Potassium in PDB 6dmc: Ppgpp Riboswitch Bound to Ppgpp, Native Structure

The structure of Ppgpp Riboswitch Bound to Ppgpp, Native Structure, PDB code: 6dmc 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)	20.00 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	78.162, 48.917, 78.723, 90.00, 97.33, 90.00
R / Rfree (%)	22.8 / 25.9

The structure of Ppgpp Riboswitch Bound to Ppgpp, Native Structure also contains other interesting chemical elements:

Magnesium	(Mg)	21 atoms
Sodium	(Na)	10 atoms

The binding sites of Potassium atom in the Ppgpp Riboswitch Bound to Ppgpp, Native Structure (pdb code 6dmc). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total only one binding site of Potassium was determined in the Ppgpp Riboswitch Bound to Ppgpp, Native Structure, PDB code: 6dmc:

Potassium binding site 1 out of 1 in the Ppgpp Riboswitch Bound to Ppgpp, Native Structure


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Ppgpp Riboswitch Bound to Ppgpp, Native Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:K220 b:67.0 occ:1.00 N7 A:G36 3.3 31.1 1.0 N6 A:A38 3.3 26.6 1.0 O A:HOH386 3.5 17.3 1.0 N7 A:G37 3.5 30.5 1.0 N1 A:A17 3.6 27.2 1.0 O A:HOH310 3.6 33.3 1.0 C5 A:G36 3.7 31.1 1.0 C6 A:A38 3.7 27.2 1.0 C8 A:G36 3.7 31.6 1.0 O6 A:G37 3.8 27.4 1.0 N3 A:A35 3.9 28.4 1.0 N6 A:A17 4.1 28.1 1.0 C6 A:G36 4.2 31.4 1.0 C5 A:A38 4.2 27.8 1.0 N1 A:A38 4.3 26.9 1.0 N9 A:G36 4.3 30.5 1.0 C5 A:G37 4.3 30.3 1.0 C4 A:G36 4.3 30.3 1.0 C6 A:A17 4.3 26.8 1.0 O6 A:G36 4.3 30.8 1.0 O2' A:A35 4.4 32.6 1.0 C6 A:G37 4.4 29.5 1.0 O6 A:G16 4.5 24.4 1.0 C2 A:A35 4.5 27.9 1.0 C2 A:A17 4.5 27.7 1.0 N7 A:A38 4.5 29.0 1.0 C8 A:G37 4.5 30.2 1.0 C1' A:A35 4.6 31.0 1.0 O3' A:A35 4.7 32.5 1.0 C4 A:A35 4.8 28.9 1.0 C5' A:G36 4.8 30.3 1.0 O A:HOH367 4.9 33.2 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