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

The structure of Crystal Structure of 2'-Dg-III Riboswitch with Guanine, PDB code: 8ked 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)	24.30 / 2.11
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	138.674, 26.182, 65.524, 90, 113.38, 90
R / Rfree (%)	21.2 / 25.3

The structure of Crystal Structure of 2'-Dg-III Riboswitch with Guanine 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 Guanine (pdb code 8ked). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of 2'-Dg-III Riboswitch with Guanine, PDB code: 8ked:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of 2'-Dg-III Riboswitch with Guanine


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 Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:59.5 occ:1.00 O6 A:G64 2.5 75.9 1.0 O4 A:U8 2.7 68.3 1.0 O4 A:U63 2.9 73.4 1.0 O6 A:G7 3.1 70.1 1.0 C4 A:U8 3.6 74.1 1.0 C6 A:G64 3.7 73.0 1.0 C4 A:U63 3.8 79.4 1.0 N6 A:A9 3.8 66.5 1.0 N3 A:U8 3.9 68.4 1.0 C6 A:G7 4.1 73.0 1.0 N4 A:C65 4.1 79.8 1.0 N7 A:G64 4.4 86.9 1.0 C5 A:G64 4.4 76.4 1.0 C5 A:U63 4.6 79.2 1.0 N3 A:U63 4.6 82.6 1.0 C6 A:A9 4.7 68.9 1.0 N1 A:G64 4.8 66.6 1.0 N1 A:G7 4.9 74.4 1.0 C5 A:G7 4.9 68.6 1.0 C5 A:U8 5.0 67.6 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of 2'-Dg-III Riboswitch with Guanine


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 Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:90.4 occ:1.00 O4 A:U5 3.7 84.3 1.0 O6 A:G66 3.8 72.2 1.0 N4 A:C6 4.3 79.7 1.0 N4 A:C65 4.3 79.8 1.0 N6 A:A67 4.7 67.5 1.0 C4 A:U5 4.8 79.3 1.0 O4 A:U4 4.8 82.5 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of 2'-Dg-III Riboswitch with Guanine


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 2'-Dg-III Riboswitch with Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:70.9 occ:1.00 O2' A:U10 2.6 74.4 1.0 O3' A:U10 2.8 81.6 1.0 O6 A:GUN102 2.8 74.4 1.0 OP2 A:A11 3.0 85.7 1.0 C2' A:U10 3.5 77.0 1.0 P A:A11 3.5 83.6 1.0 C3' A:U10 3.7 76.7 1.0 N6 A:A9 3.7 66.5 1.0 C6 A:GUN102 3.9 66.6 1.0 C1' A:U10 4.0 74.7 1.0 C6 A:A9 4.1 68.9 1.0 O2 A:U10 4.1 69.1 1.0 N7 A:A9 4.2 70.2 1.0 C5 A:A9 4.2 69.4 1.0 N7 A:GUN102 4.4 72.0 1.0 C5' A:A11 4.5 85.1 1.0 N4 A:C62 4.5 69.9 1.0 C5 A:GUN102 4.5 62.4 1.0 O5' A:A11 4.5 85.2 1.0 OP1 A:A11 4.6 86.3 1.0 OP2 A:U12 4.8 89.2 1.0 C4' A:U10 4.9 79.3 1.0 N1 A:A9 4.9 70.6 1.0 C2 A:U10 4.9 73.2 1.0 O4' A:U10 5.0 85.3 1.0 N1 A:U10 5.0 76.0 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of 2'-Dg-III Riboswitch with Guanine


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 2'-Dg-III Riboswitch with Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:132.3 occ:1.00 OP2 A:A9 2.2 105.6 1.0 OP1 A:A11 2.8 86.3 1.0 P A:A9 3.4 102.3 1.0 OP1 A:A9 4.0 103.5 1.0 P A:A11 4.1 83.6 1.0 O5' A:A9 4.2 95.0 1.0 O5' A:A11 4.3 85.2 1.0 O3' A:U8 4.6 88.7 1.0 OP2 A:U10 4.8 97.5 1.0 C3' A:U8 4.9 84.6 1.0

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