Potassium in PDB 3dil: Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine

The structure of Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, PDB code: 3dil was solved by A.A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.216, 78.953, 139.988, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 22.9

The structure of Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Sodium	(Na)	29 atoms

The binding sites of Potassium atom in the Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine (pdb code 3dil). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, PDB code: 3dil:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine within 5.0Å range: probe atom residue distance (Å) B Occ A:K200 b:13.7 occ:1.00 OXT A:LYS175 2.7 7.7 1.0 O A:HOH797 2.9 11.3 1.0 O2' A:G115 3.0 20.3 1.0 O4' A:G12 3.0 18.9 1.0 O4' A:G14 3.0 17.6 1.0 O2' A:G11 3.0 17.0 1.0 O A:HOH887 3.0 15.4 1.0 N3 A:G12 3.3 16.6 1.0 C A:LYS175 3.6 7.9 1.0 C4' A:G12 3.6 18.9 1.0 O A:LYS175 3.6 8.0 1.0 C1' A:G14 3.8 17.3 1.0 C4' A:G14 3.8 17.8 1.0 C2' A:G11 3.9 17.4 1.0 C1' A:G12 3.9 18.0 1.0 N2 A:G12 4.0 16.0 1.0 C2 A:G12 4.1 16.4 1.0 C2' A:G115 4.1 19.3 1.0 C4 A:G12 4.3 17.0 1.0 C5' A:G12 4.3 18.6 1.0 C1' A:G115 4.3 18.9 1.0 O2' A:G14 4.3 17.4 1.0 O A:HOH703 4.4 8.7 1.0 N9 A:G12 4.5 17.8 1.0 C5' A:G14 4.6 18.2 1.0 C3' A:G11 4.6 17.7 1.0 C2' A:G14 4.6 17.4 1.0 C3' A:G12 4.9 19.0 1.0 N9 A:G14 4.9 16.9 1.0 O4' A:G115 4.9 19.1 1.0 O A:HOH819 4.9 18.4 1.0 CA A:LYS175 5.0 7.9 1.0

Potassium binding site 2 out of 3 in the Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine within 5.0Å range: probe atom residue distance (Å) B Occ A:K230 b:44.4 occ:1.00 O A:HOH1045 2.6 23.2 1.0 O A:HOH1236 2.6 18.6 1.0 O A:HOH315 2.6 34.5 1.0 O A:HOH1235 2.7 18.0 1.0 O A:HOH925 2.7 15.8 1.0 NA A:NA211 3.6 16.7 1.0 O A:HOH634 3.7 23.6 1.0 O A:HOH334 3.7 22.5 1.0 O A:HOH1232 4.1 19.9 1.0 O A:HOH995 4.2 23.6 1.0 NA A:NA219 4.2 31.8 1.0 O A:HOH873 4.4 16.2 1.0 O A:HOH903 4.4 13.2 1.0 OP2 A:G116 4.6 19.4 1.0 O A:HOH357 4.6 28.5 1.0 OP2 A:A133 4.6 18.4 1.0 O A:HOH981 4.7 26.2 1.0 O A:HOH388 4.9 11.8 1.0 O A:HOH405 5.0 18.9 1.0

Potassium binding site 3 out of 3 in the Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine within 5.0Å range: probe atom residue distance (Å) B Occ A:K231 b:48.8 occ:1.00 O A:HOH792 2.5 20.4 1.0 O A:HOH689 2.7 27.2 1.0 O A:HOH456 2.8 25.4 1.0 O A:HOH1027 3.0 22.9 1.0 O4 A:U86 3.0 15.6 1.0 O A:HOH406 3.1 14.7 1.0 N6 A:A108 3.2 17.0 1.0 O A:HOH898 3.3 13.5 1.0 O A:HOH373 3.4 25.7 1.0 O A:HOH1015 3.4 17.6 1.0 N4 A:C107 3.5 17.9 1.0 O A:HOH557 3.8 24.9 1.0 O A:HOH366 3.9 23.0 1.0 O6 A:G87 4.2 17.7 1.0 C4 A:U86 4.2 15.5 1.0 NA A:NA226 4.2 35.8 1.0 O A:HOH931 4.3 20.1 1.0 C6 A:A108 4.4 17.0 1.0 O6 A:G85 4.6 17.3 1.0 C4 A:C107 4.8 18.0 1.0 O A:HOH996 4.8 9.7 1.0 N7 A:G85 4.8 17.1 1.0 O A:HOH896 5.0 21.2 1.0

A.Serganov, L.Huang, D.J.Patel. Structural Insights Into Amino Acid Binding and Gene Control By A Lysine Riboswitch. Nature V. 455 1263 2008.
ISSN: ISSN 0028-0836
PubMed: 18784651
DOI: 10.1038/NATURE07326