Potassium in PDB 2qbz: Structure of the M-Box Riboswitch Aptamer Domain

The structure of Structure of the M-Box Riboswitch Aptamer Domain, PDB code: 2qbz was solved by C.E.Dann Iii, W.C.Winkler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.67 / 2.60
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	48.655, 101.081, 285.765, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 24.6

The structure of Structure of the M-Box Riboswitch Aptamer Domain also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Potassium atom in the Structure of the M-Box Riboswitch Aptamer Domain (pdb code 2qbz). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Structure of the M-Box Riboswitch Aptamer Domain, PDB code: 2qbz:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the Structure of the M-Box Riboswitch Aptamer Domain


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of the M-Box Riboswitch Aptamer Domain within 5.0Å range: probe atom residue distance (Å) B Occ X:K301 b:26.8 occ:1.00 OP2 X:A155 2.6 18.9 1.0 O6 X:G157 2.9 18.4 1.0 O4 X:U28 2.9 15.1 1.0 O X:HOH359 3.0 11.4 1.0 O6 X:G27 3.1 24.7 1.0 N4 X:C158 3.3 20.5 1.0 N2 X:G29 3.4 24.9 1.0 O X:HOH391 3.4 45.7 1.0 C5' X:A155 3.6 21.0 1.0 N1 X:G29 3.7 22.5 1.0 P X:A155 3.8 16.8 1.0 C2 X:G29 3.8 24.6 1.0 C4 X:U28 3.8 17.0 1.0 N3 X:U28 3.9 17.4 1.0 C6 X:G157 3.9 19.6 1.0 O5' X:A155 4.1 18.1 1.0 C6 X:G27 4.2 24.8 1.0 N7 X:G157 4.3 21.5 1.0 C4 X:C158 4.4 21.4 1.0 C5 X:G157 4.5 20.3 1.0 OP1 X:A155 4.5 15.9 1.0 OP1 X:A156 4.6 17.9 1.0 O X:HOH380 4.6 14.4 1.0 C6 X:G29 4.7 22.3 1.0 N3 X:G29 4.8 23.8 1.0 N1 X:G27 4.9 24.9 1.0 N3 X:C158 5.0 22.4 1.0

Potassium binding site 2 out of 4 in the Structure of the M-Box Riboswitch Aptamer Domain


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of the M-Box Riboswitch Aptamer Domain within 5.0Å range: probe atom residue distance (Å) B Occ X:K302 b:39.7 occ:1.00 O2 X:C75 2.7 26.1 1.0 O2 X:U67 2.8 28.9 1.0 O2' X:A106 2.8 21.2 1.0 O3' X:A106 2.9 19.7 1.0 OP1 X:G107 3.1 18.2 1.0 O X:HOH407 3.2 21.2 1.0 P X:G107 3.7 18.7 1.0 C3' X:A106 3.7 20.2 1.0 C2' X:A106 3.8 20.9 1.0 N2 X:G66 3.8 25.6 1.0 C2 X:C75 3.8 25.5 1.0 C2 X:U67 3.9 28.9 1.0 C4' X:A106 3.9 21.0 1.0 C2 X:A74 4.1 24.3 1.0 C1' X:C75 4.3 23.7 1.0 O2' X:U67 4.3 30.3 1.0 O5' X:G107 4.4 17.3 1.0 N1 X:C75 4.5 24.6 1.0 C1' X:U67 4.6 27.9 1.0 N3 X:A74 4.6 23.5 1.0 O2' X:C75 4.6 21.9 1.0 C2' X:C75 4.7 23.1 1.0 N3 X:C75 4.8 26.2 1.0 O4' X:C68 4.8 26.1 1.0 N1 X:U67 4.8 29.2 1.0 C2' X:U67 4.8 28.9 1.0 N3 X:U67 4.8 29.2 1.0 O4' X:A106 4.9 21.4 1.0 C1' X:A106 4.9 21.9 1.0 OP2 X:G107 4.9 16.4 1.0 N1 X:A74 4.9 23.5 1.0 C2 X:G66 4.9 27.5 1.0 C5' X:A106 5.0 19.7 1.0

Potassium binding site 3 out of 4 in the Structure of the M-Box Riboswitch Aptamer Domain


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of the M-Box Riboswitch Aptamer Domain within 5.0Å range: probe atom residue distance (Å) B Occ X:K303 b:47.7 occ:1.00 O2 X:U161 2.9 34.2 1.0 O2' X:A72 3.0 20.1 1.0 O4' X:A25 3.0 17.6 1.0 O3' X:A72 3.2 17.2 1.0 O X:HOH418 3.2 14.3 1.0 C1' X:A25 3.7 18.6 1.0 C8 X:A25 3.8 19.4 1.0 N9 X:A25 3.8 20.4 1.0 N3 X:A162 3.8 31.8 1.0 C2 X:U161 3.9 32.3 1.0 C3' X:A72 4.0 18.2 1.0 C4' X:A72 4.0 17.9 1.0 C2' X:A72 4.0 17.9 1.0 OP1 X:G73 4.1 18.0 1.0 C2 X:A162 4.1 30.8 1.0 N3 X:U161 4.2 31.4 1.0 P X:G73 4.2 17.4 1.0 O5' X:A25 4.2 14.9 1.0 C4' X:A25 4.3 17.0 1.0 C5' X:A25 4.4 15.4 1.0 OP2 X:A25 4.5 16.4 1.0 O5' X:G73 4.5 16.9 1.0 N7 X:A25 4.7 19.7 1.0 C4 X:A162 4.8 32.1 1.0 C4 X:A25 4.8 21.7 1.0 O4' X:A72 4.8 18.8 1.0 P X:A25 4.8 15.7 1.0 O2 X:U23 4.9 10.4 1.0 C1' X:A72 5.0 19.5 1.0

Potassium binding site 4 out of 4 in the Structure of the M-Box Riboswitch Aptamer Domain


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of the M-Box Riboswitch Aptamer Domain within 5.0Å range: probe atom residue distance (Å) B Occ X:K304 b:38.0 occ:1.00 O X:HOH308 2.7 14.7 1.0 OP1 X:U24 2.8 12.6 1.0 OP1 X:U23 3.0 12.2 1.0 O X:HOH380 3.0 14.4 1.0 O X:HOH390 3.0 17.2 1.0 O X:HOH310 3.2 15.8 1.0 P X:U23 3.8 8.9 1.0 O X:HOH347 3.9 34.5 1.0 O5' X:U23 3.9 8.8 1.0 MG X:MG202 3.9 15.5 1.0 P X:U24 4.0 11.2 1.0 OP2 X:G157 4.1 18.0 1.0 O3' X:U23 4.2 11.6 1.0 O X:HOH417 4.2 31.4 1.0 OP2 X:U23 4.3 10.0 1.0 C5' X:U23 4.3 9.8 1.0 O2' X:C99 4.6 21.8 1.0 C3' X:U23 4.7 10.8 1.0 O5' X:U24 4.7 9.1 1.0 C4' X:A155 4.8 20.8 1.0

C.E.Dann Iii, C.A.Wakeman, C.L.Sieling, S.C.Baker, I.Irnov, W.C.Winkler. Structure and Mechanism of A Metal-Sensing Regulatory Rna Cell(Cambridge,Mass.) V. 130 878 2007.
ISSN: ISSN 0092-8674
PubMed: 17803910
DOI: 10.1016/J.CELL.2007.06.051