Sodium 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:

Magnesium

(Mg)

3 atoms

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

Sodium 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 Sodium with other atoms in the Na binding site number 1 of Prpp Riboswitch Bound to Prpp, Native Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:80.0 occ:0.50 OP1 A:C21 3.5 67.8 1.0 O3' A:C20 3.8 75.6 1.0 OP1 A:C33 4.1 81.7 1.0 P A:C21 4.2 78.1 1.0 OP2 A:C33 4.5 78.0 1.0 P A:C33 4.8 77.5 1.0 C3' A:C20 5.0 63.5 1.0

Sodium 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 Sodium with other atoms in the Na binding site number 2 of Prpp Riboswitch Bound to Prpp, Native Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:59.5 occ:1.00 O4' A:C39 3.8 52.1 1.0 C1' A:C39 4.0 49.9 1.0 N2 A:G36 4.0 68.5 1.0 N1 A:C39 4.1 49.2 1.0 C1' A:G24 4.2 78.0 1.0 C6 A:C39 4.4 49.8 1.0 O4' A:G24 4.4 76.6 1.0 C2 A:C39 4.5 58.8 1.0 O2 A:C39 4.8 65.3 1.0 O2' A:G24 4.8 77.8 1.0 O2 A:C23 5.0 69.5 1.0 N9 A:G24 5.0 75.0 1.0 N3 A:G24 5.0 69.3 1.0

Sodium 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 Sodium with other atoms in the Na binding site number 3 of Prpp Riboswitch Bound to Prpp, Native Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na206 b:62.6 occ:1.00 O6 A:G65 4.1 64.0 1.0 O2 A:U66 4.4 63.5 1.0 O2' A:U62 4.5 61.4 1.0 C6 A:G65 4.6 65.8 1.0 C5 A:U63 4.7 51.3 1.0 O4' A:G67 4.9 60.8 1.0 C1' A:G67 5.0 56.2 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