Potassium in PDB 4yb0: 3',3'-Cgamp Riboswitch Bound with C-Di-Gmp

The structure of 3',3'-Cgamp Riboswitch Bound with C-Di-Gmp, PDB code: 4yb0 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)	85.10 / 2.12
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	174.829, 44.901, 68.210, 90.00, 103.33, 90.00
R / Rfree (%)	22.8 / 26.2

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

Magnesium

(Mg)

5 atoms

The binding sites of Potassium atom in the 3',3'-Cgamp Riboswitch Bound with C-Di-Gmp (pdb code 4yb0). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the 3',3'-Cgamp Riboswitch Bound with C-Di-Gmp, PDB code: 4yb0:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the 3',3'-Cgamp Riboswitch Bound with C-Di-Gmp


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 C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ R:K106 b:57.7 occ:1.00 O R:HOH217 2.5 42.1 1.0 O R:HOH211 2.6 41.4 1.0 O6 R:G51 2.7 46.4 1.0 N3 R:A48 3.1 37.4 1.0 N7 R:G51 3.2 41.0 1.0 N1 R:A65 3.4 38.0 1.0 C6 R:G51 3.5 43.0 1.0 O6 R:G50 3.5 51.1 1.0 O4' R:A48 3.5 47.3 1.0 C5 R:G51 3.7 41.2 1.0 C2 R:A48 3.7 36.3 1.0 O6 R:G52 3.9 40.6 1.0 C2 R:A65 4.0 37.3 1.0 C6 R:G52 4.0 40.5 1.0 N7 R:G50 4.0 42.2 1.0 C1' R:A48 4.0 47.5 1.0 C4 R:A48 4.1 37.9 1.0 C6 R:G50 4.1 42.6 1.0 C5 R:G52 4.2 43.5 1.0 C6 R:A65 4.2 39.7 1.0 C5 R:G50 4.2 41.3 1.0 N7 R:G52 4.3 43.0 1.0 C4' R:A48 4.3 53.6 1.0 N6 R:A65 4.4 37.8 1.0 C8 R:G51 4.4 52.4 1.0 N9 R:A48 4.4 40.1 1.0 N1 R:G52 4.6 40.9 1.0 N4 R:C67 4.9 37.5 1.0 N1 R:G51 4.9 44.8 1.0 C4 R:G52 4.9 45.2 1.0 C8 R:G50 5.0 45.0 1.0 N1 R:A48 5.0 44.9 1.0

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


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 C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ R:K107 b:63.0 occ:1.00 O R:HOH221 2.6 54.0 1.0 N7 R:G35 2.6 49.7 1.0 O R:HOH223 2.7 67.1 1.0 O6 R:G36 2.8 52.2 1.0 O R:HOH216 2.9 41.6 1.0 C6 R:G36 3.4 45.8 1.0 N7 R:G34 3.5 46.2 1.0 C8 R:G35 3.5 54.3 1.0 C5 R:G35 3.7 46.6 1.0 O6 R:G35 3.9 42.9 1.0 C5 R:G36 4.0 43.5 1.0 C5 R:G34 4.0 43.6 1.0 O R:HOH220 4.1 42.9 1.0 O R:HOH224 4.1 52.1 1.0 N7 R:G36 4.1 53.4 1.0 O6 R:G34 4.1 42.6 1.0 C8 R:G34 4.1 46.6 1.0 C6 R:G35 4.2 45.3 1.0 N1 R:G36 4.3 44.5 1.0 C6 R:G34 4.3 42.8 1.0 N9 R:G35 4.7 50.3 1.0 OP2 R:G35 4.8 57.4 1.0 C4 R:G35 4.9 44.9 1.0 C4 R:G34 4.9 45.4 1.0 N9 R:G34 5.0 44.8 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