Potassium in PDB 6dlr: Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure

The structure of Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure, PDB code: 6dlr was solved by A.Peselis, A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.54 / 2.66
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	83.520, 92.677, 74.487, 90.00, 121.21, 90.00
R / Rfree (%)	19.7 / 22.2

The structure of Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure also contains other interesting chemical elements:

Magnesium	(Mg)	3 atoms
Iridium	(Ir)	18 atoms

The binding sites of Potassium atom in the Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure (pdb code 6dlr). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure, PDB code: 6dlr:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:K224 b:86.8 occ:1.00 N2 A:G36 3.6 56.7 1.0 C1' A:G24 4.1 64.3 1.0 O4' A:G24 4.2 69.0 1.0 O4' A:C39 4.2 59.0 1.0 C1' A:C39 4.3 49.2 1.0 O2' A:G24 4.4 66.8 1.0 N1 A:C39 4.6 50.4 1.0 C2 A:G36 4.8 55.4 1.0 O2 A:C23 4.8 60.0 1.0 C6 A:C39 4.9 48.2 1.0 C2' A:G24 4.9 69.7 1.0 N9 A:G24 5.0 57.9 1.0 C2 A:C39 5.0 56.2 1.0

Potassium binding site 2 out of 3 in the Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:K225 b:0.2 occ:1.00 OP1 A:G69 4.5 84.7 1.0

Potassium binding site 3 out of 3 in the Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:K226 b:0.9 occ:1.00 OP2 A:A101 3.9 0.2 1.0 OP1 A:G1 4.8 0.8 1.0

A.Peselis, A.Serganov. Ykkc Riboswitches Employ An Add-on Helix to Adjust Specificity For Polyanionic Ligands. Nat. Chem. Biol. V. 14 887 2018.
ISSN: ESSN 1552-4469
PubMed: 30120360
DOI: 10.1038/S41589-018-0114-4