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
Go back to
Fluorine Binding Sites List in 8p9w
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
Go back to
Fluorine Binding Sites List in 8p9w
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: Fri Aug 2 21:50:35 2024
|