Fluorine in PDB 8fhx: Structure of Lettuce Aptamer Bound to Dfhbi-1T
Protein crystallography data
The structure of Structure of Lettuce Aptamer Bound to Dfhbi-1T, PDB code: 8fhx
was solved by
L.F.M.Passalacqua,
A.R.Ferre-D'amare,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
41.61 /
2.50
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
25.015,
44.417,
118.921,
90,
90,
90
|
R / Rfree (%)
|
22.5 /
26.8
|
Other elements in 8fhx:
The structure of Structure of Lettuce Aptamer Bound to Dfhbi-1T also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Structure of Lettuce Aptamer Bound to Dfhbi-1T
(pdb code 8fhx). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the
Structure of Lettuce Aptamer Bound to Dfhbi-1T, PDB code: 8fhx:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
Fluorine binding site 1 out
of 5 in 8fhx
Go back to
Fluorine Binding Sites List in 8fhx
Fluorine binding site 1 out
of 5 in the Structure of Lettuce Aptamer Bound to Dfhbi-1T
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Structure of Lettuce Aptamer Bound to Dfhbi-1T within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F107
b:42.3
occ:1.00
|
F8
|
A:2ZY107
|
0.0
|
42.3
|
1.0
|
C6
|
A:2ZY107
|
1.4
|
40.9
|
1.0
|
C1
|
A:2ZY107
|
2.4
|
40.4
|
1.0
|
C5
|
A:2ZY107
|
2.4
|
36.4
|
1.0
|
O9
|
A:2ZY107
|
2.8
|
33.9
|
1.0
|
N6
|
A:DA11
|
3.0
|
34.3
|
1.0
|
N3
|
A:DC17
|
3.1
|
40.0
|
1.0
|
C4
|
A:DC17
|
3.2
|
38.2
|
1.0
|
C2
|
A:DC17
|
3.3
|
47.4
|
1.0
|
N1
|
A:DG18
|
3.4
|
35.9
|
1.0
|
C5
|
A:DC17
|
3.4
|
39.2
|
1.0
|
N1
|
A:DC17
|
3.6
|
46.9
|
1.0
|
C2
|
A:DG18
|
3.6
|
38.5
|
1.0
|
C6
|
A:DC17
|
3.6
|
41.8
|
1.0
|
C2
|
A:2ZY107
|
3.6
|
40.1
|
1.0
|
C4
|
A:2ZY107
|
3.6
|
40.7
|
1.0
|
N4
|
A:DC17
|
3.8
|
37.6
|
1.0
|
C6
|
A:DG18
|
3.8
|
34.0
|
1.0
|
N2
|
A:DG18
|
3.9
|
38.0
|
1.0
|
O2
|
A:DC17
|
4.0
|
55.9
|
1.0
|
N3
|
A:DG18
|
4.1
|
38.7
|
1.0
|
C3
|
A:2ZY107
|
4.1
|
39.9
|
1.0
|
C5
|
A:DG18
|
4.2
|
34.2
|
1.0
|
C2'
|
A:DC17
|
4.2
|
51.4
|
1.0
|
O6
|
A:DG18
|
4.3
|
34.9
|
1.0
|
C4
|
A:DG18
|
4.3
|
35.3
|
1.0
|
C6
|
A:DA11
|
4.3
|
33.9
|
1.0
|
C1'
|
A:DC17
|
4.5
|
50.1
|
1.0
|
F7
|
A:2ZY107
|
4.8
|
34.6
|
1.0
|
N7
|
A:DG10
|
4.8
|
34.6
|
1.0
|
K
|
A:K102
|
4.9
|
38.0
|
1.0
|
C10
|
A:2ZY107
|
4.9
|
47.7
|
1.0
|
O6
|
A:DG10
|
4.9
|
32.2
|
1.0
|
|
Fluorine binding site 2 out
of 5 in 8fhx
Go back to
Fluorine Binding Sites List in 8fhx
Fluorine binding site 2 out
of 5 in the Structure of Lettuce Aptamer Bound to Dfhbi-1T
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Structure of Lettuce Aptamer Bound to Dfhbi-1T within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F107
b:34.6
occ:1.00
|
F7
|
A:2ZY107
|
0.0
|
34.6
|
1.0
|
C4
|
A:2ZY107
|
1.4
|
40.7
|
1.0
|
C3
|
A:2ZY107
|
2.4
|
39.9
|
1.0
|
C5
|
A:2ZY107
|
2.4
|
36.4
|
1.0
|
O9
|
A:2ZY107
|
2.8
|
33.9
|
1.0
|
C2
|
A:DG25
|
3.0
|
34.2
|
1.0
|
N1
|
A:DG25
|
3.0
|
32.9
|
1.0
|
N2
|
A:DG44
|
3.0
|
35.0
|
1.0
|
C6
|
A:DG26
|
3.2
|
43.9
|
0.5
|
O6
|
A:DG26
|
3.2
|
43.3
|
0.5
|
O6
|
A:DG26
|
3.2
|
43.0
|
0.5
|
C6
|
A:DG26
|
3.3
|
44.0
|
0.5
|
C5
|
A:DG26
|
3.3
|
41.9
|
0.5
|
C5
|
A:DG26
|
3.4
|
42.2
|
0.5
|
N2
|
A:DG25
|
3.4
|
37.2
|
1.0
|
N3
|
A:DG25
|
3.4
|
36.2
|
1.0
|
C6
|
A:DG25
|
3.5
|
32.5
|
1.0
|
O6
|
A:DG18
|
3.5
|
34.9
|
1.0
|
N7
|
A:DG26
|
3.5
|
38.4
|
0.5
|
N7
|
A:DG26
|
3.5
|
38.6
|
0.5
|
C6
|
A:2ZY107
|
3.7
|
40.9
|
1.0
|
C2
|
A:2ZY107
|
3.7
|
40.1
|
1.0
|
C4
|
A:DG25
|
3.7
|
38.7
|
1.0
|
C5
|
A:DG25
|
3.8
|
35.2
|
1.0
|
K
|
A:K102
|
3.8
|
38.0
|
1.0
|
N1
|
A:DG26
|
3.9
|
45.2
|
0.5
|
O
|
A:HOH210
|
3.9
|
34.5
|
1.0
|
N1
|
A:DG26
|
4.0
|
45.4
|
0.5
|
C4
|
A:DG26
|
4.1
|
44.5
|
0.5
|
O6
|
A:DG25
|
4.1
|
31.8
|
1.0
|
C1
|
A:2ZY107
|
4.1
|
40.4
|
1.0
|
C4
|
A:DG26
|
4.2
|
44.7
|
0.5
|
C6
|
A:DG18
|
4.2
|
34.0
|
1.0
|
C2
|
A:DG44
|
4.3
|
39.5
|
1.0
|
C8
|
A:DG26
|
4.3
|
43.5
|
0.5
|
C8
|
A:DG26
|
4.3
|
43.7
|
0.5
|
O
|
A:HOH214
|
4.5
|
32.8
|
1.0
|
N7
|
A:DG18
|
4.5
|
37.6
|
1.0
|
C2
|
A:DG26
|
4.5
|
46.9
|
0.5
|
N9
|
A:DG26
|
4.6
|
45.8
|
0.5
|
C5
|
A:DG18
|
4.7
|
34.2
|
1.0
|
N9
|
A:DG25
|
4.7
|
36.1
|
1.0
|
N3
|
A:DG26
|
4.7
|
47.1
|
0.5
|
N1
|
A:DG44
|
4.7
|
37.8
|
1.0
|
C2
|
A:DG26
|
4.7
|
46.9
|
0.5
|
N9
|
A:DG26
|
4.7
|
45.9
|
0.5
|
F8
|
A:2ZY107
|
4.8
|
42.3
|
1.0
|
N7
|
A:DG25
|
4.8
|
34.0
|
1.0
|
N12
|
A:2ZY107
|
4.8
|
43.5
|
1.0
|
N3
|
A:DG26
|
4.8
|
47.3
|
0.5
|
N4
|
A:DC17
|
4.9
|
37.6
|
1.0
|
C10
|
A:2ZY107
|
5.0
|
47.7
|
1.0
|
|
Fluorine binding site 3 out
of 5 in 8fhx
Go back to
Fluorine Binding Sites List in 8fhx
Fluorine binding site 3 out
of 5 in the Structure of Lettuce Aptamer Bound to Dfhbi-1T
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Structure of Lettuce Aptamer Bound to Dfhbi-1T within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F107
b:100.7
occ:1.00
|
F20
|
A:2ZY107
|
0.0
|
100.7
|
1.0
|
C19
|
A:2ZY107
|
1.4
|
75.3
|
1.0
|
F22
|
A:2ZY107
|
2.2
|
62.5
|
1.0
|
F21
|
A:2ZY107
|
2.2
|
62.2
|
1.0
|
C16
|
A:2ZY107
|
2.4
|
61.1
|
1.0
|
N14
|
A:2ZY107
|
3.6
|
48.1
|
1.0
|
O18
|
A:2ZY107
|
4.3
|
54.9
|
1.0
|
C15
|
A:2ZY107
|
4.4
|
50.0
|
1.0
|
C13
|
A:2ZY107
|
4.7
|
43.6
|
1.0
|
O4'
|
A:DC20
|
4.8
|
54.5
|
1.0
|
C6
|
A:DC20
|
4.9
|
45.1
|
1.0
|
|
Fluorine binding site 4 out
of 5 in 8fhx
Go back to
Fluorine Binding Sites List in 8fhx
Fluorine binding site 4 out
of 5 in the Structure of Lettuce Aptamer Bound to Dfhbi-1T
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Structure of Lettuce Aptamer Bound to Dfhbi-1T within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F107
b:62.2
occ:1.00
|
F21
|
A:2ZY107
|
0.0
|
62.2
|
1.0
|
C19
|
A:2ZY107
|
1.4
|
75.3
|
1.0
|
F22
|
A:2ZY107
|
2.2
|
62.5
|
1.0
|
F20
|
A:2ZY107
|
2.2
|
100.7
|
1.0
|
C16
|
A:2ZY107
|
2.4
|
61.1
|
1.0
|
N14
|
A:2ZY107
|
2.7
|
48.1
|
1.0
|
O18
|
A:2ZY107
|
2.7
|
54.9
|
1.0
|
C15
|
A:2ZY107
|
2.9
|
50.0
|
1.0
|
C13
|
A:2ZY107
|
3.8
|
43.6
|
1.0
|
C5'
|
A:DG19
|
4.0
|
48.9
|
1.0
|
C11
|
A:2ZY107
|
4.1
|
48.9
|
1.0
|
C4'
|
A:DG19
|
4.3
|
44.2
|
1.0
|
C5
|
A:DC20
|
4.3
|
44.7
|
1.0
|
O4'
|
A:DG19
|
4.5
|
37.8
|
1.0
|
N12
|
A:2ZY107
|
4.5
|
43.5
|
1.0
|
C6
|
A:DC20
|
4.6
|
45.1
|
1.0
|
OP1
|
A:DG19
|
4.6
|
65.2
|
1.0
|
C17
|
A:2ZY107
|
4.7
|
47.5
|
1.0
|
C8
|
A:DG18
|
4.8
|
40.1
|
1.0
|
C4
|
A:DC20
|
4.9
|
47.7
|
1.0
|
C1'
|
A:DG18
|
4.9
|
38.4
|
1.0
|
C10
|
A:2ZY107
|
5.0
|
47.7
|
1.0
|
|
Fluorine binding site 5 out
of 5 in 8fhx
Go back to
Fluorine Binding Sites List in 8fhx
Fluorine binding site 5 out
of 5 in the Structure of Lettuce Aptamer Bound to Dfhbi-1T
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Structure of Lettuce Aptamer Bound to Dfhbi-1T within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F107
b:62.5
occ:1.00
|
F22
|
A:2ZY107
|
0.0
|
62.5
|
1.0
|
C19
|
A:2ZY107
|
1.4
|
75.3
|
1.0
|
F20
|
A:2ZY107
|
2.2
|
100.7
|
1.0
|
F21
|
A:2ZY107
|
2.2
|
62.2
|
1.0
|
C16
|
A:2ZY107
|
2.4
|
61.1
|
1.0
|
N14
|
A:2ZY107
|
2.9
|
48.1
|
1.0
|
C5
|
A:DC20
|
3.0
|
44.7
|
1.0
|
C6
|
A:DC20
|
3.1
|
45.1
|
1.0
|
C4
|
A:DC20
|
3.3
|
47.7
|
1.0
|
N1
|
A:DC20
|
3.4
|
49.1
|
1.0
|
C13
|
A:2ZY107
|
3.4
|
43.6
|
1.0
|
C17
|
A:2ZY107
|
3.5
|
47.5
|
1.0
|
N3
|
A:DC20
|
3.6
|
50.4
|
1.0
|
C2
|
A:DC20
|
3.6
|
54.3
|
1.0
|
C15
|
A:2ZY107
|
3.9
|
50.0
|
1.0
|
N4
|
A:DC20
|
4.0
|
51.6
|
1.0
|
O4'
|
A:DC20
|
4.1
|
54.5
|
1.0
|
C1'
|
A:DC20
|
4.2
|
51.4
|
1.0
|
O18
|
A:2ZY107
|
4.4
|
54.9
|
1.0
|
O2
|
A:DC20
|
4.5
|
53.0
|
1.0
|
N12
|
A:2ZY107
|
4.6
|
43.5
|
1.0
|
C4'
|
A:DG19
|
4.8
|
44.2
|
1.0
|
C11
|
A:2ZY107
|
4.8
|
48.9
|
1.0
|
O4'
|
A:DG19
|
4.9
|
37.8
|
1.0
|
|
Reference:
L.F.M.Passalacqua,
A.R.Ferre-D'amare.
Structure of Lettuce Aptamer Bound to Dfhbi-1T To Be Published.
Page generated: Fri Aug 2 19:05:10 2024
|