Magnesium in PDB 6dmc: Ppgpp Riboswitch Bound to Ppgpp, Native Structure

The structure of Ppgpp Riboswitch Bound to Ppgpp, Native Structure, PDB code: 6dmc 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 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	78.162, 48.917, 78.723, 90.00, 97.33, 90.00
R / Rfree (%)	22.8 / 25.9

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

Potassium	(K)	1 atom
Sodium	(Na)	10 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Magnesium atom in the Ppgpp Riboswitch Bound to Ppgpp, Native Structure (pdb code 6dmc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 21 binding sites of Magnesium where determined in the Ppgpp Riboswitch Bound to Ppgpp, Native Structure, PDB code: 6dmc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 21 in the Ppgpp Riboswitch Bound to Ppgpp, Native Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ppgpp Riboswitch Bound to Ppgpp, Native Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:36.9 occ:1.00 O A:HOH384 1.9 43.0 1.0 O1B A:G4P201 2.1 39.7 1.0 O2A A:G4P201 2.2 33.0 1.0 O A:HOH350 2.2 31.3 1.0 O A:HOH377 2.4 24.7 1.0 N7 A:A3 2.7 31.0 1.0 PB A:G4P201 3.1 39.6 1.0 PA A:G4P201 3.3 33.0 1.0 O3B A:G4P201 3.5 38.8 1.0 O3A A:G4P201 3.5 35.1 1.0 C8 A:A3 3.6 30.2 1.0 C5 A:A3 3.6 30.4 1.0 N6 A:A3 3.7 31.5 1.0 O A:HOH303 3.7 31.7 1.0 O5' A:G4P201 3.9 29.9 1.0 C6 A:A3 4.1 30.4 1.0 N7 A:A4 4.2 25.9 1.0 O2B A:G4P201 4.5 38.3 1.0 O A:HOH362 4.5 19.4 1.0 O6 A:G5 4.6 24.8 1.0 O1A A:G4P201 4.6 33.9 1.0 N9 A:A3 4.8 29.3 1.0 OP2 A:A3 4.8 30.0 1.0 N7 A:G2 4.8 26.0 1.0 C4 A:A3 4.8 29.9 1.0 N6 A:A4 4.9 25.0 1.0

Magnesium binding site 2 out of 21 in the Ppgpp Riboswitch Bound to Ppgpp, Native Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ppgpp Riboswitch Bound to Ppgpp, Native Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:23.5 occ:1.00 O A:HOH406 2.0 14.7 1.0 OP2 A:A13 2.1 28.1 1.0 O A:HOH378 2.1 24.0 1.0 O A:HOH318 2.1 18.2 1.0 O A:HOH360 2.2 24.1 1.0 N7 A:G14 2.3 26.9 1.0 C8 A:G14 3.1 27.3 1.0 C5 A:G14 3.4 26.6 1.0 P A:A13 3.5 27.6 1.0 O A:HOH357 3.6 32.6 1.0 O A:HOH306 3.8 19.6 1.0 O6 A:G14 3.8 25.9 1.0 C6 A:G14 4.0 26.1 1.0 OP1 A:A13 4.2 27.8 1.0 O3' A:U12 4.3 27.4 1.0 N9 A:G14 4.4 27.4 1.0 O5' A:A13 4.5 27.2 1.0 N1 A:A41 4.5 26.5 1.0 C3' A:U12 4.5 27.7 1.0 C4 A:G14 4.5 26.6 1.0 O5' A:U12 4.8 33.7 1.0 C2 A:A41 5.0 26.3 1.0

Magnesium binding site 3 out of 21 in the Ppgpp Riboswitch Bound to Ppgpp, Native Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ppgpp Riboswitch Bound to Ppgpp, Native Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:35.9 occ:1.00 O A:HOH323 2.0 29.6 1.0 OP1 A:A13 2.2 27.8 1.0 OP2 A:G14 2.3 31.5 1.0 O A:HOH357 2.4 32.6 1.0 P A:A13 3.6 27.6 1.0 P A:G14 3.7 33.1 1.0 O5' A:A13 4.1 27.2 1.0 C5' A:A13 4.2 27.7 1.0 OP2 A:A13 4.3 28.1 1.0 OP1 A:G14 4.4 32.5 1.0 O5' A:G14 4.4 32.8 1.0 O3' A:U12 4.7 27.4 1.0 O3' A:A13 4.8 29.0 1.0 O A:HOH406 4.9 14.7 1.0

Magnesium binding site 4 out of 21 in the Ppgpp Riboswitch Bound to Ppgpp, Native Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ppgpp Riboswitch Bound to Ppgpp, Native Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg205 b:30.0 occ:1.00 OP1 A:A87 1.9 30.2 1.0 OP2 A:C88 1.9 30.0 1.0 OP1 A:G43 2.0 24.6 1.0 O A:HOH358 2.1 18.8 1.0 O A:HOH389 2.1 22.3 1.0 O A:HOH363 2.2 33.9 1.0 P A:A87 3.2 30.9 1.0 P A:C88 3.3 31.0 1.0 P A:G43 3.3 23.9 1.0 OP2 A:A87 3.8 28.5 1.0 O A:HOH343 3.8 21.9 1.0 O3' A:A42 3.9 25.4 1.0 OP1 A:C88 3.9 32.3 1.0 O5' A:A87 4.0 29.9 1.0 OP2 A:G43 4.1 24.5 1.0 O3' A:A87 4.2 30.3 1.0 N7 A:G43 4.2 25.1 1.0 C5' A:A87 4.2 28.4 1.0 C8 A:G43 4.3 25.2 1.0 O5' A:C88 4.3 32.0 1.0 O3' A:G86 4.4 33.8 1.0 O5' A:G43 4.5 23.0 1.0 C3' A:A87 4.5 27.7 1.0 C4' A:A87 4.9 28.4 1.0 MG A:MG208 5.0 48.0 1.0

Magnesium binding site 5 out of 21 in the Ppgpp Riboswitch Bound to Ppgpp, Native Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ppgpp Riboswitch Bound to Ppgpp, Native Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg206 b:44.0 occ:1.00 O A:HOH314 2.4 31.9 1.0 OP2 A:U81 4.2 42.2 1.0 OP2 A:A82 4.3 42.0 1.0 OP1 A:U81 4.3 48.6 1.0 OP2 A:A83 4.5 31.8 1.0 P A:U81 4.5 46.9 1.0 O5' A:U81 4.6 44.0 1.0 OP1 A:A83 4.7 33.0 1.0 P A:A83 5.0 34.8 1.0

Magnesium binding site 6 out of 21 in the Ppgpp Riboswitch Bound to Ppgpp, Native Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Ppgpp Riboswitch Bound to Ppgpp, Native Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg207 b:24.5 occ:1.00 O A:HOH325 1.9 22.8 1.0 OP2 A:C72 2.0 25.8 1.0 O A:HOH365 2.0 29.0 1.0 O A:HOH344 2.1 21.3 1.0 O A:HOH405 2.1 21.9 1.0 O2 A:C44 2.3 22.9 1.0 C2 A:C44 3.2 22.6 1.0 P A:C72 3.4 27.9 1.0 N3 A:C44 3.6 20.8 1.0 O A:HOH426 3.8 25.8 1.0 O3' A:A71 3.9 27.2 1.0 O A:HOH341 3.9 18.5 1.0 O A:HOH423 4.0 40.5 1.0 O5' A:C72 4.2 28.7 1.0 O2' A:A71 4.2 26.1 1.0 O1D A:G4P201 4.3 22.5 1.0 N1 A:C44 4.4 22.6 1.0 OP1 A:C72 4.4 24.9 1.0 C2' A:A71 4.6 26.7 1.0 C3' A:A71 4.7 27.1 1.0 C1' A:C44 4.7 23.6 1.0 C2' A:C44 4.8 24.3 1.0 N1 A:G43 4.8 24.6 1.0 C4 A:C44 4.9 21.7 1.0 C5 A:C72 4.9 30.0 1.0 O2' A:C44 5.0 23.4 1.0

Magnesium binding site 7 out of 21 in the Ppgpp Riboswitch Bound to Ppgpp, Native Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Ppgpp Riboswitch Bound to Ppgpp, Native Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg208 b:48.0 occ:1.00 O A:HOH301 1.9 36.4 1.0 OP1 A:C88 2.4 32.3 1.0 OP2 A:G43 2.4 24.5 1.0 P A:G43 3.5 23.9 1.0 P A:C88 3.8 31.0 1.0 C5' A:G43 3.9 23.8 1.0 OP1 A:G43 3.9 24.6 1.0 O5' A:G43 4.2 23.0 1.0 OP2 A:C88 4.4 30.0 1.0 O3' A:A87 4.6 30.3 1.0 O A:HOH389 4.6 22.3 1.0 O4' A:G43 4.7 24.0 1.0 O5' A:C88 4.8 32.0 1.0 C4' A:G43 4.9 24.1 1.0 O3' A:A42 4.9 25.4 1.0 MG A:MG205 5.0 30.0 1.0

Magnesium binding site 8 out of 21 in the Ppgpp Riboswitch Bound to Ppgpp, Native Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Ppgpp Riboswitch Bound to Ppgpp, Native Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg209 b:23.5 occ:1.00 O1C A:G4P201 1.9 24.7 1.0 O A:HOH307 2.0 13.7 1.0 O A:HOH311 2.0 15.2 1.0 O A:HOH399 2.0 17.0 1.0 O A:HOH345 2.0 13.2 1.0 O A:HOH395 2.1 19.1 1.0 PC A:G4P201 3.3 24.4 1.0 O3D A:G4P201 3.8 21.6 1.0 O2D A:G4P201 3.8 22.3 1.0 O3' A:G4P201 3.8 25.6 1.0 O3C A:G4P201 4.1 23.6 1.0 O6 A:G93 4.1 28.7 1.0 PD A:G4P201 4.1 23.6 1.0 O4 A:U92 4.2 32.4 1.0 O6 A:G94 4.3 26.9 1.0 O2C A:G4P201 4.4 23.0 1.0 N7 A:G93 4.5 28.2 1.0 N4 A:C72 4.6 30.9 1.0 C4 A:U92 4.6 31.6 1.0 O A:HOH324 4.8 37.8 1.0 N3 A:U92 4.9 31.3 1.0 C6 A:G93 4.9 28.8 1.0

Magnesium binding site 9 out of 21 in the Ppgpp Riboswitch Bound to Ppgpp, Native Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Ppgpp Riboswitch Bound to Ppgpp, Native Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg210 b:39.0 occ:1.00 O A:HOH366 2.0 31.6 1.0 O A:HOH326 2.2 27.8 1.0 O A:HOH368 2.3 33.5 1.0 O A:HOH353 2.3 19.0 1.0 O A:HOH422 2.4 36.5 1.0 O A:HOH421 2.5 34.4 1.0 O4 A:U92 3.9 32.4 1.0 O6 A:G91 4.1 29.5 1.0 O6 A:G43 4.2 24.5 1.0 N7 A:G91 4.3 31.0 1.0 O A:HOH324 4.4 37.8 1.0 O2D A:G4P201 4.5 22.3 1.0 N4 A:C90 4.7 36.4 1.0 C6 A:G91 4.9 29.9 1.0 C4 A:U92 4.9 31.6 1.0 C5 A:G91 5.0 30.7 1.0

Magnesium binding site 10 out of 21 in the Ppgpp Riboswitch Bound to Ppgpp, Native Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Ppgpp Riboswitch Bound to Ppgpp, Native Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg211 b:36.3 occ:1.00 OP2 A:G37 1.8 26.0 1.0 O A:HOH418 1.9 23.3 1.0 O A:HOH386 2.0 17.3 1.0 O A:HOH313 2.0 29.5 1.0 O A:HOH334 2.1 25.1 1.0 O A:HOH346 2.2 21.2 1.0 P A:G37 3.2 28.0 1.0 OP1 A:G37 3.9 26.4 1.0 O5' A:G37 4.1 29.1 1.0 O A:HOH310 4.1 33.3 1.0 C5' A:G36 4.2 30.3 1.0 O A:HOH320 4.2 27.4 1.0 O3' A:G36 4.3 27.1 1.0 OP2 A:G36 4.4 32.1 1.0 N7 A:A38 4.5 29.0 1.0 C3' A:G36 4.6 28.6 1.0 OP2 A:A38 4.7 40.0 1.0 C4' A:G36 4.9 29.5 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