Fluorine in PDB 7kvt: Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions

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

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

Magnesium	(Mg)	2 atoms
Iridium	(Ir)	3 atoms

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 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 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 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 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 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

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