Magnesium in PDB 6dnr: Prpp Riboswitch Bound to Prpp, Ligand-Free Structure

The structure of Prpp Riboswitch Bound to Prpp, Ligand-Free Structure, PDB code: 6dnr was solved by A.Peselis, A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.81 / 2.90
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	63.773, 63.773, 376.493, 90.00, 90.00, 120.00
R / Rfree (%)	21.2 / 27.3

The binding sites of Magnesium atom in the Prpp Riboswitch Bound to Prpp, Ligand-Free Structure (pdb code 6dnr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Prpp Riboswitch Bound to Prpp, Ligand-Free Structure, PDB code: 6dnr:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Prpp Riboswitch Bound to Prpp, Ligand-Free Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Prpp Riboswitch Bound to Prpp, Ligand-Free Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:0.9 occ:1.00 OP2 A:A14 3.8 0.7 1.0 OP1 A:G41 4.1 0.4 1.0 N7 A:G15 4.3 0.0 1.0 OP1 A:A14 4.4 0.9 1.0 O6 A:G15 4.5 0.3 1.0 OP2 A:G41 4.5 0.3 1.0 P A:A14 4.6 0.2 1.0 P A:G41 4.8 0.6 1.0 O6 A:G16 4.8 0.5 1.0 N7 A:G16 4.9 91.6 1.0 C5 A:G15 5.0 0.1 1.0

Magnesium binding site 2 out of 3 in the Prpp Riboswitch Bound to Prpp, Ligand-Free Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Prpp Riboswitch Bound to Prpp, Ligand-Free Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:90.9 occ:1.00 OP1 A:C91 2.3 0.8 1.0 OP2 A:G48 2.5 83.1 1.0 P A:C91 3.7 0.9 1.0 P A:G48 4.0 0.5 1.0 O3' A:C90 4.1 0.4 1.0 C5' A:G48 4.3 91.6 1.0 OP2 A:C91 4.6 84.8 1.0 O5' A:G48 4.7 91.3 1.0 O5' A:C91 4.8 99.7 1.0 O3' A:A47 4.8 0.7 1.0 C5' A:C91 4.8 86.0 1.0 O5' A:A47 4.9 0.9 1.0 OP1 A:G48 4.9 94.7 1.0

Magnesium binding site 3 out of 3 in the Prpp Riboswitch Bound to Prpp, Ligand-Free Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Prpp Riboswitch Bound to Prpp, Ligand-Free Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:86.1 occ:1.00 OP2 A:C91 2.0 84.8 1.0 OP1 A:C90 2.1 0.0 1.0 OP1 A:G48 2.2 94.7 1.0 P A:C90 3.3 96.4 1.0 P A:C91 3.5 0.9 1.0 P A:G48 3.5 0.5 1.0 OP2 A:C90 3.7 90.1 1.0 O5' A:C90 3.9 97.2 1.0 O3' A:A47 4.1 0.7 1.0 OP2 A:G48 4.2 83.1 1.0 O5' A:C91 4.3 99.7 1.0 N7 A:G48 4.3 0.2 1.0 OP1 A:C91 4.3 0.8 1.0 O3' A:C90 4.4 0.4 1.0 O2' A:A93 4.4 0.4 1.0 C3' A:C90 4.5 0.9 1.0 C5' A:C90 4.6 0.9 1.0 O3' A:G89 4.6 93.8 1.0 C8 A:G48 4.6 0.8 1.0 O5' A:G48 4.6 91.3 1.0 OP2 A:G94 4.7 0.8 1.0 O3' A:A93 4.8 0.8 1.0 OP2 A:C92 4.9 0.3 1.0

A.Peselis, A.Serganov. Ykkc Riboswitches Employ An Add-on Helix to Adjust Specificity For Polyanionic Ligands. Nat. Chem. Biol. V. 14 887 2018.
ISSN: ESSN 1552-4469
PubMed: 30120360
DOI: 10.1038/S41589-018-0114-4