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

The structure of Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T, PDB code: 7kvv 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)	52.14 / 2.85
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	104.271, 104.271, 52.107, 90, 90, 90
R / Rfree (%)	22.1 / 24.5

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

Magnesium

(Mg)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T (pdb code 7kvv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T, PDB code: 7kvv:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 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 D:F302 b:79.6 occ:1.00 F1 D:747302 0.0 79.6 1.0 C2 D:747302 1.4 82.0 1.0 C1 D:747302 2.4 80.2 1.0 C3 D:747302 2.4 82.7 1.0 O1 D:747302 2.8 81.6 1.0 C8 D:A69 3.1 82.4 1.0 N7 D:A69 3.2 82.5 1.0 N9 D:A69 3.3 82.2 1.0 N1 D:A70 3.3 78.1 1.0 O2' D:A69 3.4 78.5 1.0 C2 D:A70 3.4 78.7 1.0 C5 D:A69 3.4 82.7 1.0 C6 D:A70 3.4 78.0 1.0 C4 D:A69 3.5 82.1 1.0 C5 D:A70 3.6 84.5 1.0 N3 D:A70 3.6 82.0 1.0 C D:747302 3.6 84.1 1.0 C4 D:747302 3.7 83.7 1.0 C4 D:A70 3.7 74.0 1.0 C2' D:A69 4.0 85.2 1.0 C1' D:A69 4.0 84.1 1.0 N6 D:A70 4.1 78.1 1.0 C5 D:747302 4.1 84.8 1.0 C6 D:A69 4.2 83.0 1.0 N3 D:A69 4.3 81.3 1.0 N3 D:U15 4.3 85.1 1.0 N7 D:A70 4.4 78.5 1.0 N9 D:A70 4.5 88.2 1.0 N2 D:G13 4.5 82.7 1.0 O4 D:U15 4.5 83.6 1.0 O2' D:A70 4.6 82.2 1.0 C4 D:U15 4.7 84.1 1.0 F D:747302 4.8 85.5 1.0 C8 D:A70 4.8 79.6 1.0 N13 D:747302 4.8 84.7 1.0 C2 D:A69 4.8 82.8 1.0 N6 D:A69 4.9 84.5 1.0 N1 D:A69 4.9 82.9 1.0 C6 D:747302 4.9 85.5 1.0 C2 D:U15 5.0 86.8 1.0

Fluorine binding site 2 out of 2 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 D:F302 b:85.5 occ:1.00 F D:747302 0.0 85.5 1.0 C D:747302 1.4 84.1 1.0 C1 D:747302 2.4 80.2 1.0 C5 D:747302 2.4 84.8 1.0 O1 D:747302 2.8 81.6 1.0 N1 D:G13 2.9 85.2 1.0 N3 D:G14 3.2 96.9 1.0 C2 D:G13 3.2 84.5 1.0 N2 D:G14 3.3 93.2 1.0 C2 D:G14 3.3 97.7 1.0 C6 D:G13 3.4 87.3 1.0 N2 D:G13 3.6 82.7 1.0 C2 D:747302 3.6 82.0 1.0 C4 D:747302 3.6 83.7 1.0 O2' D:A70 3.8 82.2 1.0 O6 D:G13 3.8 87.1 1.0 N3 D:G13 3.9 85.7 1.0 C5 D:G13 3.9 89.5 1.0 C4 D:G14 3.9 96.6 1.0 C4 D:G13 4.1 89.9 1.0 N1 D:G14 4.1 112.0 1.0 C3 D:747302 4.1 82.7 1.0 N9 D:G14 4.7 97.7 1.0 C5 D:G14 4.7 97.0 1.0 F1 D:747302 4.8 79.6 1.0 O4 D:U15 4.8 83.6 1.0 C6 D:G14 4.9 95.6 1.0 C1' D:G14 4.9 98.3 1.0 C6 D:747302 4.9 85.5 1.0 O4' D:G14 4.9 94.5 1.0 C2' D:A70 4.9 82.4 1.0 N7 D:G13 5.0 90.2 1.0

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