Potassium in PDB 2xnz: Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to Acetoguanamine Identified By Virtual Screening

The structure of Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to Acetoguanamine Identified By Virtual Screening, PDB code: 2xnz was solved by P.Daldrop, F.E.Reyes, D.A.Robinson, C.M.Hammond, D.M.J.Lilley, R.T.Batey, R.Brenk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.08 / 1.59
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	132.165, 35.068, 41.798, 90.00, 90.06, 90.00
R / Rfree (%)	19.8 / 23.4

The structure of Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to Acetoguanamine Identified By Virtual Screening also contains other interesting chemical elements:

Cobalt

(Co)

6 atoms

The binding sites of Potassium atom in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to Acetoguanamine Identified By Virtual Screening (pdb code 2xnz). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to Acetoguanamine Identified By Virtual Screening, PDB code: 2xnz:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to Acetoguanamine Identified By Virtual Screening


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to Acetoguanamine Identified By Virtual Screening within 5.0Å range: probe atom residue distance (Å) B Occ A:K1089 b:52.6 occ:1.00 C4' A:A40 3.7 15.3 1.0 O A:HOH2008 3.7 29.6 1.0 C5' A:A40 3.8 16.2 1.0 O A:HOH2091 4.0 34.2 1.0 O4' A:A40 4.3 13.2 1.0 C3' A:A40 4.9 15.1 1.0 O2' A:A40 4.9 16.4 1.0 O3' A:A40 5.0 14.4 1.0

Potassium binding site 2 out of 6 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to Acetoguanamine Identified By Virtual Screening


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to Acetoguanamine Identified By Virtual Screening within 5.0Å range: probe atom residue distance (Å) B Occ A:K1090 b:36.2 occ:1.00 O2' A:U20 3.7 33.6 1.0 OP1 A:U48 3.9 36.4 1.0 O A:HOH2205 4.1 41.2 1.0 O4 A:U49 4.2 27.2 1.0 C4 A:U49 4.6 28.1 1.0 C5 A:U49 4.8 29.0 1.0 C2' A:U20 4.9 33.4 1.0 C5 A:U48 4.9 49.5 1.0 O2 A:U20 5.0 31.1 1.0 C6 A:U48 5.0 49.0 1.0

Potassium binding site 3 out of 6 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to Acetoguanamine Identified By Virtual Screening


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to Acetoguanamine Identified By Virtual Screening within 5.0Å range: probe atom residue distance (Å) B Occ A:K1091 b:32.1 occ:1.00 O A:HOH2084 2.4 32.9 1.0 O A:HOH2079 2.7 29.9 1.0 O A:HOH2142 3.7 34.6 1.0 OP2 A:G37 4.0 13.7 1.0 O A:HOH2146 4.0 25.0 1.0 O6 A:G38 4.3 14.4 1.0 O A:HOH2085 4.4 33.2 1.0 N7 A:G38 4.5 13.5 1.0 N7 A:G37 4.5 13.4 1.0 O A:HOH2081 5.0 31.3 1.0

Potassium binding site 4 out of 6 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to Acetoguanamine Identified By Virtual Screening


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to Acetoguanamine Identified By Virtual Screening within 5.0Å range: probe atom residue distance (Å) B Occ A:K1092 b:54.8 occ:1.00 O A:HOH2204 3.5 38.7 1.0 O2' A:C50 4.2 36.8 1.0 O2 A:C50 4.5 35.6 1.0 O4' A:U51 4.9 32.6 1.0

Potassium binding site 5 out of 6 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to Acetoguanamine Identified By Virtual Screening


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to Acetoguanamine Identified By Virtual Screening within 5.0Å range: probe atom residue distance (Å) B Occ A:K1093 b:56.2 occ:1.00 OP2 A:U22 4.1 26.3 1.0 OP1 A:A21 4.4 32.0 1.0 OP1 A:U22 5.0 28.7 1.0

Potassium binding site 6 out of 6 in the Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to Acetoguanamine Identified By Virtual Screening


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Xpt-Pbux C74U Riboswitch From B. Subtilis Bound to Acetoguanamine Identified By Virtual Screening within 5.0Å range: probe atom residue distance (Å) B Occ A:K1094 b:34.9 occ:1.00 OP1 A:C26 3.7 26.1 1.0 O A:HOH2177 4.0 30.7 1.0 O3' A:U25 4.2 25.1 1.0 OP1 A:U69 4.2 17.6 1.0 OP2 A:U69 4.6 15.2 1.0 P A:C26 4.7 23.3 1.0 O A:HOH2183 4.8 30.4 1.0 P A:U69 4.9 14.5 1.0 O A:HOH2181 5.0 26.6 1.0

P.Daldrop, F.E.Reyes, D.A.Robinson, C.M.Hammond, D.M.Lilley, R.T.Batey, R.Brenk. Novel Ligands For A Purine Riboswitch Discovered By Rna-Ligand Docking. Chem. Biol. V. 18 324 2011.
ISSN: ISSN 1879-1301
PubMed: 21439477
DOI: 10.1016/J.CHEMBIOL.2010.12.020