHE448 4.6 37.6 1.0
O A:ALA259 4.7 32.8 1.0
CA A:VAL262 4.8 28.2 1.0
N A:ALA259 4.8 29.4 1.0
C A:LEU258 4.8 30.0 1.0
C22 A:C5D500 4.9 39.7 1.0
C A:ALA259 4.9 31.5 1.0
CB A:ALA259 5.0 28.6 1.0

Fluorine binding site 4 out of 6 in 3dr1

Go back to Fluorine Binding Sites List in 3dr1
Fluorine binding site 4 out of 6 in the Side-Chain Fluorine Atoms of Non-Steroidal Vitamin D3 Analogs Stabilize Helix 12 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 Side-Chain Fluorine Atoms of Non-Steroidal Vitamin D3 Analogs Stabilize Helix 12 of Vitamin D Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F500

b:41.3
occ:1.00
 F28 A:C5D500 0.0 41.3 1.0
C26 A:C5D500 1.3 43.5 1.0
F30 A:C5D500 2.2 40.8 1.0
F29 A:C5D500 2.2 46.7 1.0
C25 A:C5D500 2.4 44.1 1.0
F11 A:C5D500 2.7 45.7 1.0
O3 A:C5D500 2.9 45.8 1.0
C27 A:C5D500 3.0 44.5 1.0
CD2 A:LEU440 3.3 24.9 1.0
CD2 A:LEU430 3.4 51.2 1.0
F21 A:C5D500 3.4 44.7 1.0
CD1 A:LEU255 3.5 34.1 1.0
C24 A:C5D500 3.6 43.0 1.0
F19 A:C5D500 4.2 44.8 1.0
CE1 A:TYR427 4.5 31.5 1.0
CD1 A:TYR427 4.5 33.8 1.0
CG A:LEU440 4.6 27.0 1.0
CG A:LEU430 4.6 51.7 1.0
C23 A:C5D500 4.7 40.9 1.0
O A:ALA331 4.8 47.9 1.0
CD1 A:LEU440 4.9 27.3 1.0
CG A:LEU255 4.9 34.4 1.0
NE2 A:HIS333 4.9 45.7 1.0

Fluorine binding site 5 out of 6 in 3dr1

Go back to Fluorine Binding Sites List in 3dr1
Fluorine binding site 5 out of 6 in the Side-Chain Fluorine Atoms of Non-Steroidal Vitamin D3 Analogs Stabilize Helix 12 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 Side-Chain Fluorine Atoms of Non-Steroidal Vitamin D3 Analogs Stabilize Helix 12 of Vitamin D Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F500

b:46.7
occ:1.00
 F29 A:C5D500 0.0 46.7 1.0
C26 A:C5D500 1.3 43.5 1.0
F30 A:C5D500 2.2 40.8 1.0
F28 A:C5D500 2.2 41.3 1.0
C25 A:C5D500 2.4 44.1 1.0
F21 A:C5D500 2.7 44.7 1.0
C24 A:C5D500 2.8 43.0 1.0
C27 A:C5D500 3.0 44.5 1.0
F11 A:C5D500 3.5 45.7 1.0
CD1 A:LEU255 3.6 34.1 1.0
C23 A:C5D500 3.6 40.9 1.0
O3 A:C5D500 3.6 45.8 1.0
CA A:ALA259 3.7 30.6 1.0
N A:ALA259 3.8 29.4 1.0
C A:LEU258 4.1 30.0 1.0
CB A:ALA259 4.1 28.6 1.0
F19 A:C5D500 4.2 44.8 1.0
O A:LEU258 4.3 31.1 1.0
O A:LEU255 4.4 35.5 1.0
CB A:LEU258 4.4 28.0 1.0
CD2 A:LEU440 4.5 24.9 1.0
CG2 A:VAL262 4.8 23.4 1.0
C22 A:C5D500 4.8 39.7 1.0
CA A:LEU258 4.9 30.0 1.0
O A:ALA331 4.9 47.9 1.0
CG A:LEU255 5.0 34.4 1.0

Fluorine binding site 6 out of 6 in 3dr1

Go back to Fluorine Binding Sites List in 3dr1
Fluorine binding site 6 out of 6 in the Side-Chain Fluorine Atoms of Non-Steroidal Vitamin D3 Analogs Stabilize Helix 12 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 Side-Chain Fluorine Atoms of Non-Steroidal Vitamin D3 Analogs Stabilize Helix 12 of Vitamin D Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F500

b:40.8
occ:1.00
 F30 A:C5D500 0.0 40.8 1.0
C26 A:C5D500 1.3 43.5 1.0
F28 A:C5D500 2.2 41.3 1.0
F29 A:C5D500 2.2 46.7 1.0
C25 A:C5D500 2.4 44.1 1.0
C24 A:C5D500 2.8 43.0 1.0
O3 A:C5D500 2.8 45.8 1.0
O A:ALA331 3.2 47.9 1.0
C23 A:C5D500 3.5 40.9 1.0
CD1 A:LEU255 3.6 34.1 1.0
CD2 A:LEU430 3.6 51.2 1.0
NE2 A:HIS333 3.7 45.7 1.0
CD2 A:HIS333 3.7 47.1 1.0
C27 A:C5D500 3.8 44.5 1.0
F11 A:C5D500 4.2 45.7 1.0
F21 A:C5D500 4.2 44.7 1.0
CB A:ALA331 4.2 48.1 1.0
C A:ALA331 4.3 48.2 1.0
C22 A:C5D500 4.7 39.7 1.0
F19 A:C5D500 4.7 44.8 1.0
CA A:ALA331 4.8 48.1 1.0
CE1 A:HIS333 4.9 46.5 1.0
CG A:HIS333 4.9 47.5 1.0

Reference:

G.Eelen, N.Valle, Y.Sato, N.Rochel, L.Verlinden, P.De Clercq, D.Moras, R.Bouillon, A.Munoz, A.Verstuyf. Superagonistic Fluorinated Vitamin D3 Analogs Stabilize Helix 12 of the Vitamin D Receptor. Chem.Biol. V. 15 1029 2008.
ISSN: ISSN 1074-5521
PubMed: 18940664
DOI: 10.1016/J.CHEMBIOL.2008.08.008
Page generated: Mon Jul 14 15:57:43 2025

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