Magnesium in PDB 8keb: Crystal Structure of 2'-Dg-III Riboswitch with 2'-Dg

The structure of Crystal Structure of 2'-Dg-III Riboswitch with 2'-Dg, PDB code: 8keb was solved by W.Liao, L.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.43 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	139.516, 26.834, 65.227, 90, 112.71, 90
R / Rfree (%)	20.2 / 24.2

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

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of 2'-Dg-III Riboswitch with 2'-Dg (pdb code 8keb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of 2'-Dg-III Riboswitch with 2'-Dg, PDB code: 8keb:
Jump to Magnesium binding site number: 1; 2;

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


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 2'-Dg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:75.7 occ:1.00 O A:HOH202 2.0 61.6 1.0 O A:HOH206 2.2 68.1 1.0 O A:HOH203 2.4 73.6 1.0 O A:HOH205 2.6 72.2 1.0 O A:HOH204 3.0 75.5 1.0 N4 A:C65 4.1 56.4 1.0 O4 A:U5 4.2 66.9 1.0 N4 A:C6 4.2 62.3 1.0 O6 A:G66 4.4 57.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of 2'-Dg-III Riboswitch with 2'-Dg


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 2'-Dg-III Riboswitch with 2'-Dg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:63.6 occ:1.00 O2' A:U10 2.6 60.6 1.0 O6 A:GNG102 2.7 61.0 1.0 O3' A:U10 3.0 64.2 1.0 OP2 A:A11 3.1 62.7 1.0 C2' A:U10 3.7 60.6 1.0 P A:A11 3.7 64.8 1.0 N6 A:A9 3.8 60.2 1.0 C6 A:GNG102 3.8 56.3 1.0 N4 A:C62 3.9 57.2 1.0 C3' A:U10 4.0 62.0 1.0 C6 A:A9 4.1 57.1 1.0 C1' A:U10 4.2 61.0 1.0 O2 A:U10 4.3 60.9 1.0 C5 A:A9 4.3 54.8 1.0 N7 A:A9 4.3 58.5 1.0 N7 A:GNG102 4.5 59.5 1.0 C5 A:GNG102 4.5 58.5 1.0 N6 A:A61 4.6 66.9 1.0 C5' A:A11 4.6 63.8 1.0 O5' A:A11 4.7 60.0 1.0 OP1 A:A11 4.8 58.9 1.0 N1 A:A9 4.9 55.8 1.0 N1 A:GNG102 4.9 53.5 1.0

W.Liao, L.Huang. Crystal Structure of 2'-Dg-III Riboswitch with 2'-Dg To Be Published.