Fluorine in PDB 6cy0: Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U.
Protein crystallography data
The structure of Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U., PDB code: 6cy0
was solved by
J.M.Harp,
M.Egli,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
42.60 /
2.40
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
47.012,
47.631,
100.744,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
20.2 /
24.2
|
Other elements in 6cy0:
The structure of Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U. also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U.
(pdb code 6cy0). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the
Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U., PDB code: 6cy0:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Fluorine binding site 1 out
of 8 in 6cy0
Go back to
Fluorine Binding Sites List in 6cy0
Fluorine binding site 1 out
of 8 in the Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U.
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F5
b:32.0
occ:1.00
|
F2'
|
A:UFB5
|
0.0
|
32.0
|
1.0
|
|
C2'
|
A:UFB5
|
1.3
|
15.5
|
1.0
|
|
O5'
|
A:UFB5
|
1.9
|
30.1
|
1.0
|
|
H2'
|
A:UFB5
|
2.0
|
18.6
|
1.0
|
|
C3'
|
A:UFB5
|
2.3
|
20.0
|
1.0
|
|
C1'
|
A:UFB5
|
2.3
|
14.9
|
1.0
|
|
H1'
|
A:UFB5
|
2.4
|
17.9
|
1.0
|
|
O3'
|
A:UFB5
|
2.7
|
16.4
|
1.0
|
|
C4'
|
A:UFB5
|
2.8
|
22.5
|
1.0
|
|
C5'
|
A:UFB5
|
2.8
|
17.5
|
1.0
|
|
O4'
|
A:UFB5
|
2.8
|
15.3
|
1.0
|
|
H5'
|
A:U6
|
3.0
|
19.4
|
1.0
|
|
H2'
|
A:A4
|
3.1
|
25.6
|
1.0
|
|
P
|
A:UFB5
|
3.2
|
33.3
|
1.0
|
|
H3'
|
A:UFB5
|
3.3
|
24.0
|
1.0
|
|
H5S
|
A:UFB5
|
3.3
|
21.1
|
1.0
|
|
H3'
|
A:A4
|
3.4
|
26.6
|
1.0
|
|
OP1
|
A:UFB5
|
3.5
|
35.4
|
1.0
|
|
H5'
|
A:UFB5
|
3.6
|
21.1
|
1.0
|
|
O3'
|
A:A4
|
3.6
|
20.0
|
1.0
|
|
N1
|
A:UFB5
|
3.7
|
10.8
|
1.0
|
|
C3'
|
A:A4
|
3.8
|
22.1
|
1.0
|
|
O
|
A:HOH107
|
3.8
|
31.5
|
1.0
|
|
C2'
|
A:A4
|
3.8
|
21.3
|
1.0
|
|
C5'
|
A:U6
|
3.9
|
16.1
|
1.0
|
|
P
|
A:U6
|
4.0
|
26.3
|
1.0
|
|
O5'
|
A:U6
|
4.0
|
24.3
|
1.0
|
|
HO2'
|
A:A4
|
4.2
|
28.5
|
1.0
|
|
OM
|
A:UFB5
|
4.2
|
24.3
|
1.0
|
|
O2
|
A:UFB5
|
4.2
|
16.2
|
1.0
|
|
O4'
|
A:U6
|
4.2
|
13.8
|
1.0
|
|
H6
|
A:U6
|
4.3
|
16.1
|
1.0
|
|
OP2
|
A:UFB5
|
4.4
|
21.8
|
1.0
|
|
C2
|
A:UFB5
|
4.4
|
13.1
|
1.0
|
|
O2'
|
A:A4
|
4.5
|
23.7
|
1.0
|
|
H5''
|
A:U6
|
4.5
|
19.4
|
1.0
|
|
C4'
|
A:U6
|
4.7
|
20.0
|
1.0
|
|
H6
|
A:UFB5
|
4.7
|
14.5
|
1.0
|
|
C6
|
A:UFB5
|
4.7
|
12.1
|
1.0
|
|
OP1
|
A:U6
|
4.7
|
27.4
|
1.0
|
|
H4'
|
A:U6
|
5.0
|
24.0
|
1.0
|
|
HM2
|
A:UFB5
|
5.0
|
21.9
|
1.0
|
|
C6
|
A:U6
|
5.0
|
13.3
|
1.0
|
|
Fluorine binding site 2 out
of 8 in 6cy0
Go back to
Fluorine Binding Sites List in 6cy0
Fluorine binding site 2 out
of 8 in the Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U.
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F5
b:32.2
occ:1.00
|
F2'
|
B:UFB5
|
0.0
|
32.2
|
1.0
|
|
C2'
|
B:UFB5
|
1.3
|
15.2
|
1.0
|
|
O5'
|
B:UFB5
|
1.9
|
17.9
|
1.0
|
|
H2'
|
B:UFB5
|
2.0
|
18.3
|
1.0
|
|
C3'
|
B:UFB5
|
2.3
|
22.0
|
1.0
|
|
C1'
|
B:UFB5
|
2.3
|
17.9
|
1.0
|
|
H1'
|
B:UFB5
|
2.5
|
21.6
|
1.0
|
|
O3'
|
B:UFB5
|
2.7
|
19.1
|
1.0
|
|
O4'
|
B:UFB5
|
2.7
|
12.6
|
1.0
|
|
C4'
|
B:UFB5
|
2.8
|
17.4
|
1.0
|
|
C5'
|
B:UFB5
|
2.8
|
14.5
|
1.0
|
|
H5'
|
B:U6
|
3.0
|
20.4
|
1.0
|
|
H2'
|
B:A4
|
3.1
|
23.4
|
1.0
|
|
P
|
B:UFB5
|
3.2
|
31.6
|
1.0
|
|
H3'
|
B:UFB5
|
3.3
|
26.5
|
1.0
|
|
H3'
|
B:A4
|
3.3
|
21.1
|
1.0
|
|
H5'
|
B:UFB5
|
3.4
|
17.5
|
1.0
|
|
OP1
|
B:UFB5
|
3.5
|
37.2
|
1.0
|
|
O
|
B:HOH111
|
3.5
|
30.9
|
1.0
|
|
O3'
|
B:A4
|
3.5
|
30.8
|
1.0
|
|
H5S
|
B:UFB5
|
3.7
|
17.5
|
1.0
|
|
C3'
|
B:A4
|
3.7
|
17.5
|
1.0
|
|
N1
|
B:UFB5
|
3.7
|
10.6
|
1.0
|
|
C2'
|
B:A4
|
3.8
|
19.5
|
1.0
|
|
C5'
|
B:U6
|
3.9
|
16.9
|
1.0
|
|
P
|
B:U6
|
4.1
|
24.6
|
1.0
|
|
O5'
|
B:U6
|
4.1
|
30.6
|
1.0
|
|
HO2'
|
B:A4
|
4.1
|
17.4
|
1.0
|
|
OM
|
B:UFB5
|
4.2
|
23.0
|
1.0
|
|
O2
|
B:UFB5
|
4.2
|
17.8
|
1.0
|
|
H6
|
B:U6
|
4.2
|
20.6
|
1.0
|
|
O4'
|
B:U6
|
4.3
|
18.2
|
1.0
|
|
OP2
|
B:UFB5
|
4.4
|
15.2
|
1.0
|
|
C2
|
B:UFB5
|
4.4
|
11.3
|
1.0
|
|
O2'
|
B:A4
|
4.5
|
14.5
|
1.0
|
|
H5''
|
B:U6
|
4.5
|
20.4
|
1.0
|
|
O
|
B:HOH116
|
4.5
|
26.8
|
1.0
|
|
H6
|
B:UFB5
|
4.6
|
14.8
|
1.0
|
|
C4'
|
B:U6
|
4.7
|
12.9
|
1.0
|
|
C6
|
B:UFB5
|
4.7
|
12.3
|
1.0
|
|
OP1
|
B:U6
|
4.8
|
23.6
|
1.0
|
|
HM2
|
B:UFB5
|
4.9
|
35.2
|
1.0
|
|
H4'
|
B:U6
|
5.0
|
15.5
|
1.0
|
|
Fluorine binding site 3 out
of 8 in 6cy0
Go back to
Fluorine Binding Sites List in 6cy0
Fluorine binding site 3 out
of 8 in the Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U.
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F5
b:37.6
occ:1.00
|
F2'
|
C:UFB5
|
0.0
|
37.6
|
1.0
|
|
C2'
|
C:UFB5
|
1.3
|
20.6
|
1.0
|
|
O5'
|
C:UFB5
|
1.9
|
24.2
|
1.0
|
|
H2'
|
C:UFB5
|
2.0
|
24.8
|
1.0
|
|
C3'
|
C:UFB5
|
2.3
|
19.4
|
1.0
|
|
C1'
|
C:UFB5
|
2.3
|
18.6
|
1.0
|
|
H1'
|
C:UFB5
|
2.5
|
22.4
|
1.0
|
|
O3'
|
C:UFB5
|
2.7
|
28.6
|
1.0
|
|
O4'
|
C:UFB5
|
2.7
|
13.2
|
1.0
|
|
C4'
|
C:UFB5
|
2.8
|
18.6
|
1.0
|
|
C5'
|
C:UFB5
|
2.8
|
19.2
|
1.0
|
|
H5'
|
C:U6
|
3.0
|
28.0
|
1.0
|
|
H2'
|
C:A4
|
3.1
|
22.3
|
1.0
|
|
P
|
C:UFB5
|
3.2
|
29.6
|
1.0
|
|
H3'
|
C:UFB5
|
3.3
|
23.3
|
1.0
|
|
H5'
|
C:UFB5
|
3.4
|
23.1
|
1.0
|
|
OP1
|
C:UFB5
|
3.5
|
31.4
|
1.0
|
|
H3'
|
C:A4
|
3.6
|
14.5
|
1.0
|
|
H5S
|
C:UFB5
|
3.7
|
23.1
|
1.0
|
|
N1
|
C:UFB5
|
3.7
|
11.9
|
1.0
|
|
O3'
|
C:A4
|
3.8
|
21.9
|
1.0
|
|
O
|
C:HOH108
|
3.8
|
36.1
|
1.0
|
|
C2'
|
C:A4
|
3.8
|
18.6
|
1.0
|
|
C3'
|
C:A4
|
3.9
|
12.1
|
1.0
|
|
C5'
|
C:U6
|
3.9
|
23.3
|
1.0
|
|
P
|
C:U6
|
4.1
|
31.2
|
1.0
|
|
O5'
|
C:U6
|
4.1
|
30.5
|
1.0
|
|
OM
|
C:UFB5
|
4.2
|
23.5
|
1.0
|
|
O2
|
C:UFB5
|
4.2
|
14.6
|
1.0
|
|
O4'
|
C:U6
|
4.3
|
22.5
|
1.0
|
|
H6
|
C:U6
|
4.4
|
22.6
|
1.0
|
|
OP2
|
C:UFB5
|
4.4
|
37.1
|
1.0
|
|
C2
|
C:UFB5
|
4.4
|
9.9
|
1.0
|
|
O2'
|
C:A4
|
4.5
|
11.6
|
1.0
|
|
H5''
|
C:U6
|
4.5
|
28.0
|
1.0
|
|
H6
|
C:UFB5
|
4.7
|
12.3
|
1.0
|
|
C4'
|
C:U6
|
4.7
|
22.2
|
1.0
|
|
C6
|
C:UFB5
|
4.7
|
10.2
|
1.0
|
|
OP1
|
C:U6
|
4.8
|
27.1
|
1.0
|
|
H4'
|
C:U6
|
5.0
|
26.6
|
1.0
|
|
HM2
|
C:UFB5
|
5.0
|
17.7
|
1.0
|
|
Fluorine binding site 4 out
of 8 in 6cy0
Go back to
Fluorine Binding Sites List in 6cy0
Fluorine binding site 4 out
of 8 in the Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U.
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F5
b:40.5
occ:1.00
|
F2'
|
D:UFB5
|
0.0
|
40.5
|
1.0
|
|
C2'
|
D:UFB5
|
1.3
|
20.7
|
1.0
|
|
O5'
|
D:UFB5
|
2.0
|
16.6
|
1.0
|
|
H2'
|
D:UFB5
|
2.0
|
24.9
|
1.0
|
|
C3'
|
D:UFB5
|
2.3
|
23.4
|
1.0
|
|
C1'
|
D:UFB5
|
2.3
|
22.0
|
1.0
|
|
H1'
|
D:UFB5
|
2.5
|
26.4
|
1.0
|
|
O3'
|
D:UFB5
|
2.7
|
26.8
|
1.0
|
|
C4'
|
D:UFB5
|
2.7
|
26.7
|
1.0
|
|
O4'
|
D:UFB5
|
2.7
|
22.9
|
1.0
|
|
C5'
|
D:UFB5
|
2.8
|
28.3
|
1.0
|
|
H2'
|
D:A4
|
3.0
|
31.2
|
1.0
|
|
H5'
|
D:UFB5
|
3.2
|
34.0
|
1.0
|
|
P
|
D:UFB5
|
3.2
|
31.5
|
1.0
|
|
H3'
|
D:UFB5
|
3.3
|
28.1
|
1.0
|
|
H5'
|
D:U6
|
3.3
|
26.8
|
1.0
|
|
OP1
|
D:UFB5
|
3.6
|
43.6
|
1.0
|
|
H3'
|
D:A4
|
3.7
|
26.0
|
1.0
|
|
H5S
|
D:UFB5
|
3.7
|
34.0
|
1.0
|
|
N1
|
D:UFB5
|
3.7
|
16.9
|
1.0
|
|
O3'
|
D:A4
|
3.7
|
35.1
|
1.0
|
|
C2'
|
D:A4
|
3.8
|
26.0
|
1.0
|
|
O
|
D:HOH120
|
3.9
|
28.4
|
1.0
|
|
C3'
|
D:A4
|
3.9
|
21.6
|
1.0
|
|
O
|
D:HOH124
|
4.0
|
35.5
|
1.0
|
|
P
|
D:U6
|
4.0
|
31.3
|
1.0
|
|
O5'
|
D:U6
|
4.1
|
29.8
|
1.0
|
|
C5'
|
D:U6
|
4.1
|
22.3
|
1.0
|
|
OM
|
D:UFB5
|
4.1
|
31.9
|
1.0
|
|
O
|
D:HOH107
|
4.2
|
26.4
|
1.0
|
|
O2
|
D:UFB5
|
4.2
|
18.4
|
1.0
|
|
O2'
|
D:A4
|
4.3
|
17.3
|
1.0
|
|
C2
|
D:UFB5
|
4.4
|
12.0
|
1.0
|
|
OP2
|
D:UFB5
|
4.5
|
23.0
|
1.0
|
|
H6
|
D:U6
|
4.6
|
15.0
|
1.0
|
|
H6
|
D:UFB5
|
4.7
|
22.5
|
1.0
|
|
H5''
|
D:U6
|
4.7
|
26.8
|
1.0
|
|
OP1
|
D:U6
|
4.7
|
26.1
|
1.0
|
|
C6
|
D:UFB5
|
4.7
|
18.7
|
1.0
|
|
HM2
|
D:UFB5
|
4.8
|
39.2
|
1.0
|
|
O4'
|
D:U6
|
4.9
|
23.6
|
1.0
|
|
HO2'
|
D:A4
|
5.0
|
20.8
|
1.0
|
|
Fluorine binding site 5 out
of 8 in 6cy0
Go back to
Fluorine Binding Sites List in 6cy0
Fluorine binding site 5 out
of 8 in the Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U.
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:F5
b:38.7
occ:1.00
|
F2'
|
E:UFB5
|
0.0
|
38.7
|
1.0
|
|
C2'
|
E:UFB5
|
1.3
|
21.6
|
1.0
|
|
O5'
|
E:UFB5
|
1.9
|
24.0
|
1.0
|
|
H2'
|
E:UFB5
|
2.0
|
25.9
|
1.0
|
|
C1'
|
E:UFB5
|
2.3
|
20.6
|
1.0
|
|
C3'
|
E:UFB5
|
2.3
|
19.0
|
1.0
|
|
H1'
|
E:UFB5
|
2.5
|
24.7
|
1.0
|
|
O3'
|
E:UFB5
|
2.7
|
26.4
|
1.0
|
|
O4'
|
E:UFB5
|
2.7
|
17.0
|
1.0
|
|
C4'
|
E:UFB5
|
2.8
|
18.5
|
1.0
|
|
C5'
|
E:UFB5
|
2.8
|
18.9
|
1.0
|
|
H2'
|
E:A4
|
3.0
|
31.1
|
1.0
|
|
P
|
E:UFB5
|
3.1
|
35.0
|
1.0
|
|
H5'
|
E:U6
|
3.2
|
10.0
|
1.0
|
|
H3'
|
E:A4
|
3.3
|
24.3
|
1.0
|
|
H3'
|
E:UFB5
|
3.3
|
22.9
|
1.0
|
|
O3'
|
E:A4
|
3.4
|
18.3
|
1.0
|
|
H5'
|
E:UFB5
|
3.4
|
22.7
|
1.0
|
|
OP1
|
E:UFB5
|
3.6
|
38.2
|
1.0
|
|
C3'
|
E:A4
|
3.6
|
20.2
|
1.0
|
|
H5S
|
E:UFB5
|
3.7
|
22.7
|
1.0
|
|
C2'
|
E:A4
|
3.7
|
25.9
|
1.0
|
|
N1
|
E:UFB5
|
3.7
|
13.7
|
1.0
|
|
C5'
|
E:U6
|
4.0
|
8.3
|
1.0
|
|
HO2'
|
E:A4
|
4.1
|
19.9
|
1.0
|
|
P
|
E:U6
|
4.1
|
19.6
|
1.0
|
|
O2
|
E:UFB5
|
4.1
|
21.9
|
1.0
|
|
OM
|
E:UFB5
|
4.2
|
22.5
|
1.0
|
|
O5'
|
E:U6
|
4.2
|
18.2
|
1.0
|
|
OP2
|
E:UFB5
|
4.4
|
26.1
|
1.0
|
|
H6
|
E:U6
|
4.4
|
21.1
|
1.0
|
|
C2
|
E:UFB5
|
4.4
|
13.8
|
1.0
|
|
O4'
|
E:U6
|
4.4
|
19.9
|
1.0
|
|
O2'
|
E:A4
|
4.4
|
16.5
|
1.0
|
|
H5''
|
E:U6
|
4.7
|
10.0
|
1.0
|
|
H6
|
E:UFB5
|
4.7
|
18.9
|
1.0
|
|
C6
|
E:UFB5
|
4.7
|
15.8
|
1.0
|
|
OP1
|
E:U6
|
4.8
|
16.5
|
1.0
|
|
C4'
|
E:U6
|
4.8
|
14.0
|
1.0
|
|
C1'
|
E:A4
|
5.0
|
16.5
|
1.0
|
|
HM2
|
E:UFB5
|
5.0
|
26.3
|
1.0
|
|
Fluorine binding site 6 out
of 8 in 6cy0
Go back to
Fluorine Binding Sites List in 6cy0
Fluorine binding site 6 out
of 8 in the Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U.
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:F5
b:34.9
occ:1.00
|
F2'
|
F:UFB5
|
0.0
|
34.9
|
1.0
|
|
C2'
|
F:UFB5
|
1.3
|
16.4
|
1.0
|
|
O5'
|
F:UFB5
|
1.9
|
30.7
|
1.0
|
|
H2'
|
F:UFB5
|
2.0
|
19.7
|
1.0
|
|
C3'
|
F:UFB5
|
2.3
|
17.3
|
1.0
|
|
C1'
|
F:UFB5
|
2.3
|
23.9
|
1.0
|
|
H1'
|
F:UFB5
|
2.5
|
28.7
|
1.0
|
|
O4'
|
F:UFB5
|
2.7
|
20.7
|
1.0
|
|
C4'
|
F:UFB5
|
2.7
|
21.3
|
1.0
|
|
O3'
|
F:UFB5
|
2.7
|
20.2
|
1.0
|
|
C5'
|
F:UFB5
|
2.8
|
15.4
|
1.0
|
|
H5'
|
F:U6
|
3.0
|
18.7
|
1.0
|
|
P
|
F:UFB5
|
3.2
|
21.6
|
1.0
|
|
H2'
|
F:A4
|
3.2
|
15.6
|
1.0
|
|
H3'
|
F:UFB5
|
3.3
|
20.8
|
1.0
|
|
H5'
|
F:UFB5
|
3.3
|
18.5
|
1.0
|
|
H3'
|
F:A4
|
3.4
|
22.1
|
1.0
|
|
O3'
|
F:A4
|
3.6
|
20.4
|
1.0
|
|
OP1
|
F:UFB5
|
3.6
|
30.6
|
1.0
|
|
H5S
|
F:UFB5
|
3.7
|
18.5
|
1.0
|
|
N1
|
F:UFB5
|
3.7
|
19.3
|
1.0
|
|
C3'
|
F:A4
|
3.8
|
18.4
|
1.0
|
|
C5'
|
F:U6
|
3.8
|
15.5
|
1.0
|
|
O5'
|
F:U6
|
3.9
|
30.3
|
1.0
|
|
C2'
|
F:A4
|
3.9
|
12.9
|
1.0
|
|
P
|
F:U6
|
4.0
|
27.0
|
1.0
|
|
OM
|
F:UFB5
|
4.2
|
29.8
|
1.0
|
|
O2
|
F:UFB5
|
4.2
|
20.1
|
1.0
|
|
HO2'
|
F:A4
|
4.3
|
17.7
|
1.0
|
|
H6
|
F:U6
|
4.3
|
22.6
|
1.0
|
|
C2
|
F:UFB5
|
4.4
|
15.6
|
1.0
|
|
OP2
|
F:UFB5
|
4.4
|
16.6
|
1.0
|
|
O4'
|
F:U6
|
4.4
|
19.7
|
1.0
|
|
H5''
|
F:U6
|
4.5
|
18.7
|
1.0
|
|
O2'
|
F:A4
|
4.6
|
14.7
|
1.0
|
|
OP1
|
F:U6
|
4.6
|
17.9
|
1.0
|
|
H6
|
F:UFB5
|
4.7
|
26.4
|
1.0
|
|
C6
|
F:UFB5
|
4.7
|
22.0
|
1.0
|
|
C4'
|
F:U6
|
4.8
|
19.2
|
1.0
|
|
HM2
|
F:UFB5
|
4.9
|
39.2
|
1.0
|
|
Fluorine binding site 7 out
of 8 in 6cy0
Go back to
Fluorine Binding Sites List in 6cy0
Fluorine binding site 7 out
of 8 in the Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U.
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 7 of Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:F5
b:30.5
occ:1.00
|
F2'
|
G:UFB5
|
0.0
|
30.5
|
1.0
|
|
C2'
|
G:UFB5
|
1.3
|
16.7
|
1.0
|
|
O5'
|
G:UFB5
|
1.9
|
27.5
|
1.0
|
|
H2'
|
G:UFB5
|
2.0
|
20.1
|
1.0
|
|
C1'
|
G:UFB5
|
2.3
|
23.3
|
1.0
|
|
C3'
|
G:UFB5
|
2.3
|
14.9
|
1.0
|
|
H1'
|
G:UFB5
|
2.5
|
28.0
|
1.0
|
|
O3'
|
G:UFB5
|
2.7
|
22.2
|
1.0
|
|
C4'
|
G:UFB5
|
2.8
|
16.1
|
1.0
|
|
O4'
|
G:UFB5
|
2.8
|
17.4
|
1.0
|
|
C5'
|
G:UFB5
|
2.8
|
22.0
|
1.0
|
|
H2'
|
G:A4
|
3.0
|
24.7
|
1.0
|
|
P
|
G:UFB5
|
3.1
|
27.1
|
1.0
|
|
H5'
|
G:U6
|
3.1
|
21.5
|
1.0
|
|
H3'
|
G:A4
|
3.2
|
32.5
|
1.0
|
|
H3'
|
G:UFB5
|
3.3
|
17.9
|
1.0
|
|
OP1
|
G:UFB5
|
3.4
|
41.4
|
1.0
|
|
O3'
|
G:A4
|
3.4
|
24.7
|
1.0
|
|
H5'
|
G:UFB5
|
3.5
|
26.5
|
1.0
|
|
C3'
|
G:A4
|
3.6
|
27.1
|
1.0
|
|
H5S
|
G:UFB5
|
3.6
|
26.5
|
1.0
|
|
C2'
|
G:A4
|
3.7
|
20.5
|
1.0
|
|
N1
|
G:UFB5
|
3.7
|
18.4
|
1.0
|
|
C5'
|
G:U6
|
4.0
|
17.9
|
1.0
|
|
O2
|
G:UFB5
|
4.1
|
19.7
|
1.0
|
|
HO2'
|
G:A4
|
4.1
|
27.6
|
1.0
|
|
P
|
G:U6
|
4.1
|
17.1
|
1.0
|
|
OM
|
G:UFB5
|
4.2
|
20.5
|
1.0
|
|
O5'
|
G:U6
|
4.3
|
26.9
|
1.0
|
|
O4'
|
G:U6
|
4.3
|
12.3
|
1.0
|
|
H6
|
G:U6
|
4.3
|
22.8
|
1.0
|
|
OP2
|
G:UFB5
|
4.3
|
34.4
|
1.0
|
|
C2
|
G:UFB5
|
4.4
|
16.1
|
1.0
|
|
O2'
|
G:A4
|
4.4
|
22.9
|
1.0
|
|
H5''
|
G:U6
|
4.7
|
21.5
|
1.0
|
|
H6
|
G:UFB5
|
4.7
|
18.0
|
1.0
|
|
C6
|
G:UFB5
|
4.7
|
15.0
|
1.0
|
|
C4'
|
G:U6
|
4.8
|
18.0
|
1.0
|
|
OP1
|
G:U6
|
4.9
|
21.7
|
1.0
|
|
HM2
|
G:UFB5
|
4.9
|
30.1
|
1.0
|
|
C1'
|
G:A4
|
4.9
|
24.3
|
1.0
|
|
N9
|
G:A4
|
5.0
|
18.6
|
1.0
|
|
C6
|
G:U6
|
5.0
|
19.0
|
1.0
|
|
Fluorine binding site 8 out
of 8 in 6cy0
Go back to
Fluorine Binding Sites List in 6cy0
Fluorine binding site 8 out
of 8 in the Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U.
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 8 of Rna Octamer Containing 2'-F, 4'-Cbeta-Ome U. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:F5
b:31.3
occ:1.00
|
F2'
|
H:UFB5
|
0.0
|
31.3
|
1.0
|
|
C2'
|
H:UFB5
|
1.3
|
16.7
|
1.0
|
|
O5'
|
H:UFB5
|
1.9
|
25.7
|
1.0
|
|
H2'
|
H:UFB5
|
2.0
|
20.0
|
1.0
|
|
C3'
|
H:UFB5
|
2.3
|
19.2
|
1.0
|
|
C1'
|
H:UFB5
|
2.3
|
17.5
|
1.0
|
|
H1'
|
H:UFB5
|
2.5
|
21.0
|
1.0
|
|
O3'
|
H:UFB5
|
2.7
|
27.9
|
1.0
|
|
O4'
|
H:UFB5
|
2.8
|
20.6
|
1.0
|
|
C4'
|
H:UFB5
|
2.8
|
20.4
|
1.0
|
|
C5'
|
H:UFB5
|
2.8
|
15.8
|
1.0
|
|
H5'
|
H:U6
|
2.9
|
16.8
|
1.0
|
|
H2'
|
H:A4
|
3.0
|
28.1
|
1.0
|
|
P
|
H:UFB5
|
3.1
|
31.5
|
1.0
|
|
H3'
|
H:UFB5
|
3.3
|
23.1
|
1.0
|
|
H3'
|
H:A4
|
3.3
|
24.0
|
1.0
|
|
H5'
|
H:UFB5
|
3.4
|
19.0
|
1.0
|
|
OP1
|
H:UFB5
|
3.4
|
45.5
|
1.0
|
|
O3'
|
H:A4
|
3.5
|
26.9
|
1.0
|
|
H5S
|
H:UFB5
|
3.7
|
19.0
|
1.0
|
|
C3'
|
H:A4
|
3.7
|
20.0
|
1.0
|
|
C2'
|
H:A4
|
3.7
|
23.4
|
1.0
|
|
N1
|
H:UFB5
|
3.7
|
19.9
|
1.0
|
|
C5'
|
H:U6
|
3.8
|
13.9
|
1.0
|
|
O5'
|
H:U6
|
4.0
|
28.0
|
1.0
|
|
P
|
H:U6
|
4.1
|
30.4
|
1.0
|
|
O2
|
H:UFB5
|
4.2
|
17.6
|
1.0
|
|
OM
|
H:UFB5
|
4.2
|
33.6
|
1.0
|
|
O4'
|
H:U6
|
4.3
|
18.2
|
1.0
|
|
H6
|
H:U6
|
4.3
|
15.8
|
1.0
|
|
OP2
|
H:UFB5
|
4.4
|
31.0
|
1.0
|
|
O2'
|
H:A4
|
4.4
|
19.9
|
1.0
|
|
H5''
|
H:U6
|
4.4
|
16.8
|
1.0
|
|
C2
|
H:UFB5
|
4.4
|
18.7
|
1.0
|
|
O
|
H:HOH104
|
4.5
|
22.7
|
1.0
|
|
C4'
|
H:U6
|
4.6
|
18.0
|
1.0
|
|
H6
|
H:UFB5
|
4.7
|
19.4
|
1.0
|
|
C6
|
H:UFB5
|
4.7
|
16.2
|
1.0
|
|
OP1
|
H:U6
|
4.7
|
27.7
|
1.0
|
|
C1'
|
H:A4
|
4.9
|
21.6
|
1.0
|
|
H4'
|
H:U6
|
4.9
|
21.6
|
1.0
|
|
N9
|
H:A4
|
5.0
|
13.6
|
1.0
|
|
Reference:
J.M.Harp,
D.C.Guenther,
A.Bisbe,
L.Perkins,
S.Matsuda,
G.R.Bommineni,
I.Zlatev,
D.J.Foster,
N.Taneja,
K.Charisse,
M.A.Maier,
K.G.Rajeev,
M.Manoharan,
M.Egli.
Structural Basis For the Synergy of 4'- and 2'-Modifications on Sirna Nuclease Resistance, Thermal Stability and Rnai Activity. Nucleic Acids Res. V. 46 8090 2018.
ISSN: ESSN 1362-4962
PubMed: 30107495
DOI: 10.1093/NAR/GKY703
Page generated: Tue Jul 15 10:30:37 2025
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