Sodium in PDB 3dig: Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to S-(2-Aminoethyl)-L-Cysteine

The structure of Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to S-(2-Aminoethyl)-L-Cysteine, PDB code: 3dig 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 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.441, 78.941, 142.855, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 22.5

The structure of Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to S-(2-Aminoethyl)-L-Cysteine also contains other interesting chemical elements:

Potassium

(K)

1 atom

Pages:

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

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to S-(2-Aminoethyl)-L-Cysteine (pdb code 3dig). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 14 binding sites of Sodium where determined in the Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to S-(2-Aminoethyl)-L-Cysteine, PDB code: 3dig:
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 Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to S-(2-Aminoethyl)-L-Cysteine


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 the Thermotoga Maritima Lysine Riboswitch Bound to S-(2-Aminoethyl)-L-Cysteine within 5.0Å range: probe atom residue distance (Å) B Occ X:Na201 b:20.8 occ:1.00 O X:HOH322 2.4 12.4 1.0 O6 X:G20 2.4 22.8 1.0 O6 X:G71 2.9 23.9 1.0 N7 X:G71 3.4 21.9 1.0 C6 X:G20 3.6 23.1 1.0 C6 X:G71 3.7 22.6 1.0 OP2 X:C70 3.8 20.2 1.0 C5 X:G71 3.9 22.1 1.0 O X:HOH321 4.4 25.1 1.0 N1 X:G20 4.4 23.2 1.0 C5 X:G20 4.5 22.8 1.0 C8 X:G71 4.6 21.8 1.0 N7 X:G20 4.7 22.3 1.0 C5 X:C70 4.8 16.8 1.0 P X:C70 5.0 19.9 1.0 N1 X:G71 5.0 22.4 1.0

Sodium binding site 2 out of 14 in the Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to S-(2-Aminoethyl)-L-Cysteine


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 the Thermotoga Maritima Lysine Riboswitch Bound to S-(2-Aminoethyl)-L-Cysteine within 5.0Å range: probe atom residue distance (Å) B Occ X:Na202 b:39.0 occ:1.00 O X:HOH320 3.5 23.3 1.0 OP2 X:G69 4.4 22.3 1.0 OP1 X:G68 4.4 21.7 1.0 OP1 X:G69 4.5 22.1 1.0 C5' X:G68 4.8 21.6 1.0 P X:G69 4.9 21.8 1.0

Sodium binding site 3 out of 14 in the Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to S-(2-Aminoethyl)-L-Cysteine


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 the Thermotoga Maritima Lysine Riboswitch Bound to S-(2-Aminoethyl)-L-Cysteine within 5.0Å range: probe atom residue distance (Å) B Occ X:Na203 b:36.1 occ:1.00 O X:HOH324 2.8 21.9 1.0 O6 X:G69 2.8 19.6 1.0 N7 X:G68 3.1 23.3 1.0 N2 X:G25 3.5 23.4 1.0 C6 X:G69 3.6 19.7 1.0 N7 X:A67 3.8 22.8 1.0 C8 X:G68 4.0 23.5 1.0 O6 X:G68 4.1 22.4 1.0 C5 X:G68 4.1 23.5 1.0 C2 X:G25 4.2 23.8 1.0 C5 X:G69 4.2 19.8 1.0 C8 X:A67 4.2 22.8 1.0 N7 X:G69 4.2 20.2 1.0 O4 X:U24 4.3 18.5 1.0 N6 X:A23 4.4 13.6 1.0 OP2 X:A67 4.4 21.4 1.0 OP2 X:G68 4.4 21.4 1.0 N3 X:G25 4.4 23.9 1.0 C6 X:G68 4.5 22.8 1.0 N1 X:G69 4.6 19.6 1.0 N3 X:U24 4.6 18.7 1.0 C5 X:A67 4.6 22.6 1.0 C4 X:U24 4.9 18.7 1.0

Sodium binding site 4 out of 14 in the Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to S-(2-Aminoethyl)-L-Cysteine


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 the Thermotoga Maritima Lysine Riboswitch Bound to S-(2-Aminoethyl)-L-Cysteine within 5.0Å range: probe atom residue distance (Å) B Occ X:Na204 b:36.7 occ:1.00 NA X:NA208 3.4 39.4 1.0 OP2 X:C130 4.2 26.3 1.0 OP1 X:A129 4.4 28.6 1.0

Sodium binding site 5 out of 14 in the Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to S-(2-Aminoethyl)-L-Cysteine


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 the Thermotoga Maritima Lysine Riboswitch Bound to S-(2-Aminoethyl)-L-Cysteine within 5.0Å range: probe atom residue distance (Å) B Occ X:Na205 b:35.6 occ:1.00 OP2 X:G11 2.7 23.8 1.0 O6 X:G12 2.7 27.0 1.0 C6 X:G12 3.7 27.6 1.0 P X:G11 3.7 23.5 1.0 OP1 X:G11 4.1 22.6 1.0 N2 X:G11 4.1 26.4 1.0 N4 X:C79 4.2 18.8 1.0 N7 X:G12 4.3 26.5 1.0 C5 X:G12 4.4 26.9 1.0 O3' X:A10 4.4 27.0 1.0 OP1 X:A10 4.8 28.7 1.0 O5' X:A10 4.8 27.1 1.0 N1 X:G12 4.8 27.6 1.0 C3' X:A10 4.8 25.8 1.0 C4 X:C79 5.0 18.2 1.0

Sodium binding site 6 out of 14 in the Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to S-(2-Aminoethyl)-L-Cysteine


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 the Thermotoga Maritima Lysine Riboswitch Bound to S-(2-Aminoethyl)-L-Cysteine within 5.0Å range: probe atom residue distance (Å) B Occ X:Na206 b:31.5 occ:1.00 O2 X:C13 4.2 27.0 1.0 OP1 X:C15 4.4 20.7 1.0 OP2 X:C15 4.5 20.3 1.0 O2' X:C13 4.7 26.6 1.0 C2 X:C13 5.0 27.5 1.0 P X:C15 5.0 20.9 1.0

Sodium binding site 7 out of 14 in the Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to S-(2-Aminoethyl)-L-Cysteine


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 the Thermotoga Maritima Lysine Riboswitch Bound to S-(2-Aminoethyl)-L-Cysteine within 5.0Å range: probe atom residue distance (Å) B Occ X:Na207 b:27.0 occ:1.00 OP1 X:C15 4.0 20.7 1.0 OP1 X:C131 4.2 22.6 1.0 OP1 X:G117 4.2 24.8 1.0 OP2 X:C132 4.5 20.6 1.0 OP2 X:G117 4.7 25.1 1.0 P X:G117 4.8 24.4 1.0 OP1 X:G16 4.8 20.6 1.0 OP2 X:G16 4.9 20.7 1.0 O3' X:G116 5.0 24.1 1.0 OP1 X:C132 5.0 20.7 1.0

Sodium binding site 8 out of 14 in the Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to S-(2-Aminoethyl)-L-Cysteine


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 the Thermotoga Maritima Lysine Riboswitch Bound to S-(2-Aminoethyl)-L-Cysteine within 5.0Å range: probe atom residue distance (Å) B Occ X:Na208 b:39.4 occ:1.00 NA X:NA204 3.4 36.7 1.0 OP1 X:G118 3.9 24.3 1.0 OP2 X:G118 4.1 24.1 1.0 P X:G118 4.5 24.3 1.0 OP2 X:C130 4.8 26.3 1.0 OP1 X:C130 4.9 26.7 1.0

Sodium binding site 9 out of 14 in the Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to S-(2-Aminoethyl)-L-Cysteine


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 the Thermotoga Maritima Lysine Riboswitch Bound to S-(2-Aminoethyl)-L-Cysteine within 5.0Å range: probe atom residue distance (Å) B Occ X:Na209 b:37.2 occ:1.00 O X:HOH319 2.6 15.1 1.0 OP2 X:G8 3.9 23.3 1.0 OP1 X:C79 4.0 20.7 1.0 OP2 X:C79 4.7 20.4 1.0 P X:C79 4.9 20.6 1.0 NA X:NA210 5.0 29.3 1.0

Sodium binding site 10 out of 14 in the Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to S-(2-Aminoethyl)-L-Cysteine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of the Thermotoga Maritima Lysine Riboswitch Bound to S-(2-Aminoethyl)-L-Cysteine within 5.0Å range: probe atom residue distance (Å) B Occ X:Na210 b:29.3 occ:1.00 O X:HOH319 2.6 15.1 1.0 O6 X:G9 2.8 27.4 1.0 OP1 X:G80 3.7 18.5 1.0 C6 X:G9 3.8 27.9 1.0 N7 X:G9 4.1 27.6 1.0 C5 X:G9 4.3 27.8 1.0 N6 X:A10 4.6 27.8 1.0 N4 X:C166 4.6 19.8 1.0 O6 X:G8 4.7 22.8 1.0 O6 X:G165 4.8 18.6 1.0 NA X:NA209 5.0 37.2 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