Magnesium in PDB 9uw0: Crystal Structure of 2'-Dg-III Riboswitch with Guanosine, Manganese Saok

The structure of Crystal Structure of 2'-Dg-III Riboswitch with Guanosine, Manganese Saok, PDB code: 9uw0 was solved by X.Shen, A.M.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.50 / 1.97
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	47.206, 70.365, 116.266, 90, 90, 90
R / Rfree (%)	20.5 / 22.3

The structure of Crystal Structure of 2'-Dg-III Riboswitch with Guanosine, Manganese Saok also contains other interesting chemical elements:

Manganese

(Mn)

6 atoms

The binding sites of Magnesium atom in the Crystal Structure of 2'-Dg-III Riboswitch with Guanosine, Manganese Saok (pdb code 9uw0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of 2'-Dg-III Riboswitch with Guanosine, Manganese Saok, PDB code: 9uw0:

Magnesium binding site 1 out of 1 in the Crystal Structure of 2'-Dg-III Riboswitch with Guanosine, Manganese Saok


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 2'-Dg-III Riboswitch with Guanosine, Manganese Saok within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg108 b:36.0 occ:1.00 OP2 X:A38 2.2 34.3 1.0 O4 X:U39 2.4 31.2 1.0 O2' X:GMP101 2.4 28.6 1.0 O3' X:GMP101 2.6 31.4 1.0 O X:HOH239 2.6 37.9 1.0 C2' X:GMP101 3.3 28.8 1.0 C4 X:U39 3.4 28.0 1.0 C3' X:GMP101 3.4 33.3 1.0 P X:A38 3.7 33.5 1.0 C1' X:GMP101 3.7 29.4 1.0 C5 X:U39 3.9 30.7 1.0 N7 X:A38 4.2 27.3 1.0 C5' X:A37 4.2 32.2 1.0 N6 X:A40 4.3 30.9 1.0 O5' X:A38 4.4 32.3 1.0 O4 X:U11 4.4 28.8 1.0 OP1 X:A38 4.5 43.8 1.0 N3 X:U39 4.5 28.2 1.0 C8 X:A38 4.5 28.7 1.0 O3' X:A37 4.6 31.3 1.0 C4' X:GMP101 4.6 31.8 1.0 O4' X:GMP101 4.6 28.1 1.0 C3' X:A37 4.6 34.0 1.0 N9 X:GMP101 4.8 27.4 1.0 OP1 X:A37 4.9 37.4 1.0

X.Shen, H.Li, X.Xu, Q.Song, X.Tai, M.He, A.Ren. Structure-Based Insights Into the Ligand Specificity Tuning of 2'-Dg-III Riboswitch. Nucleic Acids Res. V. 53 2025.
ISSN: ESSN 1362-4962
PubMed: 40795954
DOI: 10.1093/NAR/GKAF773