Sodium in PDB 8khh: Crystal Structure of 2'-Dg-III Riboswitch with Guanosine

The structure of Crystal Structure of 2'-Dg-III Riboswitch with Guanosine, PDB code: 8khh 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)	31.10 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	138.727, 58.621, 57.182, 90, 96.68, 90
R / Rfree (%)	23.8 / 25.3

The binding sites of Sodium atom in the Crystal Structure of 2'-Dg-III Riboswitch with Guanosine (pdb code 8khh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Crystal Structure of 2'-Dg-III Riboswitch with Guanosine, PDB code: 8khh:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in the Crystal Structure of 2'-Dg-III Riboswitch with Guanosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of 2'-Dg-III Riboswitch with Guanosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:37.4 occ:1.00 HO2' A:C58 2.7 48.5 1.0 O2' A:C58 2.8 39.4 1.0 H5' A:U59 3.0 45.5 1.0 O3' A:C58 3.5 32.1 1.0 H4' A:C58 3.5 44.0 1.0 C5' A:U59 3.9 36.9 1.0 C2' A:C58 4.0 37.4 1.0 H5'' A:U59 4.0 45.5 1.0 C3' A:C58 4.1 37.0 1.0 C4' A:C58 4.2 35.7 1.0 OP1 A:U59 4.3 33.1 1.0 P A:U59 4.4 40.6 1.0 H2' A:C58 4.5 46.0 1.0 O5' A:U59 4.5 33.6 1.0 H4' A:U59 4.9 48.4 1.0 H1' A:C58 4.9 49.5 1.0 C1' A:C58 4.9 40.3 1.0 C4' A:U59 4.9 39.3 1.0 O4' A:C58 5.0 37.6 1.0 H3' A:C58 5.0 45.6 1.0

Sodium binding site 2 out of 9 in the Crystal Structure of 2'-Dg-III Riboswitch with Guanosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of 2'-Dg-III Riboswitch with Guanosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:61.2 occ:1.00 H2 A:A61 2.0 71.7 1.0 N1 A:A61 2.4 58.2 1.0 C2 A:A61 2.5 58.7 1.0 O2' A:A39 2.9 59.4 1.0 N3 A:A39 3.0 57.0 1.0 O4' A:C40 3.1 56.9 1.0 HO2' A:A39 3.2 72.5 1.0 H2' A:A39 3.2 72.9 1.0 HN1 A:GMP101 3.3 72.0 1.0 N3 A:C62 3.3 58.5 1.0 H1' A:A39 3.3 74.3 1.0 C2 A:C62 3.4 58.5 1.0 C2' A:A39 3.4 59.7 1.0 O2 A:C62 3.5 58.4 1.0 H2 A:A39 3.5 68.7 1.0 H1' A:C40 3.6 69.3 1.0 C6 A:A61 3.7 57.0 1.0 C2 A:A39 3.7 56.3 1.0 N3 A:A61 3.8 57.6 1.0 C1' A:A39 3.8 60.9 1.0 C4 A:C62 3.9 56.8 1.0 C1' A:C40 3.9 56.7 1.0 H4' A:C40 3.9 67.7 1.0 HN22 A:GMP101 3.9 74.5 1.0 N1 A:C62 4.0 57.3 1.0 H62 A:A61 4.0 66.8 1.0 N1 A:GMP101 4.0 58.9 1.0 H5' A:C40 4.0 68.3 1.0 C4 A:A39 4.0 59.2 1.0 C4' A:C40 4.1 55.4 1.0 H1' A:C62 4.2 70.2 1.0 N6 A:A61 4.3 54.7 1.0 N9 A:A39 4.4 61.2 1.0 C5 A:C62 4.5 56.5 1.0 C6 A:C62 4.5 57.2 1.0 N4 A:C62 4.5 55.9 1.0 H42 A:C62 4.5 68.3 1.0 C5' A:C40 4.6 55.9 1.0 N2 A:GMP101 4.6 61.1 1.0 N1 A:C40 4.7 55.9 1.0 C4 A:A61 4.7 55.9 1.0 C1' A:C62 4.7 57.5 1.0 C2 A:GMP101 4.7 60.1 1.0 C5 A:A61 4.7 55.8 1.0 H6 A:C40 4.7 68.3 1.0 C6 A:GMP101 4.8 58.4 1.0 O6 A:GMP101 4.8 57.9 1.0 C3' A:A39 4.9 59.9 1.0 C6 A:C40 5.0 55.9 1.0

Sodium binding site 3 out of 9 in the Crystal Structure of 2'-Dg-III Riboswitch with Guanosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of 2'-Dg-III Riboswitch with Guanosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:40.0 occ:1.00 OP1 A:A17 2.9 39.9 1.0 H5'' B:A47 3.0 51.4 1.0 H5'' A:A17 3.0 46.8 1.0 OP1 B:A47 3.1 41.5 1.0 H5' B:A47 3.8 51.4 1.0 C5' B:A47 3.8 41.8 1.0 C5' A:A17 3.9 39.0 1.0 H5' A:A17 4.1 46.8 1.0 P A:A17 4.2 38.3 1.0 P B:A47 4.3 40.6 1.0 O5' A:A17 4.4 40.4 1.0 O5' B:A47 4.5 40.5 1.0 O3' B:G46 4.8 40.0 1.0 O3' A:U16 4.8 38.1 1.0 H4' B:A47 4.8 51.6 1.0 C4' B:A47 4.9 42.0 1.0 H4' A:A17 5.0 47.1 1.0

Sodium binding site 4 out of 9 in the Crystal Structure of 2'-Dg-III Riboswitch with Guanosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of 2'-Dg-III Riboswitch with Guanosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:100.9 occ:1.00 H3' A:C71 2.5 144.1 1.0 C3' A:C71 3.4 119.0 1.0 H2' A:C71 3.7 144.7 1.0 O3' A:C71 3.9 139.0 1.0 C2' A:C71 4.1 119.5 1.0 C6 A:C71 4.2 119.3 1.0 H5'' A:C71 4.2 149.9 1.0 N1 A:C71 4.2 118.4 1.0 H6 A:C71 4.4 144.3 1.0 HO3' A:C71 4.4 168.1 1.0 C5 A:C71 4.4 116.4 1.0 C2 A:C71 4.5 114.1 1.0 H5' A:C71 4.5 149.9 1.0 C4' A:C71 4.5 120.3 1.0 C5' A:C71 4.6 123.9 1.0 C1' A:C71 4.7 116.1 1.0 C4 A:C71 4.7 115.3 1.0 H5 A:C71 4.7 140.9 1.0 N3 A:C71 4.8 119.3 1.0 O4' A:C71 5.0 120.5 1.0

Sodium binding site 5 out of 9 in the Crystal Structure of 2'-Dg-III Riboswitch with Guanosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of 2'-Dg-III Riboswitch with Guanosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na106 b:48.3 occ:1.00 O6 A:G33 2.8 43.0 1.0 H41 A:C13 3.4 50.9 1.0 O6 A:G32 3.8 38.1 1.0 H42 A:C13 3.8 50.9 1.0 C6 A:G33 3.9 39.9 1.0 O6 A:G34 3.9 44.9 1.0 H42 A:C40 3.9 63.9 1.0 N4 A:C13 4.0 41.4 1.0 H1 A:G34 4.1 56.7 1.0 C6 A:G34 4.2 44.3 1.0 N4 A:C40 4.3 52.2 1.0 N1 A:G34 4.3 46.2 1.0 H42 A:C14 4.3 48.5 1.0 N7 A:G33 4.3 41.3 1.0 N3 A:C40 4.4 52.8 1.0 C5 A:G33 4.5 43.9 1.0 C4 A:C40 4.5 54.4 1.0 H41 A:C40 4.7 63.9 1.0 C6 A:G32 4.7 43.0 1.0 H41 A:C14 4.7 48.5 1.0 N4 A:C14 4.8 39.4 1.0 N7 A:G32 5.0 38.3 1.0

Sodium binding site 6 out of 9 in the Crystal Structure of 2'-Dg-III Riboswitch with Guanosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of 2'-Dg-III Riboswitch with Guanosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na107 b:52.7 occ:1.00 OP1 A:G32 4.9 43.8 1.0 H5'' A:A31 4.9 43.8 1.0

Sodium binding site 7 out of 9 in the Crystal Structure of 2'-Dg-III Riboswitch with Guanosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of 2'-Dg-III Riboswitch with Guanosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:168.3 occ:1.00 O4 B:U63 3.2 68.3 1.0 O6 B:G64 3.4 82.5 1.0 O6 B:G7 3.5 107.3 1.0 H41 B:C65 3.5 107.4 1.0 H61 B:A9 3.5 96.8 1.0 O4 B:U8 3.6 101.2 1.0 H42 B:C65 3.7 107.4 1.0 N4 B:C65 3.9 88.5 1.0 N6 B:A9 4.0 79.6 1.0 C4 B:U63 4.1 65.8 1.0 H62 B:A9 4.1 96.8 1.0 H3 B:U8 4.1 111.9 1.0 C6 B:G64 4.4 80.6 1.0 C4 B:U8 4.5 96.2 1.0 C6 B:G7 4.6 106.4 1.0 N3 B:U8 4.6 92.2 1.0 H5 B:U63 4.7 76.2 1.0 N7 B:G64 4.8 75.8 1.0 C5 B:U63 4.8 62.5 1.0 H3 B:U63 4.8 81.8 1.0 N3 B:U63 4.9 67.2 1.0

Sodium binding site 8 out of 9 in the Crystal Structure of 2'-Dg-III Riboswitch with Guanosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of 2'-Dg-III Riboswitch with Guanosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na103 b:41.5 occ:1.00 H41 B:C14 2.7 53.6 1.0 H5 B:C14 3.1 56.0 1.0 N4 B:C14 3.5 43.7 1.0 H5 B:C13 3.8 60.2 1.0 H41 B:C13 3.8 57.4 1.0 C5 B:C14 3.9 45.6 1.0 C5 B:C13 3.9 49.2 1.0 N4 B:C13 3.9 46.8 1.0 C4 B:C13 4.0 48.4 1.0 OP2 B:C13 4.1 49.1 1.0 H42 B:C14 4.1 53.6 1.0 C4 B:C14 4.1 45.3 1.0 H42 B:C13 4.4 57.4 1.0 C6 B:C13 4.6 49.3 1.0 N3 B:C13 4.7 48.4 1.0 H6 B:C13 4.9 60.3 1.0 H2' B:C40 5.0 62.8 1.0

Sodium binding site 9 out of 9 in the Crystal Structure of 2'-Dg-III Riboswitch with Guanosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of 2'-Dg-III Riboswitch with Guanosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na104 b:51.8 occ:1.00 O6 B:G33 3.3 47.1 1.0 O6 B:G32 3.6 46.3 1.0 H42 B:C13 3.8 57.4 1.0 H41 B:C40 3.8 59.5 1.0 N4 B:C40 3.9 48.5 1.0 H42 B:C40 4.2 59.5 1.0 H41 B:C13 4.2 57.4 1.0 C4 B:C40 4.2 50.3 1.0 O6 B:G34 4.3 50.6 1.0 H42 B:C14 4.3 53.6 1.0 N4 B:C13 4.3 46.8 1.0 C6 B:G33 4.3 48.6 1.0 N3 B:C40 4.4 50.9 1.0 C6 B:G32 4.6 46.6 1.0 H1 B:G34 4.7 63.4 1.0 N7 B:G33 4.7 49.1 1.0 H41 B:C14 4.7 53.6 1.0 C6 B:G34 4.8 51.1 1.0 N7 B:G32 4.8 46.9 1.0 N4 B:C14 4.8 43.7 1.0 C5 B:G33 4.9 49.3 1.0 N1 B:G34 4.9 51.8 1.0 C5 B:C40 4.9 51.7 1.0

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