Iridium 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
Fluorine	(F)	5 atoms

The binding sites of Iridium 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 Iridium atom.
In total 3 binding sites of Iridium where determined in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T with Iridium (III) Ions, PDB code: 7kvt:
Jump to Iridium binding site number: 1; 2; 3;

Iridium binding site 1 out of 3 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 Iridium with other atoms in the Ir 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:Ir102 b:160.3 occ:0.56 IR B:IRI102 0.0 160.3 0.6 N2 B:IRI102 2.3 92.3 0.6 N3 B:IRI102 2.3 99.6 0.6 N6 B:IRI102 2.3 133.7 0.6 N1 B:IRI102 2.3 134.1 0.6 N4 B:IRI102 2.3 135.9 0.6 N5 B:IRI102 2.3 100.2 0.6 O6 B:G2 3.8 71.2 1.0 O6 B:G3 4.1 78.3 1.0 N7 B:G2 4.4 82.7 1.0 C6 B:G2 4.6 75.8 1.0 C5 B:G2 4.9 76.4 1.0

Iridium binding site 2 out of 3 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 Iridium with other atoms in the Ir 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:Ir103 b:130.6 occ:0.43 IR B:IRI103 0.0 130.6 0.4 N1 B:IRI103 2.3 85.1 0.4 N2 B:IRI103 2.3 85.9 0.4 N6 B:IRI103 2.3 95.3 0.4 N3 B:IRI103 2.3 91.1 0.4 N4 B:IRI103 2.3 95.2 0.4 N5 B:IRI103 2.3 84.5 0.4 O2' B:A17 3.6 75.4 1.0 OP2 B:U33 3.9 64.8 1.0 OP2 B:A49 4.4 71.9 1.0 OP2 B:G18 4.7 82.2 1.0 O3' B:A17 4.7 70.7 1.0 C2' B:A17 4.9 68.6 1.0

Iridium binding site 3 out of 3 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 Iridium with other atoms in the Ir 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:Ir104 b:148.0 occ:0.48 IR B:IRI104 0.0 148.0 0.5 N1 B:IRI104 2.3 91.7 0.5 N5 B:IRI104 2.3 90.1 0.5 N4 B:IRI104 2.3 88.3 0.5 N3 B:IRI104 2.3 105.8 0.5 N6 B:IRI104 2.3 91.1 0.5 N2 B:IRI104 2.3 92.1 0.5 O6 B:G37 4.2 84.9 1.0 O4 B:U38 4.4 89.6 1.0 O6 B:G36 4.4 82.2 1.0 N7 B:G36 4.4 81.5 1.0 N7 B:G37 4.5 79.6 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