Fluorine in PDB 7kvt: Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions
Protein crystallography data
The structure of Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions, PDB code: 7kvt
was solved by
L.Truong,
A.R.Ferre-D'amare,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.47 /
2.73
|
Space group
|
P 42 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
103.9,
103.9,
51.699,
90,
90,
90
|
R / Rfree (%)
|
20.9 /
25.1
|
Other elements in 7kvt:
The structure of Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions
(pdb code 7kvt). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the
Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions, PDB code: 7kvt:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
Fluorine binding site 1 out
of 5 in 7kvt
Go back to
Fluorine Binding Sites List in 7kvt
Fluorine binding site 1 out
of 5 in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F101
b:65.3
occ:1.00
|
F8
|
B:2ZY101
|
0.0
|
65.3
|
1.0
|
C6
|
B:2ZY101
|
1.4
|
56.8
|
1.0
|
C1
|
B:2ZY101
|
2.3
|
56.2
|
1.0
|
C5
|
B:2ZY101
|
2.4
|
53.8
|
1.0
|
O2'
|
B:A69
|
2.5
|
59.9
|
1.0
|
O9
|
B:2ZY101
|
2.9
|
52.6
|
1.0
|
C8
|
B:A69
|
3.0
|
51.9
|
1.0
|
N9
|
B:A69
|
3.2
|
49.8
|
1.0
|
C2
|
B:A70
|
3.3
|
53.2
|
1.0
|
N3
|
B:A70
|
3.3
|
53.9
|
1.0
|
C2'
|
B:A69
|
3.3
|
55.0
|
1.0
|
C4
|
B:A70
|
3.3
|
49.7
|
1.0
|
N7
|
B:A69
|
3.5
|
53.3
|
1.0
|
N1
|
B:A70
|
3.5
|
59.1
|
1.0
|
C5
|
B:A70
|
3.5
|
49.0
|
1.0
|
C6
|
B:A70
|
3.5
|
54.0
|
1.0
|
C1'
|
B:A69
|
3.6
|
48.4
|
1.0
|
C2
|
B:2ZY101
|
3.6
|
59.8
|
1.0
|
C4
|
B:2ZY101
|
3.6
|
56.0
|
1.0
|
C4
|
B:A69
|
3.7
|
49.9
|
1.0
|
C5
|
B:A69
|
3.8
|
45.1
|
1.0
|
O2'
|
B:A70
|
4.0
|
54.9
|
1.0
|
N9
|
B:A70
|
4.0
|
51.9
|
1.0
|
C3
|
B:2ZY101
|
4.2
|
50.5
|
1.0
|
N7
|
B:A70
|
4.3
|
55.9
|
1.0
|
N6
|
B:A70
|
4.3
|
49.1
|
1.0
|
O4
|
B:U15
|
4.4
|
58.0
|
1.0
|
N2
|
B:G13
|
4.4
|
57.4
|
1.0
|
C2'
|
B:A70
|
4.4
|
54.8
|
1.0
|
N3
|
B:U15
|
4.5
|
47.2
|
1.0
|
C8
|
B:A70
|
4.5
|
53.4
|
1.0
|
N3
|
B:A69
|
4.6
|
52.6
|
1.0
|
C4
|
B:U15
|
4.6
|
58.2
|
1.0
|
F7
|
B:2ZY101
|
4.7
|
66.4
|
1.0
|
C10
|
B:2ZY101
|
4.7
|
56.9
|
1.0
|
C3'
|
B:A69
|
4.8
|
59.3
|
1.0
|
C1'
|
B:A70
|
4.8
|
51.5
|
1.0
|
C6
|
B:A69
|
4.8
|
49.3
|
1.0
|
O4'
|
B:A69
|
4.9
|
55.7
|
1.0
|
|
Fluorine binding site 2 out
of 5 in 7kvt
Go back to
Fluorine Binding Sites List in 7kvt
Fluorine binding site 2 out
of 5 in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F101
b:66.4
occ:1.00
|
F7
|
B:2ZY101
|
0.0
|
66.4
|
1.0
|
C4
|
B:2ZY101
|
1.4
|
56.0
|
1.0
|
C5
|
B:2ZY101
|
2.3
|
53.8
|
1.0
|
C3
|
B:2ZY101
|
2.5
|
50.5
|
1.0
|
O9
|
B:2ZY101
|
2.6
|
52.6
|
1.0
|
N3
|
B:G14
|
3.2
|
61.0
|
1.0
|
C2
|
B:G13
|
3.4
|
60.2
|
1.0
|
N1
|
B:G13
|
3.5
|
58.4
|
1.0
|
C6
|
B:2ZY101
|
3.6
|
56.8
|
1.0
|
C2
|
B:2ZY101
|
3.7
|
59.8
|
1.0
|
N3
|
B:G13
|
3.7
|
65.2
|
1.0
|
C1'
|
B:G14
|
3.8
|
63.2
|
1.0
|
N2
|
B:G13
|
3.8
|
57.4
|
1.0
|
C4
|
B:G14
|
3.8
|
70.6
|
1.0
|
C2
|
B:G14
|
3.8
|
77.0
|
1.0
|
O4'
|
B:G14
|
3.9
|
70.4
|
1.0
|
C6
|
B:G13
|
4.0
|
62.1
|
1.0
|
C4
|
B:G13
|
4.0
|
65.4
|
1.0
|
N9
|
B:G14
|
4.0
|
73.5
|
1.0
|
N2
|
B:G14
|
4.0
|
84.0
|
1.0
|
C1
|
B:2ZY101
|
4.1
|
56.2
|
1.0
|
C5
|
B:G13
|
4.1
|
62.0
|
1.0
|
O2'
|
B:A70
|
4.4
|
54.9
|
1.0
|
C5
|
B:U15
|
4.4
|
63.5
|
1.0
|
O4
|
B:U15
|
4.4
|
58.0
|
1.0
|
C4
|
B:U15
|
4.6
|
58.2
|
1.0
|
O6
|
B:G13
|
4.6
|
63.3
|
1.0
|
F8
|
B:2ZY101
|
4.7
|
65.3
|
1.0
|
N9
|
B:G13
|
4.8
|
67.0
|
1.0
|
N1
|
B:G14
|
4.9
|
66.6
|
1.0
|
C5
|
B:G14
|
4.9
|
67.3
|
1.0
|
|
Fluorine binding site 3 out
of 5 in 7kvt
Go back to
Fluorine Binding Sites List in 7kvt
Fluorine binding site 3 out
of 5 in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F101
b:72.4
occ:1.00
|
F20
|
B:2ZY101
|
0.0
|
72.4
|
1.0
|
C19
|
B:2ZY101
|
1.4
|
70.1
|
1.0
|
F22
|
B:2ZY101
|
2.3
|
68.5
|
1.0
|
F21
|
B:2ZY101
|
2.3
|
73.1
|
1.0
|
C16
|
B:2ZY101
|
2.4
|
68.6
|
1.0
|
O2'
|
B:U39
|
2.9
|
67.1
|
1.0
|
N14
|
B:2ZY101
|
3.6
|
63.9
|
1.0
|
O2
|
B:U39
|
3.7
|
67.3
|
1.0
|
C1'
|
B:U39
|
4.0
|
75.7
|
1.0
|
C2'
|
B:U39
|
4.0
|
72.3
|
1.0
|
C17
|
B:2ZY101
|
4.3
|
70.2
|
1.0
|
C13
|
B:2ZY101
|
4.3
|
68.2
|
1.0
|
C15
|
B:2ZY101
|
4.5
|
59.1
|
1.0
|
N6
|
B:A48
|
4.5
|
69.3
|
1.0
|
O2'
|
B:U15
|
4.7
|
64.3
|
1.0
|
O18
|
B:2ZY101
|
4.7
|
58.1
|
1.0
|
C2
|
B:U39
|
4.7
|
68.9
|
1.0
|
O4'
|
B:U39
|
4.8
|
87.0
|
1.0
|
O4'
|
B:A40
|
4.9
|
63.4
|
1.0
|
N1
|
B:U39
|
4.9
|
72.5
|
1.0
|
|
Fluorine binding site 4 out
of 5 in 7kvt
Go back to
Fluorine Binding Sites List in 7kvt
Fluorine binding site 4 out
of 5 in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F101
b:73.1
occ:1.00
|
F21
|
B:2ZY101
|
0.0
|
73.1
|
1.0
|
C19
|
B:2ZY101
|
1.4
|
70.1
|
1.0
|
F22
|
B:2ZY101
|
2.2
|
68.5
|
1.0
|
F20
|
B:2ZY101
|
2.3
|
72.4
|
1.0
|
C16
|
B:2ZY101
|
2.3
|
68.6
|
1.0
|
N6
|
B:A48
|
2.8
|
69.3
|
1.0
|
N14
|
B:2ZY101
|
2.9
|
63.9
|
1.0
|
O18
|
B:2ZY101
|
3.0
|
58.1
|
1.0
|
O2
|
B:U39
|
3.1
|
67.3
|
1.0
|
O2'
|
B:U15
|
3.1
|
64.3
|
1.0
|
C15
|
B:2ZY101
|
3.2
|
59.1
|
1.0
|
C6
|
B:A48
|
3.7
|
66.5
|
1.0
|
C13
|
B:2ZY101
|
4.0
|
68.2
|
1.0
|
O2'
|
B:U39
|
4.1
|
67.1
|
1.0
|
N1
|
B:A48
|
4.1
|
68.9
|
1.0
|
C1'
|
B:U15
|
4.2
|
66.1
|
1.0
|
C2
|
B:U39
|
4.2
|
68.9
|
1.0
|
C2'
|
B:U15
|
4.2
|
64.8
|
1.0
|
C11
|
B:2ZY101
|
4.4
|
57.3
|
1.0
|
O4'
|
B:U15
|
4.5
|
69.6
|
1.0
|
C5
|
B:A48
|
4.6
|
63.4
|
1.0
|
C17
|
B:2ZY101
|
4.7
|
70.2
|
1.0
|
C1'
|
B:U39
|
4.7
|
75.7
|
1.0
|
C4'
|
B:U15
|
4.7
|
64.4
|
1.0
|
N12
|
B:2ZY101
|
4.7
|
66.4
|
1.0
|
C2'
|
B:U39
|
4.8
|
72.3
|
1.0
|
N1
|
B:U39
|
5.0
|
72.5
|
1.0
|
|
Fluorine binding site 5 out
of 5 in 7kvt
Go back to
Fluorine Binding Sites List in 7kvt
Fluorine binding site 5 out
of 5 in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F101
b:68.5
occ:1.00
|
F22
|
B:2ZY101
|
0.0
|
68.5
|
1.0
|
C19
|
B:2ZY101
|
1.4
|
70.1
|
1.0
|
F21
|
B:2ZY101
|
2.2
|
73.1
|
1.0
|
F20
|
B:2ZY101
|
2.3
|
72.4
|
1.0
|
C16
|
B:2ZY101
|
2.3
|
68.6
|
1.0
|
N14
|
B:2ZY101
|
2.6
|
63.9
|
1.0
|
C13
|
B:2ZY101
|
2.9
|
68.2
|
1.0
|
C17
|
B:2ZY101
|
3.0
|
70.2
|
1.0
|
O4'
|
B:U15
|
3.1
|
69.6
|
1.0
|
C4'
|
B:U15
|
3.1
|
64.4
|
1.0
|
O2'
|
B:U15
|
3.2
|
64.3
|
1.0
|
C15
|
B:2ZY101
|
3.5
|
59.1
|
1.0
|
C1'
|
B:U15
|
3.6
|
66.1
|
1.0
|
C2'
|
B:U15
|
3.9
|
64.8
|
1.0
|
N12
|
B:2ZY101
|
3.9
|
66.4
|
1.0
|
O18
|
B:2ZY101
|
4.0
|
58.1
|
1.0
|
C3'
|
B:U15
|
4.1
|
70.0
|
1.0
|
C5'
|
B:U15
|
4.1
|
59.7
|
1.0
|
C11
|
B:2ZY101
|
4.2
|
57.3
|
1.0
|
N6
|
B:A48
|
4.6
|
69.3
|
1.0
|
O3'
|
B:U15
|
4.6
|
71.1
|
1.0
|
O2'
|
B:U39
|
4.8
|
67.1
|
1.0
|
N1
|
B:U15
|
4.9
|
60.4
|
1.0
|
|
Reference:
L.Truong,
H.Kooshapur,
S.K.Dey,
X.Li,
N.Tjandra,
S.R.Jaffrey,
A.R.Ferre-D'amare.
The Fluorescent Aptamer Squash Extensively Repurposes the Adenine Riboswitch Fold. Nat.Chem.Biol. V. 18 191 2022.
ISSN: ESSN 1552-4469
PubMed: 34937911
DOI: 10.1038/S41589-021-00931-2
Page generated: Fri Aug 2 08:31:11 2024
|