Magnesium in PDB 6db9: Structural Basis For Promiscuous Binding and Activation of Fluorogenic Dyes By DIR2S Rna Aptamer

The structure of Structural Basis For Promiscuous Binding and Activation of Fluorogenic Dyes By DIR2S Rna Aptamer, PDB code: 6db9 was solved by Y.Shao, S.A.Shelke, A.Laski, J.A.Piccirilli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.64 / 2.03
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	83.780, 83.805, 109.926, 90.00, 90.00, 90.00
R / Rfree (%)	23 / 25.7

The binding sites of Magnesium atom in the Structural Basis For Promiscuous Binding and Activation of Fluorogenic Dyes By DIR2S Rna Aptamer (pdb code 6db9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structural Basis For Promiscuous Binding and Activation of Fluorogenic Dyes By DIR2S Rna Aptamer, PDB code: 6db9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structural Basis For Promiscuous Binding and Activation of Fluorogenic Dyes By DIR2S Rna Aptamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Basis For Promiscuous Binding and Activation of Fluorogenic Dyes By DIR2S Rna Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg101 b:52.4 occ:1.00 OP2 R:G12 2.0 55.6 1.0 O R:HOH226 2.0 51.2 1.0 O R:HOH235 2.0 42.4 1.0 O R:HOH241 2.1 54.2 1.0 O R:HOH204 2.1 57.6 1.0 O R:HOH237 2.3 60.2 1.0 P R:G12 3.1 52.0 1.0 OP1 R:G12 3.5 52.2 1.0 O R:HOH233 4.1 45.5 1.0 O3' R:U11 4.2 51.7 1.0 O5' R:G12 4.3 50.7 1.0 N7 R:G33 4.3 49.3 1.0 O6 R:G33 4.4 49.5 1.0 N6 R:A32 4.5 50.4 1.0 O R:HOH216 4.6 46.3 1.0 C3' R:U11 4.7 50.4 1.0 N7 R:A32 4.7 58.1 1.0

Magnesium binding site 2 out of 2 in the Structural Basis For Promiscuous Binding and Activation of Fluorogenic Dyes By DIR2S Rna Aptamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Basis For Promiscuous Binding and Activation of Fluorogenic Dyes By DIR2S Rna Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg102 b:53.6 occ:1.00 O R:HOH254 2.1 55.3 1.0 OP1 R:G12 2.1 52.2 1.0 O R:HOH255 2.1 53.6 1.0 O R:HOH243 2.1 49.4 1.0 O R:HOH234 2.2 48.6 1.0 O R:HOH216 2.2 46.3 1.0 P R:G12 3.5 52.0 1.0 O3' R:U11 3.8 51.7 1.0 O R:HOH235 3.9 42.4 1.0 C5' R:G12 4.0 59.7 1.0 O5' R:G12 4.2 50.7 1.0 O R:HOH208 4.3 52.7 1.0 N7 R:A46 4.5 50.1 1.0 OP2 R:G12 4.6 55.6 1.0 N7 R:G47 4.6 52.2 1.0 O6 R:G47 4.7 44.7 1.0 N4 R:C48 4.7 44.4 1.0 N6 R:A46 4.8 46.3 1.0

S.A.Shelke, Y.Shao, A.Laski, D.Koirala, B.P.Weissman, J.R.Fuller, X.Tan, T.P.Constantin, A.S.Waggoner, M.P.Bruchez, B.A.Armitage, J.A.Piccirilli. Structural Basis For Activation of Fluorogenic Dyes By An Rna Aptamer Lacking A G-Quadruplex Motif. Nat Commun V. 9 4542 2018.
ISSN: ESSN 2041-1723
PubMed: 30382099
DOI: 10.1038/S41467-018-06942-3