Sodium in PDB 3dix: Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, K+ Anomalous Data

The structure of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, K+ Anomalous Data, PDB code: 3dix 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 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.108, 78.902, 140.167, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 20.5

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

Potassium

(K)

1 atom

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

Sodium binding site 1 out of 5 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, K+ Anomalous Data


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, K+ Anomalous Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:30.1 occ:1.00 O6 A:G20 2.5 27.0 1.0 O6 A:G71 2.7 31.0 1.0 N7 A:G71 3.4 29.2 1.0 C6 A:G71 3.6 29.5 1.0 C6 A:G20 3.6 25.5 1.0 C5 A:G71 3.8 29.2 1.0 OP2 A:C70 4.1 26.5 1.0 C5 A:G20 4.4 25.1 1.0 N7 A:G20 4.5 24.6 1.0 N1 A:G20 4.6 24.6 1.0 C8 A:G71 4.6 29.5 1.0 N1 A:G71 4.9 29.1 1.0 C5 A:C70 4.9 26.8 1.0

Sodium binding site 2 out of 5 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, K+ Anomalous Data


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, K+ Anomalous Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:55.7 occ:1.00 O6 A:G146 3.4 33.1 1.0 O6 A:G147 3.6 32.5 1.0 N4 A:C145 3.6 30.7 1.0 N7 A:G146 3.7 32.3 1.0 C6 A:G146 4.1 32.9 1.0 C4 A:C145 4.1 30.7 1.0 C5 A:G146 4.2 32.5 1.0 N7 A:G147 4.2 32.7 1.0 C5 A:C145 4.3 31.2 1.0 C6 A:G147 4.5 32.6 1.0 C5 A:G147 4.7 32.5 1.0 C8 A:G146 4.8 32.4 1.0

Sodium binding site 3 out of 5 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, K+ Anomalous Data


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, K+ Anomalous Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:47.6 occ:1.00 N7 A:G68 3.0 27.0 1.0 O6 A:G69 3.2 26.1 1.0 C8 A:G68 3.6 26.9 1.0 N7 A:A67 3.7 29.8 1.0 OP2 A:G68 3.8 32.1 1.0 N2 A:G25 3.8 23.6 1.0 C8 A:A67 3.8 30.1 1.0 C6 A:G69 4.0 25.0 1.0 OP2 A:A67 4.0 36.2 1.0 N7 A:G69 4.0 25.0 1.0 C5 A:G68 4.2 26.9 1.0 C5 A:G69 4.3 24.9 1.0 O5' A:A67 4.5 35.8 1.0 O6 A:G68 4.5 26.9 1.0 C5 A:A67 4.6 29.6 1.0 N9 A:A67 4.7 30.4 1.0 C2 A:G25 4.7 23.6 1.0 C6 A:G68 4.7 26.8 1.0 C3' A:A67 4.9 31.9 1.0 P A:A67 4.9 36.0 1.0 N6 A:A23 4.9 22.0 1.0 N9 A:G68 5.0 27.2 1.0

Sodium binding site 4 out of 5 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, K+ Anomalous Data


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, K+ Anomalous Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:30.6 occ:1.00 NA A:NA205 3.4 37.4 1.0 O2 A:C13 4.5 37.6 1.0

Sodium binding site 5 out of 5 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, K+ Anomalous Data


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, K+ Anomalous Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:37.4 occ:1.00 OP1 A:C131 3.1 32.4 1.0 NA A:NA204 3.4 30.6 1.0 OP1 A:G117 4.2 27.9 1.0 P A:C131 4.3 33.8 1.0 OP2 A:C131 4.6 33.2 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