Magnesium in PDB 6dlr: Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure

The structure of Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure, PDB code: 6dlr 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)	19.54 / 2.66
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	83.520, 92.677, 74.487, 90.00, 121.21, 90.00
R / Rfree (%)	19.7 / 22.2

The structure of Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure also contains other interesting chemical elements:

Potassium	(K)	3 atoms
Iridium	(Ir)	18 atoms

The binding sites of Magnesium atom in the Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure (pdb code 6dlr). 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, Iridium-Hexamine Soaked Structure, PDB code: 6dlr:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked 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, Iridium-Hexamine Soaked Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg220 b:56.0 occ:1.00 OP2 A:C91 2.2 60.3 1.0 OP1 A:G48 2.2 51.3 1.0 OP1 A:C90 2.2 59.6 1.0 P A:C90 3.4 46.6 1.0 P A:C91 3.5 50.4 1.0 P A:G48 3.6 56.5 1.0 OP2 A:C90 3.8 47.0 1.0 N7 A:G48 4.0 56.5 1.0 O3' A:A47 4.1 55.2 1.0 OP1 A:C91 4.1 56.3 1.0 C8 A:G48 4.3 50.6 1.0 O5' A:C90 4.3 44.6 1.0 O5' A:C91 4.4 48.9 1.0 O2' A:A93 4.5 52.2 1.0 OP2 A:G48 4.5 53.0 1.0 O5' A:G48 4.6 51.4 1.0 O3' A:G89 4.6 51.3 1.0 O3' A:C90 4.6 58.9 1.0 C5' A:C90 4.6 49.3 1.0 OP2 A:G94 4.7 50.7 1.0 O3' A:A93 4.8 47.5 1.0 C3' A:C90 4.9 46.8 1.0

Magnesium binding site 2 out of 3 in the Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked 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, Iridium-Hexamine Soaked Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg221 b:75.7 occ:1.00 OP1 A:C91 2.1 56.3 1.0 OP2 A:G48 2.2 53.0 1.0 P A:G48 3.4 56.5 1.0 P A:C91 3.6 50.4 1.0 OP1 A:G48 3.7 51.3 1.0 C5' A:G48 4.0 46.7 1.0 O5' A:G48 4.1 51.4 1.0 O3' A:C90 4.3 58.9 1.0 OP2 A:C91 4.3 60.3 1.0 N2 A:IRI205 4.3 54.9 0.6 O5' A:C91 4.6 48.9 1.0 O3' A:A47 4.6 55.2 1.0 C5' A:C91 4.9 46.2 1.0

Magnesium binding site 3 out of 3 in the Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked 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, Iridium-Hexamine Soaked Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg222 b:60.6 occ:1.00 O2P A:PRP201 2.0 49.4 1.0 OP2 A:C75 2.4 53.9 1.0 O2 A:U49 2.4 61.3 1.0 P A:PRP201 2.9 46.2 1.0 O3P A:PRP201 3.0 48.9 1.0 O1P A:PRP201 3.5 47.1 1.0 C2 A:U49 3.6 61.4 1.0 P A:C75 3.8 58.3 1.0 O2' A:A74 4.1 45.7 1.0 N3 A:U49 4.2 58.3 1.0 O5' A:C75 4.2 58.1 1.0 O5 A:PRP201 4.3 45.7 1.0 O3' A:A74 4.3 57.9 1.0 C5 A:C75 4.4 49.9 1.0 C2' A:A74 4.5 52.1 1.0 N2 A:G48 4.7 48.2 1.0 N1 A:U49 4.7 54.8 1.0 C6 A:C75 4.7 54.3 1.0 N1 A:G48 4.7 53.8 1.0 N3 A:IRI208 4.7 39.1 0.8 N6 A:IRI208 4.8 76.6 0.8 OP2 A:C76 4.8 54.4 1.0 C5 A:C76 4.8 42.0 1.0 C1' A:U49 4.9 53.7 1.0 OP1 A:C75 5.0 56.0 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