Potassium in PDB 4yaz: 3',3'-Cgamp Riboswitch Bound with 3',3'-Cgamp

The structure of 3',3'-Cgamp Riboswitch Bound with 3',3'-Cgamp, PDB code: 4yaz was solved by A.M.Ren, D.J.Patel, R.K.Rajashankar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.50 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.623, 50.517, 78.657, 90.00, 90.92, 90.00
R / Rfree (%)	21.3 / 25

The structure of 3',3'-Cgamp Riboswitch Bound with 3',3'-Cgamp also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Potassium atom in the 3',3'-Cgamp Riboswitch Bound with 3',3'-Cgamp (pdb code 4yaz). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the 3',3'-Cgamp Riboswitch Bound with 3',3'-Cgamp, PDB code: 4yaz:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the 3',3'-Cgamp Riboswitch Bound with 3',3'-Cgamp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of 3',3'-Cgamp Riboswitch Bound with 3',3'-Cgamp within 5.0Å range: probe atom residue distance (Å) B Occ R:K105 b:40.6 occ:1.00 N3 R:A48 2.6 14.1 1.0 O R:HOH247 2.7 34.1 1.0 O4' R:A48 2.8 21.3 1.0 O R:HOH284 3.1 33.1 1.0 N7 R:G51 3.2 22.2 1.0 O6 R:G51 3.3 29.5 1.0 C2 R:A48 3.3 13.8 1.0 O R:HOH248 3.4 37.5 1.0 C1' R:A48 3.6 22.5 1.0 C4 R:A48 3.7 14.1 1.0 C4' R:A48 3.8 26.1 1.0 C5 R:G51 3.9 18.0 1.0 C6 R:G51 3.9 19.2 1.0 N1 R:A65 4.0 16.9 1.0 O6 R:G50 4.0 27.5 1.0 O6 R:G52 4.0 23.9 1.0 N9 R:A48 4.1 17.9 1.0 C2 R:A65 4.2 18.4 1.0 N7 R:G50 4.2 29.4 1.0 C8 R:G51 4.3 21.0 1.0 C6 R:G50 4.4 28.0 1.0 C5 R:G50 4.5 25.1 1.0 C6 R:G52 4.5 20.9 1.0 N1 R:A48 4.6 13.6 1.0 C5' R:A48 4.7 29.2 1.0 O3' R:A48 4.8 37.2 1.0 C3' R:A48 4.8 33.2 1.0 C5 R:G52 4.8 21.3 1.0 N4 R:C64 4.9 14.2 1.0 C6 R:A65 4.9 14.1 1.0 N7 R:G52 4.9 21.9 1.0 C5 R:A48 4.9 13.9 1.0 C2' R:A48 5.0 27.9 1.0

Potassium binding site 2 out of 3 in the 3',3'-Cgamp Riboswitch Bound with 3',3'-Cgamp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of 3',3'-Cgamp Riboswitch Bound with 3',3'-Cgamp within 5.0Å range: probe atom residue distance (Å) B Occ R:K107 b:60.4 occ:1.00 N3 A:A18 2.5 27.5 1.0 O2' R:A19 2.6 25.6 1.0 O2' A:A18 3.0 18.7 1.0 O A:HOH267 3.1 37.4 1.0 C2' A:A18 3.3 20.0 1.0 C2 A:A18 3.3 24.6 1.0 C2' R:A19 3.4 18.0 1.0 C1' A:A18 3.5 17.9 1.0 C4 A:A18 3.5 25.2 1.0 O4' A:A19 3.6 23.6 1.0 N3 R:A19 3.7 21.2 1.0 O R:HOH244 3.9 43.3 1.0 N9 A:A18 3.9 21.6 1.0 O4' R:C20 3.9 25.5 1.0 C1' R:A19 4.0 17.4 1.0 O2 A:C38 4.2 20.7 1.0 C4' R:C20 4.3 22.9 1.0 C1' A:A19 4.3 21.0 1.0 C5' R:C20 4.3 24.8 1.0 C2 R:A19 4.5 18.6 1.0 C4 R:A19 4.6 18.2 1.0 C4' A:A19 4.7 22.4 1.0 N1 A:A18 4.7 22.5 1.0 C3' R:A19 4.7 15.8 1.0 N9 R:A19 4.8 15.2 1.0 O4' A:A18 4.8 24.8 1.0 C5 A:A18 4.8 23.3 1.0 C3' A:A18 4.8 19.9 1.0 N9 A:A19 4.9 25.8 1.0 O2' A:C38 4.9 27.2 1.0 N2 A:G66 5.0 27.8 1.0

Potassium binding site 3 out of 3 in the 3',3'-Cgamp Riboswitch Bound with 3',3'-Cgamp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of 3',3'-Cgamp Riboswitch Bound with 3',3'-Cgamp within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:92.6 occ:1.00 N4 A:C58 2.8 47.4 1.0 C5 A:C58 3.0 34.9 1.0 C4 A:C58 3.3 38.5 1.0 C6 A:C58 4.2 24.0 1.0 N3 A:C58 4.7 27.8 1.0

A.Ren, X.C.Wang, C.A.Kellenberger, K.R.Rajashankar, R.A.Jones, M.C.Hammond, D.J.Patel. Structural Basis For Molecular Discrimination By A 3',3'-Cgamp Sensing Riboswitch. Cell Rep V. 11 1 2015.
ISSN: ESSN 2211-1247
PubMed: 25818298
DOI: 10.1016/J.CELREP.2015.03.004