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Fluorine in PDB 7kvu: Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T

Protein crystallography data

The structure of Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T, PDB code: 7kvu 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) 46.46 / 2.68
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 103.731, 103.731, 51.959, 90, 90, 90
R / Rfree (%) 20.9 / 24.7

Other elements in 7kvu:

The structure of Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T also contains other interesting chemical elements:

Potassium (K) 3 atoms
Magnesium (Mg) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T (pdb code 7kvu). 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, PDB code: 7kvu:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 7kvu

Go back to Fluorine Binding Sites List in 7kvu
Fluorine binding site 1 out of 5 in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F106

b:62.0
occ:1.00
F8 G:2ZY106 0.0 62.0 1.0
C6 G:2ZY106 1.4 62.1 1.0
C5 G:2ZY106 2.4 61.1 1.0
C1 G:2ZY106 2.4 61.3 1.0
O9 G:2ZY106 2.8 61.0 1.0
C8 G:A69 3.0 60.1 1.0
C2 G:A70 3.1 57.3 1.0
N1 G:A70 3.1 60.5 1.0
N7 G:A69 3.1 60.8 1.0
N9 G:A69 3.4 57.0 1.0
O2' G:A69 3.4 64.8 1.0
C6 G:A70 3.4 57.6 1.0
N3 G:A70 3.4 59.8 1.0
C5 G:A69 3.5 55.3 1.0
C4 G:2ZY106 3.6 62.4 1.0
C4 G:A69 3.6 56.9 1.0
C2 G:2ZY106 3.6 62.9 1.0
C4 G:A70 3.7 55.9 1.0
C5 G:A70 3.7 54.3 1.0
N3 G:U15 3.9 59.1 1.0
C2' G:A69 4.0 60.3 1.0
C3 G:2ZY106 4.1 62.8 1.0
N6 G:A70 4.1 53.9 1.0
C1' G:A69 4.1 56.9 1.0
O4 G:U15 4.2 63.4 1.0
C6 G:A69 4.3 58.2 1.0
C4 G:U15 4.3 63.4 1.0
N3 G:A69 4.5 58.6 1.0
N2 G:G13 4.5 62.2 1.0
N9 G:A70 4.6 55.0 1.0
O2' G:A70 4.6 58.7 1.0
N7 G:A70 4.6 57.4 1.0
C2 G:U15 4.7 65.5 1.0
F7 G:2ZY106 4.7 66.0 1.0
O2 G:U15 4.8 67.6 1.0
N6 G:A69 4.8 61.4 1.0
O G:HOH201 4.9 62.7 1.0
C10 G:2ZY106 4.9 64.6 1.0
N12 G:2ZY106 5.0 65.5 1.0

Fluorine binding site 2 out of 5 in 7kvu

Go back to Fluorine Binding Sites List in 7kvu
Fluorine binding site 2 out of 5 in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F106

b:66.0
occ:1.00
F7 G:2ZY106 0.0 66.0 1.0
C4 G:2ZY106 1.4 62.4 1.0
C5 G:2ZY106 2.4 61.1 1.0
C3 G:2ZY106 2.4 62.8 1.0
O G:HOH201 2.7 62.7 1.0
O9 G:2ZY106 2.7 61.0 1.0
N1 G:G13 3.0 64.7 1.0
C2 G:G13 3.3 64.9 1.0
N3 G:G14 3.3 71.4 1.0
C6 G:G13 3.5 66.5 1.0
N2 G:G13 3.6 62.2 1.0
C6 G:2ZY106 3.6 62.1 1.0
C2 G:2ZY106 3.7 62.9 1.0
O2' G:A70 3.7 58.7 1.0
C2 G:G14 3.7 83.2 1.0
N2 G:G14 3.8 86.0 1.0
N3 G:G13 3.8 67.3 1.0
C5 G:G13 4.0 68.0 1.0
O6 G:G13 4.0 68.0 1.0
C4 G:G14 4.0 72.7 1.0
C4 G:G13 4.1 68.9 1.0
C1 G:2ZY106 4.2 61.3 1.0
C1' G:G14 4.4 70.1 1.0
N9 G:G14 4.4 73.6 1.0
O4 G:U15 4.5 63.4 1.0
O4' G:G14 4.6 74.3 1.0
N1 G:G14 4.7 73.4 1.0
F8 G:2ZY106 4.7 62.0 1.0
C10 G:2ZY106 4.9 64.6 1.0
C4 G:U15 4.9 63.4 1.0
N7 G:G13 4.9 72.3 1.0
C5 G:G14 5.0 72.2 1.0
C2' G:A70 5.0 59.7 1.0

Fluorine binding site 3 out of 5 in 7kvu

Go back to Fluorine Binding Sites List in 7kvu
Fluorine binding site 3 out of 5 in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F106

b:72.5
occ:1.00
F20 G:2ZY106 0.0 72.5 1.0
C19 G:2ZY106 1.4 75.0 1.0
F21 G:2ZY106 2.3 76.4 1.0
F22 G:2ZY106 2.3 74.1 1.0
C16 G:2ZY106 2.3 76.8 1.0
N14 G:2ZY106 2.7 68.9 1.0
O18 G:2ZY106 2.9 75.2 1.0
C15 G:2ZY106 3.0 69.0 1.0
O4' G:U15 3.1 72.2 1.0
C4' G:U15 3.3 71.3 1.0
C13 G:2ZY106 3.7 66.7 1.0
C1' G:U15 3.8 69.4 1.0
O2' G:U15 3.8 70.0 1.0
C5' G:U15 4.1 69.8 1.0
C11 G:2ZY106 4.1 65.6 1.0
C2' G:U15 4.3 71.2 1.0
C3' G:U15 4.4 72.9 1.0
N12 G:2ZY106 4.5 65.5 1.0
C17 G:2ZY106 4.5 67.6 1.0
O2' G:U39 4.7 76.4 1.0
N6 G:A48 4.9 74.5 1.0
C10 G:2ZY106 5.0 64.6 1.0

Fluorine binding site 4 out of 5 in 7kvu

Go back to Fluorine Binding Sites List in 7kvu
Fluorine binding site 4 out of 5 in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F106

b:76.4
occ:1.00
F21 G:2ZY106 0.0 76.4 1.0
C19 G:2ZY106 1.4 75.0 1.0
F22 G:2ZY106 2.2 74.1 1.0
F20 G:2ZY106 2.3 72.5 1.0
C16 G:2ZY106 2.4 76.8 1.0
O2' G:U39 2.9 76.4 1.0
N14 G:2ZY106 3.6 68.9 1.0
O2 G:U39 3.7 76.6 1.0
C2' G:U39 3.9 81.4 1.0
C1' G:U39 4.0 82.9 1.0
C15 G:2ZY106 4.5 69.0 1.0
C13 G:2ZY106 4.5 66.7 1.0
O18 G:2ZY106 4.5 75.2 1.0
N6 G:A48 4.6 74.5 1.0
C17 G:2ZY106 4.6 67.6 1.0
C2 G:U39 4.7 76.5 1.0
O2' G:U15 4.9 70.0 1.0
O4' G:A40 4.9 69.6 1.0
O4' G:U39 4.9 92.4 1.0
N1 G:U39 4.9 78.9 1.0

Fluorine binding site 5 out of 5 in 7kvu

Go back to Fluorine Binding Sites List in 7kvu
Fluorine binding site 5 out of 5 in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F106

b:74.1
occ:1.00
F22 G:2ZY106 0.0 74.1 1.0
C19 G:2ZY106 1.4 75.0 1.0
F21 G:2ZY106 2.2 76.4 1.0
F20 G:2ZY106 2.3 72.5 1.0
C16 G:2ZY106 2.3 76.8 1.0
N14 G:2ZY106 2.8 68.9 1.0
N6 G:A48 2.8 74.5 1.0
O2' G:U15 3.0 70.0 1.0
C17 G:2ZY106 3.1 67.6 1.0
C13 G:2ZY106 3.1 66.7 1.0
O2 G:U39 3.3 76.6 1.0
C6 G:A48 3.7 72.8 1.0
C15 G:2ZY106 3.8 69.0 1.0
C1' G:U15 4.0 69.4 1.0
O4' G:U15 4.1 72.2 1.0
C2' G:U15 4.1 71.2 1.0
N1 G:A48 4.1 73.9 1.0
N12 G:2ZY106 4.2 65.5 1.0
O18 G:2ZY106 4.3 75.2 1.0
C4' G:U15 4.3 71.3 1.0
O2' G:U39 4.3 76.4 1.0
C11 G:2ZY106 4.5 65.6 1.0
C2 G:U39 4.5 76.5 1.0
C5 G:A48 4.8 72.4 1.0
C3' G:U15 4.8 72.9 1.0
C1' G:U39 5.0 82.9 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: Tue Jul 15 20:57:15 2025

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