Sodium in PDB 3dj0: Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to L-4-Oxalysine

The structure of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to L-4-Oxalysine, PDB code: 3dj0 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 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.541, 79.095, 142.535, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 26.8

The structure of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to L-4-Oxalysine also contains other interesting chemical elements:

Potassium

(K)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Sodium atom in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to L-4-Oxalysine (pdb code 3dj0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 17 binding sites of Sodium where determined in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to L-4-Oxalysine, PDB code: 3dj0:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 17 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to L-4-Oxalysine


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 L-4-Oxalysine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:18.2 occ:1.00 O A:HOH272 2.3 12.6 1.0 O6 A:G71 2.5 26.3 1.0 O A:HOH239 2.6 11.8 1.0 O6 A:G20 2.6 26.8 1.0 C6 A:G71 3.6 26.0 1.0 C6 A:G20 3.8 26.4 1.0 N7 A:G71 4.0 25.7 1.0 O A:HOH226 4.1 11.3 1.0 C5 A:G71 4.2 25.5 1.0 OP2 A:C70 4.3 25.5 1.0 N7 A:G20 4.4 25.5 1.0 C5 A:G20 4.5 25.7 1.0 OP2 A:C19 4.5 27.0 1.0 O A:HOH288 4.7 21.4 1.0 N1 A:G71 4.8 24.8 1.0 N1 A:G20 4.8 26.1 1.0 O A:HOH230 4.8 10.1 1.0

Sodium binding site 2 out of 17 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to L-4-Oxalysine


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 L-4-Oxalysine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:23.2 occ:1.00 O A:HOH258 2.1 19.2 1.0 O A:HOH228 2.3 27.6 1.0 O A:HOH245 2.7 15.2 1.0 O6 A:G69 2.7 24.1 1.0 N7 A:G68 2.8 25.3 1.0 C6 A:G69 3.5 23.7 1.0 C8 A:G68 3.7 25.5 1.0 N7 A:A67 3.7 26.5 1.0 N2 A:G25 3.8 22.7 1.0 N7 A:G69 3.8 23.1 1.0 C5 A:G68 3.9 25.3 1.0 C5 A:G69 3.9 24.0 1.0 O6 A:G68 4.0 24.8 1.0 C8 A:A67 4.1 26.6 1.0 OP2 A:G68 4.2 26.4 1.0 C6 A:G68 4.3 25.0 1.0 C5 A:A67 4.4 26.3 1.0 C2 A:G25 4.5 23.1 1.0 OP2 A:A67 4.5 28.7 1.0 N1 A:G69 4.5 23.4 1.0 N6 A:A23 4.5 20.3 1.0 N3 A:G25 4.6 22.9 1.0 O4 A:U24 4.6 22.0 1.0 N3 A:U24 4.7 21.4 1.0 N9 A:G68 4.9 25.8 1.0 N9 A:A67 4.9 27.1 1.0 N6 A:A67 5.0 26.1 1.0 C8 A:G69 5.0 23.6 1.0

Sodium binding site 3 out of 17 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to L-4-Oxalysine


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 L-4-Oxalysine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:44.6 occ:1.00 OP2 A:C130 3.2 28.7 1.0 OP1 A:A129 3.5 29.7 1.0 NA A:NA217 3.8 36.5 1.0 P A:C130 4.6 29.5 1.0 C5' A:A129 4.6 29.2 1.0 P A:A129 4.7 30.6 1.0 O5' A:A129 4.8 30.2 1.0

Sodium binding site 4 out of 17 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to L-4-Oxalysine


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 L-4-Oxalysine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:31.6 occ:1.00 OP2 A:G11 2.6 27.3 1.0 O6 A:G12 2.7 26.4 1.0 N4 A:C79 3.8 27.3 1.0 C6 A:G12 3.8 26.4 1.0 N2 A:G11 3.9 24.3 1.0 P A:G11 4.0 27.2 1.0 OP1 A:A10 4.4 27.7 1.0 O5' A:A10 4.5 28.0 1.0 C4 A:C79 4.5 28.8 1.0 OP2 A:A10 4.6 28.2 1.0 OP1 A:G11 4.6 26.6 1.0 P A:A10 4.7 27.9 1.0 N1 A:G12 4.7 26.5 1.0 C5 A:G12 4.7 26.6 1.0 O3' A:A10 4.7 27.0 1.0 O A:HOH265 4.7 9.7 1.0 N3 A:C79 4.8 29.1 1.0 N7 A:G12 4.9 26.8 1.0 C3' A:A10 4.9 28.4 1.0 O A:HOH240 5.0 16.1 1.0

Sodium binding site 5 out of 17 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to L-4-Oxalysine


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 L-4-Oxalysine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:35.1 occ:1.00 O A:HOH251 3.1 25.8 1.0 O A:HOH234 4.0 12.6 1.0 O A:HOH276 4.2 16.0 1.0 OP1 A:C15 4.4 22.9 1.0 OP2 A:C15 4.9 24.1 1.0 O2 A:C13 4.9 33.9 1.0

Sodium binding site 6 out of 17 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to L-4-Oxalysine


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 L-4-Oxalysine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na206 b:30.2 occ:1.00 OP1 A:C131 2.5 29.8 1.0 P A:C131 3.6 29.8 1.0 C5' A:C131 3.6 28.9 1.0 O A:HOH251 3.7 25.8 1.0 O3' A:C130 3.7 29.2 1.0 O5' A:C131 4.1 29.2 1.0 O A:HOH234 4.4 12.6 1.0 O2' A:C130 4.9 31.2 1.0 C4' A:C131 4.9 29.0 1.0 OP2 A:C131 4.9 28.9 1.0

Sodium binding site 7 out of 17 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to L-4-Oxalysine


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 L-4-Oxalysine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na207 b:21.7 occ:1.00 O A:HOH234 2.6 12.6 1.0 OP2 A:C132 4.2 28.1 1.0 OP1 A:G117 4.2 28.8 1.0 OP1 A:C15 4.2 22.9 1.0 O A:HOH251 4.2 25.8 1.0 OP1 A:C131 4.4 29.8 1.0 OP1 A:C132 4.5 28.3 1.0 OP1 A:G16 4.5 23.8 1.0 OP2 A:G117 4.6 28.9 1.0 O A:HOH293 4.8 24.8 1.0 P A:G117 4.8 29.1 1.0 P A:C132 4.9 28.8 1.0

Sodium binding site 8 out of 17 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to L-4-Oxalysine


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 L-4-Oxalysine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na208 b:41.1 occ:1.00 O A:HOH266 2.8 22.0 1.0 OP1 A:G116 4.1 26.9 1.0 OP2 A:A133 4.3 26.2 1.0 OP2 A:G116 4.3 26.8 1.0 OP1 A:A133 4.4 26.0 1.0 OP1 A:C132 4.5 28.3 1.0 P A:G116 4.7 25.0 1.0 P A:A133 4.9 26.3 1.0 O2' A:G83 4.9 23.5 1.0

Sodium binding site 9 out of 17 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to L-4-Oxalysine


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 L-4-Oxalysine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na209 b:32.0 occ:1.00 O A:HOH249 2.3 23.8 1.0 O A:HOH294 2.6 12.2 1.0 O6 A:G9 2.7 27.4 1.0 C6 A:G9 3.7 27.1 1.0 N7 A:G9 3.7 25.3 1.0 O A:HOH242 3.9 24.1 1.0 OP1 A:G80 4.0 26.7 1.0 C5 A:G9 4.1 26.4 1.0 N4 A:C166 4.3 21.5 1.0 O A:HOH274 4.3 22.5 1.0 O6 A:G8 4.5 27.6 1.0 O A:HOH292 4.6 9.9 1.0 N6 A:A10 4.8 26.6 1.0 O6 A:G165 4.8 23.1 1.0 N1 A:G9 4.9 26.7 1.0 C8 A:G9 5.0 27.4 1.0

Sodium binding site 10 out of 17 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to L-4-Oxalysine


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 L-4-Oxalysine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na210 b:31.0 occ:1.00 OP1 A:A164 2.3 28.5 1.0 O A:HOH256 2.5 14.7 1.0 N7 A:G80 2.8 23.8 1.0 C8 A:G80 3.5 23.2 1.0 P A:A164 3.7 29.8 1.0 O4 A:U113 3.7 25.5 1.0 C5 A:U113 3.8 25.8 1.0 C5 A:G80 3.9 23.2 1.0 C4 A:U113 3.9 25.9 1.0 O6 A:G80 4.3 24.1 1.0 C3' A:G163 4.3 28.5 1.0 O3' A:G163 4.3 29.6 1.0 OP2 A:A164 4.4 30.3 1.0 N7 A:A164 4.5 35.3 1.0 C6 A:G80 4.5 23.2 1.0 C8 A:A164 4.5 35.8 1.0 C6 A:U113 4.7 26.1 1.0 O5' A:A164 4.7 30.3 1.0 N9 A:G80 4.8 24.2 1.0 O2' A:G163 4.9 29.0 1.0 OP2 A:G163 5.0 29.3 1.0 C4 A:G80 5.0 24.0 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