Sodium in PDB 6dmd: Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure

The structure of Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure, PDB code: 6dmd 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)	30.00 / 2.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	78.741, 49.595, 79.365, 90.00, 97.29, 90.00
R / Rfree (%)	21.7 / 27.2

The structure of Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure also contains other interesting chemical elements:

Magnesium	(Mg)	8 atoms
Potassium	(K)	1 atom
Manganese	(Mn)	10 atoms

The binding sites of Sodium atom in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure (pdb code 6dmd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure, PDB code: 6dmd:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na208 b:23.7 occ:1.00 OP2 A:C11 3.0 47.3 1.0 N7 A:A41 3.5 23.6 1.0 OP2 A:A41 4.0 24.5 1.0 C8 A:A41 4.3 23.1 1.0 P A:C11 4.4 49.2 1.0 C5 A:A41 4.5 23.3 1.0 N6 A:A41 4.6 22.4 1.0 OP2 A:C40 4.7 29.0 1.0 C5 A:C40 5.0 21.2 1.0 C6 A:A41 5.0 22.4 1.0 OP1 A:C11 5.0 55.9 1.0

Sodium binding site 2 out of 8 in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na209 b:35.6 occ:1.00 N7 A:G32 4.1 39.6 1.0 O6 A:G32 4.3 36.8 1.0 N7 A:G33 4.8 33.5 1.0 C5 A:G32 4.9 38.3 1.0 C6 A:G32 5.0 37.4 1.0 O A:HOH303 5.0 36.2 1.0 O6 A:G33 5.0 32.1 1.0

Sodium binding site 3 out of 8 in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na210 b:50.2 occ:1.00 O A:HOH316 2.6 41.6 1.0

Sodium binding site 4 out of 8 in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na211 b:22.0 occ:1.00 O6 A:G45 4.3 26.0 1.0 OP2 A:C44 4.3 20.5 1.0 O6 A:G46 4.3 24.3 1.0 OP1 A:C44 4.4 21.9 1.0 N7 A:G45 4.4 27.1 1.0 N7 A:G46 4.5 24.4 1.0 C5' A:A42 4.7 22.5 1.0 P A:C44 4.7 21.3 1.0 C6 A:G45 4.8 26.4 1.0 O A:HOH308 4.8 19.6 1.0 C5 A:G45 4.8 26.1 1.0 O5' A:A42 4.9 23.0 1.0

Sodium binding site 5 out of 8 in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na212 b:71.7 occ:1.00 OP2 A:A84 2.5 37.2 1.0 O4 A:U81 3.1 36.3 1.0 N7 A:A80 3.5 40.5 1.0 P A:A84 3.8 38.1 1.0 C4 A:U81 4.1 37.6 1.0 C8 A:A80 4.2 41.2 1.0 O5' A:A84 4.3 35.4 1.0 OP1 A:A84 4.3 38.2 1.0 C5 A:A80 4.5 39.7 1.0 C5 A:U81 4.5 38.4 1.0 N6 A:A80 4.6 39.5 1.0 OP2 A:A80 4.8 49.9 1.0 C6 A:A80 5.0 38.3 1.0

Sodium binding site 6 out of 8 in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Na206 b:36.3 occ:1.00 OP1 B:C44 4.1 46.7 1.0 OP2 B:C44 4.1 46.4 1.0 N7 B:G46 4.1 61.7 1.0 O6 B:G45 4.2 50.8 1.0 N7 B:G45 4.3 49.3 1.0 O6 B:G46 4.5 60.0 1.0 P B:C44 4.5 46.8 1.0 C6 B:G45 4.7 50.0 1.0 C5 B:G45 4.7 50.2 1.0 C5' B:A42 4.9 42.1 1.0

Sodium binding site 7 out of 8 in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Na207 b:33.8 occ:1.00 O6 B:G32 3.8 50.3 1.0 N7 B:G32 3.9 48.0 1.0 C6 B:G32 4.5 50.0 1.0 C5 B:G32 4.6 50.2 1.0 O6 B:G33 4.7 49.1 1.0

Sodium binding site 8 out of 8 in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Na208 b:47.6 occ:1.00 OP1 B:G66 2.3 75.3 1.0 P B:G66 3.4 80.2 1.0 OP2 B:G66 3.6 73.7 1.0 O5' B:G66 4.3 73.3 1.0 OP2 B:U67 4.4 57.7 1.0 O3' B:G65 4.6 78.8 1.0 C5' B:G66 4.8 72.0 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