Magnesium in PDB 6yl5: Crystal Structure of the Sam-Sah Riboswitch with Sah

The structure of Crystal Structure of the Sam-Sah Riboswitch with Sah, PDB code: 6yl5 was solved by L.Huang, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	74.61 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	86.750, 147.610, 74.660, 90.00, 92.07, 90.00
R / Rfree (%)	17.2 / 20

The structure of Crystal Structure of the Sam-Sah Riboswitch with Sah also contains other interesting chemical elements:

Bromine	(Br)	6 atoms
Sodium	(Na)	14 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Sam-Sah Riboswitch with Sah (pdb code 6yl5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of the Sam-Sah Riboswitch with Sah, PDB code: 6yl5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of the Sam-Sah Riboswitch with Sah


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 the Sam-Sah Riboswitch with Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:67.5 occ:1.00 H3 A:U20 2.6 0.6 1.0 N3 A:U20 3.3 0.3 1.0 O2 A:U20 3.8 0.9 1.0 C2 A:U20 3.9 0.1 1.0 O4 A:U20 4.1 0.2 1.0 C4 A:U20 4.1 0.6 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of the Sam-Sah Riboswitch with Sah


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 the Sam-Sah Riboswitch with Sah within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg102 b:68.4 occ:1.00 H42 C:C31 2.9 91.4 1.0 H42 C:C32 2.9 0.3 1.0 N4 C:C31 3.6 76.1 1.0 N4 C:C32 3.7 96.9 1.0 H5 C:C31 3.9 98.4 1.0 O C:HOH212 4.0 70.4 1.0 H41 C:C31 4.0 91.4 1.0 H41 C:C32 4.0 0.3 1.0 C4 C:C31 4.4 82.3 1.0 H5 C:C32 4.4 0.2 1.0 C5 C:C31 4.5 82.0 1.0 C4 C:C32 4.8 83.3 1.0 C5 C:C32 5.0 95.2 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of the Sam-Sah Riboswitch with Sah


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 the Sam-Sah Riboswitch with Sah within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg102 b:86.9 occ:1.00 H41 D:C50 2.8 51.4 1.0 H62 D:A51 3.4 51.9 1.0 N4 D:C50 3.6 42.8 1.0 H5 D:C50 3.8 52.2 1.0 H42 D:C50 4.0 51.4 1.0 N6 D:A51 4.1 43.2 1.0 H61 D:A51 4.3 51.9 1.0 C5 D:C50 4.5 43.5 1.0 C4 D:C50 4.5 40.8 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of the Sam-Sah Riboswitch with Sah


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Sam-Sah Riboswitch with Sah within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg102 b:66.9 occ:1.00 H4' H:C50 3.3 51.7 1.0 HO2' H:G49 3.4 40.0 1.0 O2' H:G49 3.5 33.3 1.0 H5' H:C50 3.9 54.7 1.0 O H:HOH210 3.9 41.3 1.0 O H:HOH208 4.0 46.4 1.0 C4' H:C50 4.1 43.0 1.0 O H:HOH215 4.2 51.4 1.0 O4' H:C50 4.2 38.8 1.0 C5' H:C50 4.4 45.5 1.0 H2' H:G49 4.6 41.2 1.0 HO2' H:C50 4.6 47.6 1.0 C2' H:G49 4.6 34.4 1.0 H5'' H:C50 4.7 54.7 1.0 H1' H:G49 4.9 42.0 1.0 H1' H:C50 4.9 46.9 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of the Sam-Sah Riboswitch with Sah


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Sam-Sah Riboswitch with Sah within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg103 b:60.1 occ:1.00 H42 H:C50 2.3 43.2 1.0 O H:HOH206 3.2 54.0 1.0 N4 H:C50 3.2 35.9 1.0 H5 H:C50 3.4 48.8 1.0 O H:HOH219 3.4 50.6 1.0 H62 H:A51 3.5 53.8 1.0 H41 H:C50 3.7 43.2 1.0 C5 H:C50 4.0 40.6 1.0 C4 H:C50 4.1 40.1 1.0 N6 H:A51 4.1 44.8 1.0 O H:HOH204 4.4 51.6 1.0 H61 H:A51 4.4 53.8 1.0 N7 H:G49 4.9 35.0 1.0

L.Huang, T.W.Liao, J.Wang, T.Ha, D.M.J.Lilley. Crystal Structure and Ligand-Induced Folding of the Sam/Sah Riboswitch. Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962
PubMed: 32520325
DOI: 10.1093/NAR/GKAA493