Magnesium in PDB 7e9e: Crystal Structure of A Class I PREQ1 Riboswitch Aptamer (AB13-14) Complexed with A Cognate Ligand-Derived Photoaffinity Probe

The structure of Crystal Structure of A Class I PREQ1 Riboswitch Aptamer (AB13-14) Complexed with A Cognate Ligand-Derived Photoaffinity Probe, PDB code: 7e9e was solved by T.Numata, J.S.Schneekloth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.60 / 1.57
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	52.691, 52.691, 176.999, 90, 90, 120
R / Rfree (%)	19 / 20.8

The binding sites of Magnesium atom in the Crystal Structure of A Class I PREQ1 Riboswitch Aptamer (AB13-14) Complexed with A Cognate Ligand-Derived Photoaffinity Probe (pdb code 7e9e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of A Class I PREQ1 Riboswitch Aptamer (AB13-14) Complexed with A Cognate Ligand-Derived Photoaffinity Probe, PDB code: 7e9e:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of A Class I PREQ1 Riboswitch Aptamer (AB13-14) Complexed with A Cognate Ligand-Derived Photoaffinity Probe


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Class I PREQ1 Riboswitch Aptamer (AB13-14) Complexed with A Cognate Ligand-Derived Photoaffinity Probe within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:52.0 occ:1.00 OP2 A:A31 2.2 46.0 1.0 O A:HOH232 2.5 37.9 1.0 O A:HOH219 2.7 48.8 1.0 P A:A31 3.2 50.7 1.0 O5' A:A31 3.2 41.1 1.0 C8 A:A31 3.3 29.3 1.0 C3' A:C30 3.5 37.4 1.0 O3' A:C30 3.9 47.7 1.0 O A:HOH249 3.9 38.6 1.0 N7 A:A31 3.9 31.4 1.0 O5' A:C30 4.1 43.5 1.0 C2' A:C30 4.1 33.9 1.0 C2' A:A31 4.2 33.6 1.0 N9 A:A31 4.4 28.6 1.0 O2 A:SO4102 4.5 143.0 1.0 C6 A:C30 4.5 32.3 1.0 OP1 A:A31 4.5 55.6 1.0 C5' A:A31 4.6 38.3 1.0 N6 A:A10 4.7 35.8 1.0 C4' A:C30 4.7 42.9 1.0 OP2 A:C30 4.7 45.4 1.0 N1 A:C30 4.8 31.1 1.0 C1' A:A31 4.8 31.8 1.0 C5' A:C30 4.8 41.6 1.0 P A:C30 4.9 45.8 1.0 C3' A:A31 4.9 35.5 1.0 C1' A:C30 4.9 36.1 1.0 O2' A:A31 4.9 34.3 1.0 O4' A:A31 5.0 33.6 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of A Class I PREQ1 Riboswitch Aptamer (AB13-14) Complexed with A Cognate Ligand-Derived Photoaffinity Probe


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Class I PREQ1 Riboswitch Aptamer (AB13-14) Complexed with A Cognate Ligand-Derived Photoaffinity Probe within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:59.2 occ:1.00 OP1 A:G4 2.0 50.7 1.0 O3' A:G3 2.0 45.9 1.0 P A:G4 2.4 43.0 1.0 O A:HOH222 2.7 46.4 1.0 C5' A:G4 3.3 42.2 1.0 O5' A:G4 3.3 37.8 1.0 C3' A:G3 3.3 39.3 1.0 OP2 A:G4 3.8 46.3 1.0 O2' A:G3 3.8 36.3 1.0 C4' A:G3 4.0 43.1 1.0 C2' A:G3 4.1 38.6 1.0 C5' A:G3 4.5 42.0 1.0 C4' A:G4 4.7 37.4 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of A Class I PREQ1 Riboswitch Aptamer (AB13-14) Complexed with A Cognate Ligand-Derived Photoaffinity Probe


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Class I PREQ1 Riboswitch Aptamer (AB13-14) Complexed with A Cognate Ligand-Derived Photoaffinity Probe within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:59.8 occ:1.00 OP2 A:G8 2.1 51.1 1.0 O A:HOH234 2.9 41.1 1.0 O A:HOH268 3.1 50.3 1.0 P A:G8 3.3 44.8 1.0 O5' A:G8 3.4 41.1 1.0 C8 A:G8 3.5 45.5 1.0 O A:HOH281 3.6 52.0 1.0 N7 A:G8 3.6 37.9 1.0 OP1 A:G8 4.3 48.4 1.0 O3' A:C7 4.4 45.9 1.0 C3' A:C7 4.4 41.7 1.0 O5' A:C7 4.5 44.8 1.0 OP2 A:C9 4.6 47.9 1.0 OP2 A:C7 4.7 46.8 1.0 N9 A:G8 4.7 35.3 1.0 C5' A:G8 4.8 38.9 1.0 C5 A:G8 4.9 37.2 1.0 P A:C7 4.9 49.2 1.0 OP1 A:C7 5.0 51.1 1.0 O A:HOH286 5.0 57.6 1.0

S.Balaratnam, C.Rhodes, D.D.Bume, C.Connelly, C.C.Lai, J.A.Kelley, K.Yazdani, P.J.Homan, D.Incarnato, T.Numata, J.S.Schneekloth Jr.. A Chemical Probe Based on the Preq 1 Metabolite Enables Transcriptome-Wide Mapping of Binding Sites. Nat Commun V. 12 5856 2021.
ISSN: ESSN 2041-1723
PubMed: 34615874
DOI: 10.1038/S41467-021-25973-X