Magnesium in PDB 4jf2: Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold

The structure of Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold, PDB code: 4jf2 was solved by J.A.Liberman, J.E.Wedekind, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.70 / 2.28
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	58.036, 85.972, 98.120, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 24.4

The structure of Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold also contains other interesting chemical elements:

Caesium

(Cs)

15 atoms

The binding sites of Magnesium atom in the Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold (pdb code 4jf2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold, PDB code: 4jf2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg117 b:28.4 occ:1.00 O A:HOH315 2.0 24.1 1.0 O A:HOH312 2.1 31.9 1.0 OP1 A:U41 2.1 14.2 1.0 O A:HOH314 2.1 38.3 1.0 O A:HOH316 2.1 15.5 1.0 O A:HOH313 2.1 11.7 1.0 P A:U41 3.5 12.3 1.0 O A:HOH269 3.9 38.9 1.0 O5' A:U41 4.0 12.3 1.0 O A:HOH341 4.1 37.5 1.0 OP1 A:A24 4.1 25.7 1.0 O A:HOH239 4.1 14.4 1.0 OP2 A:A24 4.2 11.3 1.0 C5' A:U41 4.2 12.0 1.0 O A:HOH245 4.2 33.0 1.0 OP1 A:G23 4.3 21.3 1.0 O2' A:U53 4.3 20.0 1.0 OP2 A:A55 4.4 23.5 1.0 OP2 A:U41 4.4 12.3 1.0 O3' A:U40 4.5 12.6 1.0 P A:A24 4.6 11.2 1.0 O A:HOH222 4.7 34.4 1.0

Magnesium binding site 2 out of 4 in the Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg118 b:41.4 occ:1.00 O A:HOH320 2.1 22.6 1.0 OP1 A:U53 2.1 33.7 1.0 O A:HOH317 2.1 28.4 1.0 O A:HOH318 2.1 22.3 1.0 O A:HOH319 2.1 34.3 1.0 P A:U53 3.5 27.8 1.0 O5' A:U53 4.0 36.7 1.0 OP2 A:U54 4.2 26.0 1.0 OP2 A:U53 4.4 27.1 1.0 O A:HOH266 4.4 14.5 1.0 O3' A:A52 4.5 42.5 1.0 O A:HOH352 4.5 43.9 1.0 OP1 A:U54 4.7 27.9 1.0 P A:U54 4.8 23.4 1.0

Magnesium binding site 3 out of 4 in the Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg119 b:50.8 occ:1.00 OP1 A:G42 2.0 23.1 1.0 O A:HOH330 2.0 46.8 1.0 O A:HOH326 2.1 66.7 1.0 O A:HOH327 2.1 46.1 1.0 O A:HOH329 2.1 41.5 1.0 O A:HOH328 2.1 19.8 1.0 P A:G42 3.4 17.5 1.0 O A:HOH269 3.9 38.9 1.0 O3' A:U41 4.2 11.8 1.0 O5' A:G42 4.3 17.4 1.0 OP2 A:G42 4.3 23.9 1.0 OP1 A:C22 4.3 35.4 1.0 C5' A:G42 4.4 15.2 1.0 OP1 A:G23 4.4 21.3 1.0 OP2 A:G23 4.5 23.2 1.0 O A:HOH240 4.6 27.0 1.0 O A:HOH206 4.6 23.9 1.0 O A:HOH245 4.6 33.0 1.0 P A:G23 4.8 23.5 1.0 O A:HOH314 4.8 38.3 1.0 OP2 A:A43 4.8 19.0 1.0 O3' A:C22 5.0 25.6 1.0

Magnesium binding site 4 out of 4 in the Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg120 b:30.8 occ:1.00 O A:HOH333 2.0 14.1 1.0 O A:HOH335 2.0 33.1 1.0 OP1 A:A10 2.1 23.4 1.0 O A:HOH334 2.1 38.6 1.0 O A:HOH331 2.1 23.9 1.0 O A:HOH332 2.1 13.7 1.0 P A:A10 3.4 20.3 1.0 OP2 A:A10 3.9 20.1 1.0 CS A:CS102 4.3 20.5 0.8 O5' A:A10 4.3 23.6 1.0 O4' A:A10 4.4 17.4 1.0 C8 A:A10 4.4 16.6 1.0 O3' A:G9 4.4 19.0 1.0 O A:HOH294 4.4 43.9 1.0 C5' A:A10 4.4 19.4 1.0 O A:HOH264 4.6 28.3 1.0

J.A.Liberman, M.Salim, J.Krucinska, J.E.Wedekind. Structure of A Class II PREQ1 Riboswitch Reveals Ligand Recognition By A New Fold. Nat.Chem.Biol. V. 9 353 2013.
ISSN: ISSN 1552-4450
PubMed: 23584677
DOI: 10.1038/NCHEMBIO.1231