Fluorine in PDB 3ips: X-Ray Structure of Benzisoxazole Synthetic Agonist Bound to the Lxr- Alpha
Enzymatic activity of X-Ray Structure of Benzisoxazole Synthetic Agonist Bound to the Lxr- Alpha
All present enzymatic activity of X-Ray Structure of Benzisoxazole Synthetic Agonist Bound to the Lxr- Alpha:
2.3.1.48;
Protein crystallography data
The structure of X-Ray Structure of Benzisoxazole Synthetic Agonist Bound to the Lxr- Alpha, PDB code: 3ips
was solved by
X.Fradera,
D.Vu,
O.Nimz,
R.Skene,
D.Hosfield,
R.Wijnands,
A.J.Cooke,
A.Haunso,
A.King,
D.J.Bennet,
R.Mcguire,
J.C.M.Uitdehaag,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.30 /
2.26
|
Space group
|
P 4 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
123.051,
123.051,
91.636,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
25.5 /
31.5
|
Other elements in 3ips:
The structure of X-Ray Structure of Benzisoxazole Synthetic Agonist Bound to the Lxr- Alpha also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the X-Ray Structure of Benzisoxazole Synthetic Agonist Bound to the Lxr- Alpha
(pdb code 3ips). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
X-Ray Structure of Benzisoxazole Synthetic Agonist Bound to the Lxr- Alpha, PDB code: 3ips:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 3ips
Go back to
Fluorine Binding Sites List in 3ips
Fluorine binding site 1 out
of 6 in the X-Ray Structure of Benzisoxazole Synthetic Agonist Bound to the Lxr- Alpha
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of X-Ray Structure of Benzisoxazole Synthetic Agonist Bound to the Lxr- Alpha within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1
b:65.6
occ:1.00
|
F33
|
A:O901
|
0.0
|
65.6
|
1.0
|
C32
|
A:O901
|
1.4
|
63.2
|
1.0
|
F34
|
A:O901
|
2.2
|
66.9
|
1.0
|
F35
|
A:O901
|
2.2
|
65.2
|
1.0
|
C29
|
A:O901
|
2.4
|
62.1
|
1.0
|
N30
|
A:O901
|
2.7
|
61.7
|
1.0
|
CD1
|
A:LEU428
|
3.4
|
59.8
|
1.0
|
CG
|
A:GLN424
|
3.6
|
53.2
|
1.0
|
C24
|
A:O901
|
3.6
|
61.1
|
1.0
|
CG2
|
A:VAL425
|
4.0
|
53.2
|
1.0
|
O31
|
A:O901
|
4.1
|
61.2
|
1.0
|
CD
|
A:GLN424
|
4.3
|
55.1
|
1.0
|
NE2
|
A:HIS421
|
4.3
|
46.3
|
1.0
|
CD2
|
A:LEU435
|
4.4
|
53.5
|
1.0
|
C23
|
A:O901
|
4.5
|
61.1
|
1.0
|
CG
|
A:LEU428
|
4.5
|
59.6
|
1.0
|
C25
|
A:O901
|
4.6
|
61.2
|
1.0
|
OE1
|
A:GLN424
|
4.6
|
56.2
|
1.0
|
CD2
|
A:HIS421
|
4.7
|
46.7
|
1.0
|
CA
|
A:VAL425
|
4.8
|
54.3
|
1.0
|
CD1
|
A:LEU331
|
4.8
|
52.8
|
1.0
|
N
|
A:VAL425
|
4.8
|
53.7
|
1.0
|
CB
|
A:GLN424
|
4.8
|
52.8
|
1.0
|
CZ3
|
A:TRP443
|
4.9
|
41.2
|
1.0
|
CE3
|
A:TRP443
|
4.9
|
41.0
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 3ips
Go back to
Fluorine Binding Sites List in 3ips
Fluorine binding site 2 out
of 6 in the X-Ray Structure of Benzisoxazole Synthetic Agonist Bound to the Lxr- Alpha
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of X-Ray Structure of Benzisoxazole Synthetic Agonist Bound to the Lxr- Alpha within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1
b:66.9
occ:1.00
|
F34
|
A:O901
|
0.0
|
66.9
|
1.0
|
C32
|
A:O901
|
1.4
|
63.2
|
1.0
|
F33
|
A:O901
|
2.2
|
65.6
|
1.0
|
F35
|
A:O901
|
2.2
|
65.2
|
1.0
|
C29
|
A:O901
|
2.3
|
62.1
|
1.0
|
CZ3
|
A:TRP443
|
2.9
|
41.2
|
1.0
|
C24
|
A:O901
|
3.1
|
61.1
|
1.0
|
CE3
|
A:TRP443
|
3.3
|
41.0
|
1.0
|
N30
|
A:O901
|
3.3
|
61.7
|
1.0
|
CD2
|
A:LEU435
|
3.5
|
53.5
|
1.0
|
C25
|
A:O901
|
3.6
|
61.2
|
1.0
|
CH2
|
A:TRP443
|
4.0
|
41.5
|
1.0
|
NE2
|
A:HIS421
|
4.1
|
46.3
|
1.0
|
C23
|
A:O901
|
4.2
|
61.1
|
1.0
|
O31
|
A:O901
|
4.3
|
61.2
|
1.0
|
CD1
|
A:LEU435
|
4.4
|
54.2
|
1.0
|
CD2
|
A:TRP443
|
4.5
|
41.0
|
1.0
|
CG2
|
A:VAL425
|
4.5
|
53.2
|
1.0
|
CG
|
A:LEU435
|
4.5
|
54.4
|
1.0
|
CD1
|
A:LEU428
|
4.7
|
59.8
|
1.0
|
CD1
|
A:LEU439
|
4.8
|
43.0
|
1.0
|
C27
|
A:O901
|
5.0
|
61.3
|
1.0
|
CD2
|
A:HIS421
|
5.0
|
46.7
|
1.0
|
CG2
|
A:THR258
|
5.0
|
50.5
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 3ips
Go back to
Fluorine Binding Sites List in 3ips
Fluorine binding site 3 out
of 6 in the X-Ray Structure of Benzisoxazole Synthetic Agonist Bound to the Lxr- Alpha
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of X-Ray Structure of Benzisoxazole Synthetic Agonist Bound to the Lxr- Alpha within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1
b:65.2
occ:1.00
|
F35
|
A:O901
|
0.0
|
65.2
|
1.0
|
C32
|
A:O901
|
1.4
|
63.2
|
1.0
|
F34
|
A:O901
|
2.2
|
66.9
|
1.0
|
F33
|
A:O901
|
2.2
|
65.6
|
1.0
|
C29
|
A:O901
|
2.4
|
62.1
|
1.0
|
C24
|
A:O901
|
2.9
|
61.1
|
1.0
|
C25
|
A:O901
|
3.1
|
61.2
|
1.0
|
N30
|
A:O901
|
3.5
|
61.7
|
1.0
|
CD2
|
A:LEU435
|
3.8
|
53.5
|
1.0
|
CG2
|
A:THR258
|
3.8
|
50.5
|
1.0
|
CD1
|
A:LEU428
|
3.8
|
59.8
|
1.0
|
C23
|
A:O901
|
4.1
|
61.1
|
1.0
|
CE1
|
A:PHE254
|
4.2
|
63.1
|
1.0
|
CD1
|
A:LEU331
|
4.2
|
52.8
|
1.0
|
C27
|
A:O901
|
4.4
|
61.3
|
1.0
|
O31
|
A:O901
|
4.5
|
61.2
|
1.0
|
CZ
|
A:PHE254
|
4.7
|
63.4
|
1.0
|
CD1
|
A:PHE254
|
5.0
|
63.2
|
1.0
|
CZ3
|
A:TRP443
|
5.0
|
41.2
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 3ips
Go back to
Fluorine Binding Sites List in 3ips
Fluorine binding site 4 out
of 6 in the X-Ray Structure of Benzisoxazole Synthetic Agonist Bound to the Lxr- Alpha
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of X-Ray Structure of Benzisoxazole Synthetic Agonist Bound to the Lxr- Alpha within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F1
b:64.1
occ:1.00
|
F33
|
B:O901
|
0.0
|
64.1
|
1.0
|
C32
|
B:O901
|
1.4
|
63.2
|
1.0
|
F34
|
B:O901
|
2.2
|
64.6
|
1.0
|
F35
|
B:O901
|
2.3
|
63.5
|
1.0
|
C29
|
B:O901
|
2.3
|
62.9
|
1.0
|
N30
|
B:O901
|
2.7
|
62.6
|
1.0
|
CD2
|
B:LEU428
|
3.5
|
51.9
|
1.0
|
C24
|
B:O901
|
3.6
|
62.0
|
1.0
|
CG
|
B:GLN424
|
3.8
|
44.9
|
1.0
|
NE2
|
B:HIS421
|
3.9
|
38.9
|
1.0
|
O31
|
B:O901
|
4.1
|
62.7
|
1.0
|
CG2
|
B:VAL425
|
4.2
|
45.9
|
1.0
|
CD2
|
B:LEU435
|
4.3
|
44.0
|
1.0
|
CD2
|
B:HIS421
|
4.4
|
38.9
|
1.0
|
C23
|
B:O901
|
4.4
|
61.9
|
1.0
|
C25
|
B:O901
|
4.5
|
61.9
|
1.0
|
CZ3
|
B:TRP443
|
4.5
|
38.1
|
1.0
|
CE3
|
B:TRP443
|
4.6
|
37.4
|
1.0
|
CD
|
B:GLN424
|
4.7
|
47.6
|
1.0
|
CE1
|
B:HIS421
|
4.9
|
39.6
|
1.0
|
CG
|
B:LEU428
|
4.9
|
52.0
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 3ips
Go back to
Fluorine Binding Sites List in 3ips
Fluorine binding site 5 out
of 6 in the X-Ray Structure of Benzisoxazole Synthetic Agonist Bound to the Lxr- Alpha
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of X-Ray Structure of Benzisoxazole Synthetic Agonist Bound to the Lxr- Alpha within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F1
b:64.6
occ:1.00
|
F34
|
B:O901
|
0.0
|
64.6
|
1.0
|
C32
|
B:O901
|
1.4
|
63.2
|
1.0
|
F35
|
B:O901
|
2.2
|
63.5
|
1.0
|
F33
|
B:O901
|
2.2
|
64.1
|
1.0
|
C29
|
B:O901
|
2.4
|
62.9
|
1.0
|
C24
|
B:O901
|
2.9
|
62.0
|
1.0
|
C25
|
B:O901
|
3.1
|
61.9
|
1.0
|
CD2
|
B:LEU435
|
3.4
|
44.0
|
1.0
|
N30
|
B:O901
|
3.5
|
62.6
|
1.0
|
CZ3
|
B:TRP443
|
3.6
|
38.1
|
1.0
|
CE3
|
B:TRP443
|
4.1
|
37.4
|
1.0
|
C23
|
B:O901
|
4.1
|
61.9
|
1.0
|
CG2
|
B:THR258
|
4.3
|
36.6
|
1.0
|
C27
|
B:O901
|
4.4
|
62.2
|
1.0
|
O31
|
B:O901
|
4.4
|
62.7
|
1.0
|
CH2
|
B:TRP443
|
4.6
|
38.6
|
1.0
|
CD2
|
B:LEU428
|
4.6
|
51.9
|
1.0
|
CD1
|
B:LEU439
|
4.6
|
34.2
|
1.0
|
CG
|
B:LEU435
|
4.7
|
44.8
|
1.0
|
CD1
|
B:LEU435
|
4.9
|
43.8
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 3ips
Go back to
Fluorine Binding Sites List in 3ips
Fluorine binding site 6 out
of 6 in the X-Ray Structure of Benzisoxazole Synthetic Agonist Bound to the Lxr- Alpha
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of X-Ray Structure of Benzisoxazole Synthetic Agonist Bound to the Lxr- Alpha within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F1
b:63.5
occ:1.00
|
F35
|
B:O901
|
0.0
|
63.5
|
1.0
|
C32
|
B:O901
|
1.4
|
63.2
|
1.0
|
F34
|
B:O901
|
2.2
|
64.6
|
1.0
|
F33
|
B:O901
|
2.3
|
64.1
|
1.0
|
C29
|
B:O901
|
2.4
|
62.9
|
1.0
|
C24
|
B:O901
|
3.0
|
62.0
|
1.0
|
C25
|
B:O901
|
3.3
|
61.9
|
1.0
|
N30
|
B:O901
|
3.4
|
62.6
|
1.0
|
CD1
|
B:LEU331
|
3.5
|
45.2
|
1.0
|
CD2
|
B:LEU428
|
3.9
|
51.9
|
1.0
|
CG
|
B:LEU331
|
4.1
|
44.2
|
1.0
|
CE1
|
B:PHE254
|
4.1
|
46.1
|
1.0
|
C23
|
B:O901
|
4.2
|
61.9
|
1.0
|
O31
|
B:O901
|
4.4
|
62.7
|
1.0
|
CD2
|
B:LEU435
|
4.5
|
44.0
|
1.0
|
C27
|
B:O901
|
4.6
|
62.2
|
1.0
|
CG2
|
B:THR258
|
4.7
|
36.6
|
1.0
|
CD1
|
B:PHE254
|
4.8
|
47.1
|
1.0
|
CD2
|
B:LEU331
|
4.9
|
44.0
|
1.0
|
CZ
|
B:PHE254
|
4.9
|
45.6
|
1.0
|
CG
|
B:GLN424
|
5.0
|
44.9
|
1.0
|
|
Reference:
X.Fradera,
D.Vu,
O.Nimz,
R.Skene,
D.Hosfield,
R.Wynands,
A.J.Cooke,
A.Haunso,
A.King,
D.J.Bennett,
R.Mcguire,
J.C.Uitdehaag.
X-Ray Structures of the Lxralpha Lbd in Its Homodimeric Form and Implications For Heterodimer Signaling. J.Mol.Biol. V. 399 120 2010.
ISSN: ISSN 0022-2836
PubMed: 20382159
DOI: 10.1016/J.JMB.2010.04.005
Page generated: Wed Jul 31 19:33:39 2024
|