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Fluorine in PDB 8p9w: Vitamin D Receptor Complex with XE4MECF3 Analog

Enzymatic activity of Vitamin D Receptor Complex with XE4MECF3 Analog

All present enzymatic activity of Vitamin D Receptor Complex with XE4MECF3 Analog:
2.3.1.48;

Protein crystallography data

The structure of Vitamin D Receptor Complex with XE4MECF3 Analog, PDB code: 8p9w was solved by A.Y.Belorusova, N.Rochel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.90 / 2.90
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 65.82, 65.82, 263.22, 90, 90, 120
R / Rfree (%) 17.7 / 23.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Vitamin D Receptor Complex with XE4MECF3 Analog (pdb code 8p9w). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Vitamin D Receptor Complex with XE4MECF3 Analog, PDB code: 8p9w:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8p9w

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Fluorine binding site 1 out of 6 in the Vitamin D Receptor Complex with XE4MECF3 Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Vitamin D Receptor Complex with XE4MECF3 Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:100.7
occ:1.00
 F5 A:XDO4000 0.0 100.7 1.0
C26 A:XDO4000 1.3 102.6 1.0
F4 A:XDO4000 2.1 109.4 1.0
F3 A:XDO4000 2.1 96.7 1.0
C24 A:XDO4000 2.3 101.6 1.0
F1 A:XDO4000 2.5 110.1 1.0
C25 A:XDO4000 2.6 107.0 1.0
F2 A:XDO4000 2.7 93.5 1.0
O2 A:XDO4000 2.9 98.7 1.0
CD2 A:LEU440 3.5 62.0 1.0
C23 A:XDO4000 3.6 92.3 1.0
CG1 A:VAL444 3.7 59.0 1.0
F A:XDO4000 3.9 123.2 1.0
CD1 A:TYR427 4.0 63.9 1.0
CE1 A:TYR427 4.1 63.4 1.0
CD2 A:PHE448 4.5 75.4 1.0
CE2 A:PHE448 4.6 74.3 1.0
C22 A:XDO4000 4.7 89.7 1.0
CG A:LEU440 4.7 61.2 1.0
CD1 A:LEU440 4.7 62.9 1.0
CG2 A:VAL444 4.7 56.8 1.0
CB A:VAL444 4.8 56.9 1.0
CB A:ALA259 4.9 51.3 1.0
CA A:ALA259 4.9 56.2 1.0

Fluorine binding site 2 out of 6 in 8p9w

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Fluorine binding site 2 out of 6 in the Vitamin D Receptor Complex with XE4MECF3 Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Vitamin D Receptor Complex with XE4MECF3 Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:96.7
occ:1.00
 F3 A:XDO4000 0.0 96.7 1.0
C26 A:XDO4000 1.3 102.6 1.0
F5 A:XDO4000 2.1 100.7 1.0
F4 A:XDO4000 2.2 109.4 1.0
C24 A:XDO4000 2.4 101.6 1.0
O2 A:XDO4000 2.6 98.7 1.0
CE2 A:PHE448 3.0 74.3 1.0
CD2 A:PHE448 3.1 75.4 1.0
C23 A:XDO4000 3.1 92.3 1.0
NE2 A:HIS423 3.4 74.2 1.0
CD1 A:TYR427 3.6 63.9 1.0
CE1 A:HIS423 3.7 75.6 1.0
C25 A:XDO4000 3.7 107.0 1.0
C22 A:XDO4000 4.0 89.7 1.0
F1 A:XDO4000 4.0 110.1 1.0
CE1 A:TYR427 4.0 63.4 1.0
F2 A:XDO4000 4.1 93.5 1.0
CZ A:PHE448 4.2 79.8 1.0
CG A:PHE448 4.2 72.6 1.0
CG1 A:VAL444 4.3 59.0 1.0
CG A:TYR427 4.5 67.8 1.0
CG1 A:VAL262 4.6 50.7 1.0
CD2 A:HIS423 4.7 73.8 1.0
F A:XDO4000 4.8 123.2 1.0
CB A:TYR427 4.8 66.2 1.0
ND1 A:HIS423 5.0 75.3 1.0
CG2 A:VAL262 5.0 53.4 1.0
CB A:PHE448 5.0 67.2 1.0

Fluorine binding site 3 out of 6 in 8p9w

Go back to Fluorine Binding Sites List in 8p9w
Fluorine binding site 3 out of 6 in the Vitamin D Receptor Complex with XE4MECF3 Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Vitamin D Receptor Complex with XE4MECF3 Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:109.4
occ:1.00
 F4 A:XDO4000 0.0 109.4 1.0
C26 A:XDO4000 1.3 102.6 1.0
F5 A:XDO4000 2.1 100.7 1.0
F3 A:XDO4000 2.2 96.7 1.0
C24 A:XDO4000 2.4 101.6 1.0
C23 A:XDO4000 2.7 92.3 1.0
F2 A:XDO4000 2.7 93.5 1.0
C25 A:XDO4000 3.1 107.0 1.0
CG2 A:VAL262 3.2 53.4 1.0
CB A:VAL262 3.3 57.4 1.0
C22 A:XDO4000 3.4 89.7 1.0
CG1 A:VAL262 3.5 50.7 1.0
O2 A:XDO4000 3.6 98.7 1.0
F1 A:XDO4000 3.8 110.1 1.0
CE2 A:PHE448 3.9 74.3 1.0
F A:XDO4000 4.2 123.2 1.0
O A:LEU258 4.3 67.7 1.0
CD2 A:PHE448 4.5 75.4 1.0
C21 A:XDO4000 4.5 87.7 1.0
CG1 A:VAL444 4.6 59.0 1.0
CA A:ALA259 4.6 56.2 1.0
CG2 A:VAL444 4.7 56.8 1.0
NE2 A:HIS423 4.8 74.2 1.0
CA A:VAL262 4.8 57.8 1.0
CZ A:PHE448 5.0 79.8 1.0

Fluorine binding site 4 out of 6 in 8p9w

Go back to Fluorine Binding Sites List in 8p9w
Fluorine binding site 4 out of 6 in the Vitamin D Receptor Complex with XE4MECF3 Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Vitamin D Receptor Complex with XE4MECF3 Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:93.5
occ:1.00
 F2 A:XDO4000 0.0 93.5 1.0
C25 A:XDO4000 1.3 107.0 1.0
F1 A:XDO4000 2.1 110.1 1.0
F A:XDO4000 2.1 123.2 1.0
C24 A:XDO4000 2.4 101.6 1.0
F4 A:XDO4000 2.7 109.4 1.0
C26 A:XDO4000 2.7 102.6 1.0
F5 A:XDO4000 2.7 100.7 1.0
C23 A:XDO4000 2.9 92.3 1.0
O2 A:XDO4000 3.5 98.7 1.0
C22 A:XDO4000 3.7 89.7 1.0
CA A:ALA259 3.8 56.2 1.0
N A:ALA259 3.8 59.7 1.0
O A:LEU258 3.9 67.7 1.0
C A:LEU258 3.9 63.3 1.0
CD1 A:LEU255 3.9 59.9 1.0
F3 A:XDO4000 4.1 96.7 1.0
CB A:ALA259 4.1 51.3 1.0
CB A:LEU258 4.3 67.2 1.0
CD2 A:LEU440 4.6 62.0 1.0
CG2 A:VAL262 4.6 53.4 1.0
O A:LEU255 4.7 77.0 1.0
CA A:LEU258 4.7 64.6 1.0
C21 A:XDO4000 4.8 87.7 1.0

Fluorine binding site 5 out of 6 in 8p9w

Go back to Fluorine Binding Sites List in 8p9w
Fluorine binding site 5 out of 6 in the Vitamin D Receptor Complex with XE4MECF3 Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Vitamin D Receptor Complex with XE4MECF3 Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:110.1
occ:1.00
 F1 A:XDO4000 0.0 110.1 1.0
C25 A:XDO4000 1.3 107.0 1.0
F A:XDO4000 2.1 123.2 1.0
F2 A:XDO4000 2.1 93.5 1.0
C24 A:XDO4000 2.3 101.6 1.0
F5 A:XDO4000 2.5 100.7 1.0
O2 A:XDO4000 2.6 98.7 1.0
C26 A:XDO4000 3.0 102.6 1.0
CD1 A:LEU255 3.2 59.9 1.0
CD2 A:LEU440 3.5 62.0 1.0
C23 A:XDO4000 3.6 92.3 1.0
F4 A:XDO4000 3.8 109.4 1.0
F3 A:XDO4000 4.0 96.7 1.0
CD2 A:LEU430 4.2 94.3 1.0
CD1 A:LEU430 4.2 93.9 1.0
O A:ALA331 4.3 95.2 1.0
CG A:LEU255 4.7 67.2 1.0
C22 A:XDO4000 4.7 89.7 1.0
CG A:LEU430 4.8 88.7 1.0
CG A:LEU440 4.8 61.2 1.0
NE2 A:HIS333 4.9 90.8 1.0
CD1 A:TYR427 4.9 63.9 1.0

Fluorine binding site 6 out of 6 in 8p9w

Go back to Fluorine Binding Sites List in 8p9w
Fluorine binding site 6 out of 6 in the Vitamin D Receptor Complex with XE4MECF3 Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Vitamin D Receptor Complex with XE4MECF3 Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:123.2
occ:1.00
 F A:XDO4000 0.0 123.2 1.0
C25 A:XDO4000 1.3 107.0 1.0
F1 A:XDO4000 2.1 110.1 1.0
F2 A:XDO4000 2.1 93.5 1.0
C24 A:XDO4000 2.4 101.6 1.0
C23 A:XDO4000 2.7 92.3 1.0
O2 A:XDO4000 3.0 98.7 1.0
O A:ALA331 3.3 95.2 1.0
C22 A:XDO4000 3.5 89.7 1.0
CD2 A:HIS333 3.7 93.5 1.0
C26 A:XDO4000 3.7 102.6 1.0
NE2 A:HIS333 3.7 90.8 1.0
CD1 A:LEU255 3.9 59.9 1.0
F5 A:XDO4000 3.9 100.7 1.0
CB A:ALA331 4.1 76.8 1.0
F4 A:XDO4000 4.2 109.4 1.0
C A:ALA331 4.3 89.5 1.0
C21 A:XDO4000 4.5 87.7 1.0
CD1 A:LEU430 4.6 93.9 1.0
F3 A:XDO4000 4.8 96.7 1.0
CB A:LEU258 4.8 67.2 1.0
CA A:ALA331 4.9 78.9 1.0
CE1 A:HIS333 4.9 92.4 1.0
CG A:HIS333 4.9 94.1 1.0

Reference:

A.Y.Belorusova, N.Rochel. A Vitamin D-Based Strategy Overcomes Chemoresistant Prostate Cancer To Be Published.
Page generated: Wed Jul 16 06:25:40 2025

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