Potassium in PDB 7kvu: 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: 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

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

Magnesium	(Mg)	4 atoms
Fluorine	(F)	5 atoms

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

Potassium binding site 1 out of 3 in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K103 b:91.6 occ:1.00 O G:HOH208 4.2 77.4 1.0 O6 G:G36 4.2 85.7 1.0 O6 G:G37 4.2 93.3 1.0 N7 G:G36 4.3 86.2 1.0 N7 G:G37 4.6 84.2 1.0 C6 G:G36 4.8 84.9 1.0 C5 G:G36 4.9 83.7 1.0 O4 G:U38 4.9 93.0 1.0 N7 G:G35 4.9 84.5 1.0

Potassium binding site 2 out of 3 in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K104 b:94.1 occ:1.00 O2' G:A17 3.7 77.9 1.0 OP2 G:U33 3.9 73.4 1.0 OP2 G:A49 4.3 73.0 1.0 O3' G:A17 4.7 75.1 1.0 OP2 G:G18 4.8 83.9 1.0

Potassium binding site 3 out of 3 in the Crystal Structure of Squash Rna Aptamer in Complex with Dfhbi-1T


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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:K105 b:99.5 occ:1.00 O6 G:G2 4.0 73.9 1.0 N7 G:G2 4.4 83.1 1.0 O6 G:G3 4.6 76.1 1.0 C6 G:G2 4.8 76.2 1.0 C5 G:G2 5.0 79.1 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