Sodium in PDB 3diy: Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak

The structure of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak, PDB code: 3diy was solved by A.A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.71
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.193, 78.662, 140.522, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 23.7

The structure of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak also contains other interesting chemical elements:

Potassium	(K)	1 atom
Manganese	(Mn)	2 atoms

The binding sites of Sodium atom in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak (pdb code 3diy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak, PDB code: 3diy:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:23.5 occ:1.00 O A:HOH326 2.5 18.5 1.0 O6 A:G71 2.5 26.9 1.0 O6 A:G20 2.5 24.7 1.0 O A:HOH325 3.1 30.0 1.0 O A:HOH324 3.3 34.9 1.0 C6 A:G71 3.5 26.1 1.0 C6 A:G20 3.6 24.1 1.0 N7 A:G71 3.7 25.2 1.0 C5 A:G71 3.9 25.7 1.0 N7 A:G20 4.3 23.0 1.0 C5 A:G20 4.3 23.8 1.0 OP2 A:C70 4.3 28.2 1.0 N1 A:G71 4.7 26.0 1.0 N1 A:G20 4.7 23.6 1.0 OP2 A:C19 4.8 28.1 1.0 C8 A:G71 4.9 25.6 1.0 C5 A:C70 5.0 28.9 1.0

Sodium binding site 2 out of 8 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:33.5 occ:1.00 O A:HOH312 2.6 17.2 1.0 N7 A:G68 2.8 24.1 1.0 O6 A:G69 2.9 28.9 1.0 C8 A:G68 3.6 24.7 1.0 C6 A:G69 3.7 29.2 1.0 N7 A:A67 3.8 30.2 1.0 N2 A:G25 3.9 23.2 1.0 OP2 A:G68 3.9 30.8 1.0 C8 A:A67 4.0 30.7 1.0 N7 A:G69 4.0 28.7 1.0 C5 A:G68 4.0 24.1 1.0 C5 A:G69 4.1 28.9 1.0 O6 A:G68 4.3 24.8 1.0 OP2 A:A67 4.4 35.4 1.0 C5 A:A67 4.6 30.1 1.0 C6 A:G68 4.6 24.1 1.0 O5' A:A67 4.8 34.7 1.0 C2 A:G25 4.8 23.3 1.0 N1 A:G69 4.8 29.4 1.0 N9 A:A67 4.8 30.8 1.0 N9 A:G68 4.9 25.5 1.0 N6 A:A23 5.0 20.3 1.0 C3' A:A67 5.0 32.3 1.0

Sodium binding site 3 out of 8 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:28.1 occ:1.00 OP2 A:A72 2.2 32.4 1.0 O A:HOH322 2.8 29.3 1.0 N7 A:G73 2.9 30.4 1.0 O A:HOH315 2.9 32.1 1.0 O A:HOH323 3.1 20.6 1.0 O6 A:G73 3.5 30.4 1.0 P A:A72 3.6 33.1 1.0 C5 A:G73 3.8 30.3 1.0 C8 A:G73 3.9 30.2 1.0 C6 A:G73 4.0 30.3 1.0 OP1 A:A72 4.2 32.8 1.0 O5' A:A72 4.4 31.7 1.0 N2 A:G20 4.5 23.2 1.0 O3' A:G71 4.6 31.0 1.0 C3' A:G71 4.7 29.0 1.0 O5' A:G71 5.0 27.8 1.0 C4 A:G73 5.0 30.3 1.0

Sodium binding site 4 out of 8 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:51.2 occ:1.00 OP1 A:C15 3.9 25.9 1.0 OP1 A:C131 4.1 36.5 1.0 OP2 A:C132 4.4 34.5 1.0 OP1 A:G117 4.5 32.9 1.0 OP1 A:G16 4.6 27.3 1.0 OP2 A:G16 4.7 26.4 1.0 OP1 A:C132 4.8 34.4 1.0

Sodium binding site 5 out of 8 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:45.0 occ:1.00 O6 A:G12 2.8 32.9 1.0 OP2 A:G11 2.8 26.4 1.0 O A:HOH336 3.0 32.5 1.0 C6 A:G12 3.9 32.2 1.0 P A:G11 4.1 27.2 1.0 N4 A:C79 4.3 23.2 1.0 N2 A:G11 4.4 23.9 1.0 OP1 A:A10 4.4 28.3 1.0 OP1 A:G11 4.5 26.8 1.0 N7 A:G12 4.6 32.0 1.0 C5 A:G12 4.6 32.1 1.0 N1 A:G12 4.9 31.7 1.0 O3' A:A10 4.9 26.4 1.0

Sodium binding site 6 out of 8 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Na206 b:44.9 occ:1.00 O A:HOH311 2.9 30.7 1.0 OP2 A:G106 4.1 34.2 1.0 OP1 A:G106 4.3 33.8 1.0 OP1 A:G83 4.5 23.3 1.0 OP1 A:U105 4.7 34.3 1.0 P A:G106 4.7 34.1 1.0

Sodium binding site 7 out of 8 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Na207 b:35.1 occ:1.00 OP1 A:A164 2.2 27.9 1.0 O A:HOH329 2.4 25.3 1.0 N7 A:G80 2.7 24.2 1.0 C8 A:G80 3.4 24.2 1.0 P A:A164 3.6 28.8 1.0 O4 A:U113 3.7 28.3 1.0 C5 A:U113 3.8 28.2 1.0 C5 A:G80 3.9 23.9 1.0 C4 A:U113 4.0 28.3 1.0 O3' A:G163 4.2 27.6 1.0 OP2 A:A164 4.3 28.6 1.0 O6 A:G80 4.3 24.3 1.0 C3' A:G163 4.4 25.6 1.0 C6 A:G80 4.5 23.8 1.0 O5' A:A164 4.7 29.8 1.0 N9 A:G80 4.7 24.1 1.0 C8 A:A164 4.8 38.5 1.0 C6 A:U113 4.8 28.2 1.0 N7 A:A164 4.9 38.8 1.0 O2' A:G163 4.9 25.0 1.0 C8 A:G110 5.0 57.1 1.0 C4 A:G80 5.0 24.1 1.0

Sodium binding site 8 out of 8 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Na208 b:50.6 occ:1.00 O A:HOH300 2.6 25.9 1.0 O6 A:G9 2.7 26.7 1.0 C6 A:G9 3.7 25.9 1.0 N7 A:G9 3.9 25.9 1.0 OP1 A:G80 4.0 23.0 1.0 C5 A:G9 4.2 25.8 1.0 O6 A:G8 4.5 27.7 1.0 N4 A:C166 4.7 22.9 1.0 N1 A:G9 5.0 26.1 1.0

A.Serganov, L.Huang, D.J.Patel. Structural Insights Into Amino Acid Binding and Gene Control By A Lysine Riboswitch. Nature V. 455 1263 2008.
ISSN: ISSN 0028-0836
PubMed: 18784651
DOI: 10.1038/NATURE07326