Magnesium in PDB 6dlt: Prpp Riboswitch Bound to Prpp, Native Structure

The structure of Prpp Riboswitch Bound to Prpp, Native Structure, PDB code: 6dlt 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)	20.00 / 2.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	83.567, 90.756, 74.174, 90.00, 122.00, 90.00
R / Rfree (%)	22.5 / 24.3

The structure of Prpp Riboswitch Bound to Prpp, Native Structure also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

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

Magnesium binding site 1 out of 3 in the Prpp Riboswitch Bound to Prpp, Native 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, Native Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:53.1 occ:1.00 OP2 A:C91 2.1 45.6 1.0 OP1 A:C90 2.1 51.0 1.0 OP1 A:G48 2.2 53.6 1.0 P A:C90 3.3 49.8 1.0 P A:C91 3.5 55.2 1.0 P A:G48 3.6 54.4 1.0 OP2 A:C90 3.7 42.0 1.0 O A:HOH301 3.7 42.9 1.0 O3' A:A47 4.1 49.3 1.0 OP1 A:C91 4.1 49.3 1.0 O5' A:C90 4.1 45.6 1.0 N7 A:G48 4.2 52.5 1.0 O5' A:C91 4.3 40.1 1.0 OP2 A:G48 4.5 55.9 1.0 C8 A:G48 4.5 48.3 1.0 O3' A:G89 4.5 42.9 1.0 O2' A:A93 4.5 44.6 1.0 O3' A:C90 4.6 49.6 1.0 OP2 A:G94 4.6 43.5 1.0 C5' A:C90 4.6 44.3 1.0 O5' A:G48 4.7 54.9 1.0 O3' A:A93 4.8 49.6 1.0 C3' A:C90 4.8 40.9 1.0

Magnesium binding site 2 out of 3 in the Prpp Riboswitch Bound to Prpp, Native 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, Native Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:53.1 occ:1.00 OP1 A:C91 2.2 49.3 1.0 OP2 A:G48 2.5 55.9 1.0 P A:C91 3.6 55.2 1.0 P A:G48 3.8 54.4 1.0 O3' A:C90 4.1 49.6 1.0 OP1 A:G48 4.4 53.6 1.0 C5' A:G48 4.4 54.6 1.0 O5' A:C91 4.6 40.1 1.0 O5' A:G48 4.6 54.9 1.0 OP2 A:C91 4.6 45.6 1.0 C5' A:C91 4.7 36.0 1.0

Magnesium binding site 3 out of 3 in the Prpp Riboswitch Bound to Prpp, Native 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, Native Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:59.6 occ:1.00 O2P A:PRP207 2.2 49.2 1.0 O2 A:U49 2.7 53.5 1.0 OP2 A:C75 2.8 55.5 1.0 P A:PRP207 3.1 52.9 1.0 O3P A:PRP207 3.2 53.2 1.0 C2 A:U49 3.8 56.6 1.0 O1P A:PRP207 3.8 47.9 1.0 P A:C75 4.0 58.3 1.0 O5' A:C75 4.1 56.3 1.0 N3 A:U49 4.2 54.5 1.0 OP2 A:C76 4.2 44.8 1.0 C5 A:C75 4.4 51.4 1.0 O2' A:A74 4.5 54.5 1.0 O5 A:PRP207 4.5 55.1 1.0 C6 A:C75 4.6 48.6 1.0 O3' A:A74 4.6 55.5 1.0 C5 A:C76 4.7 44.4 1.0 N1 A:U49 5.0 57.0 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