Potassium in PDB 6ck5: Prpp Riboswitch From T. Mathranii Bound to Prpp

The structure of Prpp Riboswitch From T. Mathranii Bound to Prpp, PDB code: 6ck5 was solved by A.J.Knappenberger, C.W.Reiss, S.A.Strobel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.35 / 2.49
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	33.977, 89.575, 136.367, 90.00, 96.90, 90.00
R / Rfree (%)	21.5 / 25.2

The structure of Prpp Riboswitch From T. Mathranii Bound to Prpp also contains other interesting chemical elements:

Magnesium	(Mg)	8 atoms
Barium	(Ba)	20 atoms

The binding sites of Potassium atom in the Prpp Riboswitch From T. Mathranii Bound to Prpp (pdb code 6ck5). 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 From T. Mathranii Bound to Prpp, PDB code: 6ck5:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the Prpp Riboswitch From T. Mathranii Bound to Prpp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Prpp Riboswitch From T. Mathranii Bound to Prpp within 5.0Å range: probe atom residue distance (Å) B Occ A:K216 b:83.5 occ:1.00 N7 A:G99 3.1 74.8 1.0 O6 A:G99 3.6 73.6 1.0 C5 A:G99 3.9 71.0 1.0 N7 A:G100 4.1 81.0 1.0 C8 A:G99 4.1 67.7 1.0 C6 A:G99 4.1 66.2 1.0 N7 A:A98 4.1 76.2 1.0 O6 A:G100 4.3 67.6 1.0 C5 A:A98 4.4 60.6 1.0 C8 A:A98 4.6 66.6 1.0 C6 A:A98 4.7 60.4 1.0 N6 A:A98 4.7 62.8 1.0 C5 A:G100 4.8 78.1 1.0 C6 A:G100 4.9 75.0 1.0 OP2 A:G99 5.0 84.9 1.0

Potassium binding site 2 out of 3 in the Prpp Riboswitch From T. Mathranii Bound to Prpp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Prpp Riboswitch From T. Mathranii Bound to Prpp within 5.0Å range: probe atom residue distance (Å) B Occ B:K214 b:94.4 occ:1.00 OP1 B:C49 3.5 76.0 1.0 O6 B:G51 4.3 59.2 1.0 N7 B:G51 4.4 69.1 1.0 O6 B:G50 4.5 64.8 1.0 N7 B:G50 4.5 74.4 1.0 P B:C49 4.5 67.4 1.0 O4 B:U52 4.6 0.3 1.0 OP2 B:C49 4.6 84.0 1.0 C5' B:A47 4.7 49.2 1.0 C6 B:G50 4.8 68.2 1.0 C5 B:G50 4.8 68.8 1.0

Potassium binding site 3 out of 3 in the Prpp Riboswitch From T. Mathranii Bound to Prpp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Prpp Riboswitch From T. Mathranii Bound to Prpp within 5.0Å range: probe atom residue distance (Å) B Occ B:K215 b:65.0 occ:1.00 OP2 B:C45 2.5 44.2 1.0 OP2 B:C12 3.1 75.1 1.0 N7 B:G46 3.2 54.2 1.0 O6 B:G46 3.3 55.7 1.0 C5 B:G46 3.9 62.8 1.0 C6 B:G46 4.0 71.6 1.0 P B:C45 4.0 82.6 1.0 C5 B:C45 4.1 49.3 1.0 C8 B:G46 4.3 55.5 1.0 C6 B:C45 4.4 53.7 1.0 P B:C12 4.5 83.3 1.0 O3' B:C44 4.8 56.8 1.0 OP1 B:C45 4.8 55.0 1.0 O5' B:C45 4.8 60.4 1.0 C5' B:C12 5.0 97.1 1.0

A.J.Knappenberger, C.W.Reiss, S.A.Strobel. Structures of Two Aptamers with Differing Ligand Specificity Reveal Ruggedness in the Functional Landscape of Rna. Elife V. 7 2018.
ISSN: ESSN 2050-084X
PubMed: 29877798
DOI: 10.7554/ELIFE.36381