Sodium in PDB 3dio: Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Iridium Hexamine Soak

The structure of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Iridium Hexamine Soak, PDB code: 3dio 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 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.918, 78.004, 140.835, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 24.3

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

Potassium	(K)	1 atom
Iridium	(Ir)	18 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Sodium atom in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Iridium Hexamine Soak (pdb code 3dio). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 14 binding sites of Sodium where determined in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Iridium Hexamine Soak, PDB code: 3dio:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 14 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Iridium Hexamine 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, Iridium Hexamine Soak within 5.0Å range: probe atom residue distance (Å) B Occ X:Na201 b:15.9 occ:1.00 O X:HOH381 2.2 10.9 1.0 O6 X:G71 2.5 13.0 1.0 O6 X:G20 2.5 10.3 1.0 O X:HOH393 2.6 8.2 1.0 O X:HOH486 3.1 15.6 1.0 C6 X:G71 3.5 11.7 1.0 C6 X:G20 3.6 9.6 1.0 O X:HOH509 3.9 31.2 1.0 N7 X:G20 4.1 9.9 1.0 N7 X:G71 4.1 10.4 1.0 C5 X:G71 4.2 11.1 1.0 OP2 X:C19 4.2 18.3 1.0 C5 X:G20 4.2 10.1 1.0 O X:HOH421 4.2 13.9 1.0 O X:HOH308 4.6 9.2 1.0 N1 X:G71 4.6 11.4 1.0 C5 X:C19 4.6 13.5 1.0 O X:HOH485 4.6 12.0 1.0 O X:HOH484 4.7 32.6 1.0 N1 X:G20 4.8 9.0 1.0 OP2 X:C70 4.8 13.4 1.0

Sodium binding site 2 out of 14 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Iridium Hexamine 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, Iridium Hexamine Soak within 5.0Å range: probe atom residue distance (Å) B Occ X:Na202 b:17.7 occ:1.00 O X:HOH305 2.4 19.9 1.0 O X:HOH307 2.4 12.5 1.0 O X:HOH306 2.5 9.8 1.0 O6 X:G69 2.8 9.8 1.0 NA X:NA212 2.9 18.6 1.0 N7 X:G68 3.0 13.3 1.0 C6 X:G69 3.6 9.1 1.0 C8 X:G68 3.8 13.4 1.0 N7 X:A67 3.8 16.5 1.0 N2 X:G25 3.9 15.2 1.0 N7 X:G69 4.0 9.4 1.0 C5 X:G69 4.1 9.3 1.0 C5 X:G68 4.1 13.1 1.0 C8 X:A67 4.2 16.8 1.0 OP2 X:G68 4.2 19.4 1.0 O6 X:G68 4.3 13.2 1.0 N6 X:A23 4.4 10.4 1.0 O4 X:U24 4.4 11.2 1.0 C2 X:G25 4.5 15.9 1.0 OP2 X:A67 4.6 24.9 1.0 C6 X:G68 4.6 13.2 1.0 N1 X:G69 4.6 7.9 1.0 N3 X:U24 4.6 11.3 1.0 C5 X:A67 4.6 16.0 1.0 N3 X:G25 4.7 15.9 1.0

Sodium binding site 3 out of 14 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Iridium Hexamine 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, Iridium Hexamine Soak within 5.0Å range: probe atom residue distance (Å) B Occ X:Na203 b:22.3 occ:1.00 O X:HOH309 2.3 10.7 1.0 O6 X:G12 2.6 15.7 1.0 OP2 X:G11 2.6 9.7 1.0 O X:HOH447 3.0 12.3 1.0 P X:G11 3.6 9.3 1.0 C6 X:G12 3.7 15.3 1.0 N2 X:G11 3.9 7.9 1.0 OP1 X:G11 4.0 11.0 1.0 N4 X:C79 4.0 8.3 1.0 OP1 X:A10 4.2 14.4 1.0 O3' X:A10 4.3 10.3 1.0 O X:HOH310 4.5 10.8 1.0 C5 X:G12 4.5 14.8 1.0 O5' X:A10 4.6 12.7 1.0 N7 X:G12 4.6 14.6 1.0 N1 X:G12 4.7 15.2 1.0 P X:A10 4.7 13.3 1.0 OP2 X:A10 4.7 14.2 1.0 C3' X:A10 4.8 10.5 1.0 C4 X:C79 4.8 7.9 1.0

Sodium binding site 4 out of 14 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Iridium Hexamine 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, Iridium Hexamine Soak within 5.0Å range: probe atom residue distance (Å) B Occ X:Na204 b:26.5 occ:1.00 O X:HOH398 2.3 13.8 1.0 O X:HOH512 2.9 16.2 1.0 N2 X:IRI264 3.2 69.6 0.2 OP2 X:G8 3.2 17.0 1.0 O X:HOH313 3.5 16.1 1.0 OP1 X:C79 4.4 16.7 1.0 P X:G8 4.4 16.2 1.0 O X:HOH411 4.7 20.3 1.0 OP2 X:C79 4.7 16.5 1.0 N1 X:IRI264 4.7 69.6 0.2 OP1 X:G8 4.9 16.8 1.0 O5' X:G8 4.9 16.4 1.0 IR X:IRI264 5.0 69.7 0.2

Sodium binding site 5 out of 14 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Iridium Hexamine 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, Iridium Hexamine Soak within 5.0Å range: probe atom residue distance (Å) B Occ X:Na205 b:20.5 occ:1.00 O X:HOH314 2.3 10.0 1.0 O X:HOH316 2.4 20.0 1.0 OP1 X:A164 2.5 12.7 1.0 O X:HOH481 2.6 21.1 1.0 N7 X:G80 2.7 8.6 1.0 C8 X:G80 3.5 7.7 1.0 P X:A164 3.6 13.4 1.0 O4 X:U113 3.8 9.7 1.0 C3' X:G163 3.8 11.5 1.0 C5 X:G80 3.9 8.2 1.0 C5 X:U113 3.9 9.8 1.0 O3' X:G163 3.9 12.4 1.0 C4 X:U113 4.0 9.8 1.0 O X:HOH480 4.0 31.9 1.0 O6 X:G80 4.1 9.0 1.0 O X:HOH315 4.3 10.2 1.0 C6 X:G80 4.4 8.7 1.0 OP2 X:A164 4.4 14.3 1.0 O2' X:G163 4.4 11.4 1.0 N7 X:A164 4.5 25.1 1.0 C8 X:A164 4.5 24.8 1.0 C2' X:G163 4.5 10.5 1.0 O5' X:G163 4.6 15.6 1.0 C6 X:U113 4.8 10.2 1.0 N9 X:G80 4.8 9.2 1.0 O5' X:A164 4.9 16.0 1.0 OP2 X:G163 4.9 16.8 1.0 N3 X:U113 5.0 10.1 1.0 C4 X:G80 5.0 8.2 1.0

Sodium binding site 6 out of 14 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Iridium Hexamine 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, Iridium Hexamine Soak within 5.0Å range: probe atom residue distance (Å) B Occ X:Na206 b:27.6 occ:1.00 O X:HOH319 2.4 4.1 1.0 O X:HOH352 2.5 10.2 1.0 O X:HOH516 2.7 15.8 1.0 O X:HOH452 3.6 7.6 1.0 NA X:NA214 3.9 17.7 1.0 OP2 X:A133 4.1 12.6 1.0 OP1 X:C132 4.2 15.7 1.0 O X:HOH382 4.2 9.8 1.0 O X:HOH454 4.3 13.8 1.0 OP1 X:G116 4.3 10.8 1.0 O X:HOH384 4.3 16.5 1.0 OP1 X:A133 4.3 12.0 1.0 OP2 X:G116 4.4 10.3 1.0 O2' X:G83 4.6 12.8 1.0 P X:A133 4.7 12.4 1.0 O X:HOH453 4.8 16.7 1.0 P X:G116 4.9 9.9 1.0

Sodium binding site 7 out of 14 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Iridium Hexamine 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, Iridium Hexamine Soak within 5.0Å range: probe atom residue distance (Å) B Occ X:Na207 b:27.9 occ:1.00 O X:HOH437 2.2 28.7 1.0 O6 X:G92 2.6 16.4 1.0 O4 X:U93 2.9 17.4 1.0 C6 X:G92 3.6 15.1 1.0 C4 X:U93 3.9 16.9 1.0 N4 X:C102 4.0 13.8 1.0 N7 X:G92 4.1 15.1 1.0 N6 X:A91 4.1 14.7 1.0 O6 X:G101 4.2 15.6 1.0 C5 X:G92 4.2 15.0 1.0 N3 X:U93 4.4 17.4 1.0 N1 X:G92 4.8 15.1 1.0 C6 X:A91 4.9 13.8 1.0 C5 X:U93 5.0 17.4 1.0

Sodium binding site 8 out of 14 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Iridium Hexamine 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, Iridium Hexamine Soak within 5.0Å range: probe atom residue distance (Å) B Occ X:Na208 b:31.4 occ:1.00 OP2 X:U169 3.8 16.2 1.0 C8 X:G168 3.9 12.6 1.0 C5 X:U169 4.0 15.1 1.0 O X:HOH400 4.0 5.8 1.0 O X:HOH401 4.0 16.7 1.0 N7 X:G168 4.2 12.9 1.0 O5' X:G168 4.2 16.1 1.0 C3' X:G168 4.4 14.8 1.0 N9 X:G168 4.5 12.8 1.0 OP2 X:G168 4.6 17.9 1.0 C6 X:U169 4.8 15.6 1.0 O4 X:U169 4.8 16.0 1.0 O4' X:G168 4.9 14.1 1.0 C4 X:U169 4.9 15.2 1.0 C5 X:G168 4.9 12.4 1.0

Sodium binding site 9 out of 14 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Iridium Hexamine Soak


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Iridium Hexamine Soak within 5.0Å range: probe atom residue distance (Å) B Occ X:Na209 b:37.9 occ:1.00 OP2 X:A29 4.1 37.7 1.0 O6 X:G31 4.7 54.6 1.0

Sodium binding site 10 out of 14 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Iridium Hexamine Soak


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Iridium Hexamine Soak within 5.0Å range: probe atom residue distance (Å) B Occ X:Na210 b:37.4 occ:1.00 C5' X:C13 3.8 16.1 1.0 O X:HOH551 4.1 27.2 1.0 C4' X:C13 4.1 16.1 1.0 O4' X:C13 4.2 16.7 1.0 O5' X:C13 4.9 16.5 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