Thallium in PDB 3dj2: Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak

The structure of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak, PDB code: 3dj2 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 (°)	54.086, 78.751, 140.992, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 25.1

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

Sodium

(Na)

8 atoms

Pages:

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

Binding sites:

The binding sites of Thallium atom in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak (pdb code 3dj2). This binding sites where shown within 5.0 Angstroms radius around Thallium atom.
In total 11 binding sites of Thallium where determined in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak, PDB code: 3dj2:
Jump to Thallium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Thallium binding site 1 out of 11 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 1 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Tl250 b:29.4 occ:0.20 OP1 A:A164 2.6 24.8 1.0 N7 A:G80 2.6 23.6 1.0 C5 A:U113 3.4 26.6 1.0 O6 A:G80 3.4 24.0 1.0 C5 A:G80 3.5 23.3 1.0 C8 A:G80 3.6 23.4 1.0 O4 A:U113 3.6 26.2 1.0 C4 A:U113 3.6 26.6 1.0 C6 A:G80 3.8 23.3 1.0 P A:A164 3.8 25.2 1.0 C3' A:G163 4.1 24.9 1.0 C6 A:U113 4.2 26.5 1.0 O3' A:G163 4.2 25.2 1.0 O A:HOH371 4.3 21.8 1.0 O2' A:G163 4.5 25.2 1.0 OP2 A:A164 4.6 26.3 1.0 N3 A:U113 4.6 27.1 1.0 C2' A:G163 4.7 24.8 1.0 C4 A:G80 4.7 23.5 1.0 N9 A:G80 4.8 23.5 1.0

Thallium binding site 2 out of 11 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 2 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Tl251 b:35.9 occ:0.30 N7 A:G116 2.8 26.3 1.0 O6 A:G116 2.9 26.6 1.0 N7 A:G115 3.3 24.0 1.0 C5 A:G115 3.4 23.9 1.0 C5 A:G116 3.4 26.5 1.0 C6 A:G116 3.5 26.6 1.0 C6 A:G115 3.6 23.7 1.0 O6 A:G115 3.6 24.1 1.0 O A:HOH372 3.9 25.2 1.0 C8 A:G116 3.9 26.2 1.0 C8 A:G115 4.0 23.7 1.0 C4 A:G115 4.2 23.8 1.0 N1 A:G115 4.5 23.6 1.0 N9 A:G115 4.5 23.9 1.0 C4 A:G116 4.8 26.7 1.0 N7 A:G117 4.8 27.5 1.0 O6 A:G117 4.8 27.6 1.0 N1 A:G116 4.9 26.9 1.0 N9 A:G116 5.0 26.6 1.0

Thallium binding site 3 out of 11 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 3 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Tl252 b:40.8 occ:0.20 O6 A:G114 2.9 24.6 1.0 N7 A:G114 3.0 25.1 1.0 C6 A:G114 3.5 24.9 1.0 C5 A:G114 3.5 24.9 1.0 O6 A:G115 3.5 24.1 1.0 O A:HOH372 3.6 25.2 1.0 N6 A:A162 3.8 25.4 1.0 C8 A:G114 4.1 24.6 1.0 N7 A:G115 4.2 24.0 1.0 C6 A:G115 4.3 23.7 1.0 N4 A:C139 4.4 27.3 1.0 OP1 A:G114 4.5 26.1 1.0 C6 A:A162 4.6 25.6 1.0 C5 A:G115 4.6 23.9 1.0 O4 A:U140 4.8 27.7 1.0 C4 A:G114 4.8 24.7 1.0 N1 A:G114 4.8 24.8 1.0 O6 A:G141 5.0 25.4 1.0

Thallium binding site 4 out of 11 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 4 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Tl253 b:42.5 occ:0.30 N3 A:G43 2.4 25.1 1.0 C2 A:G43 2.7 25.7 1.0 O2' A:G43 2.8 26.0 1.0 N2 A:G43 2.8 25.9 1.0 N7 A:G45 2.9 24.8 1.0 N7 A:G44 3.2 25.6 1.0 O A:HOH327 3.3 18.0 1.0 C4 A:G43 3.3 25.5 1.0 C5 A:G44 3.4 25.4 1.0 C6 A:G44 3.6 25.6 1.0 O6 A:G45 3.7 24.7 1.0 N1 A:G43 3.8 25.6 1.0 C8 A:G44 3.8 25.7 1.0 O6 A:G44 3.8 25.9 1.0 C2' A:G43 3.8 25.8 1.0 C5 A:G45 3.8 24.6 1.0 C8 A:G45 3.9 24.9 1.0 N9 A:G43 4.0 25.8 1.0 C4 A:G44 4.1 25.3 1.0 C6 A:G45 4.1 24.8 1.0 C1' A:G43 4.1 25.8 1.0 C5 A:G43 4.3 25.8 1.0 N9 A:G44 4.3 25.7 1.0 OP2 A:G45 4.5 27.7 1.0 C6 A:G43 4.5 25.7 1.0 N1 A:G44 4.5 25.4 1.0 N7 A:G46 4.8 24.3 1.0 N3 A:G44 4.9 25.5 1.0

Thallium binding site 5 out of 11 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 5 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Tl254 b:43.4 occ:0.30 N7 A:G83 2.7 22.0 1.0 O A:HOH400 2.7 14.2 1.0 O A:HOH348 3.0 9.2 1.0 O6 A:G83 3.1 23.1 1.0 O A:HOH347 3.3 22.5 1.0 C5 A:G83 3.5 22.3 1.0 C6 A:G83 3.6 23.0 1.0 C8 A:G83 3.8 21.9 1.0 N7 A:A82 3.9 23.3 1.0 N6 A:A82 3.9 22.5 1.0 C5 A:A82 4.0 22.9 1.0 C6 A:A82 4.1 23.2 1.0 O A:HOH387 4.1 28.9 1.0 C8 A:A82 4.6 22.7 1.0 O6 A:G84 4.7 23.5 1.0 N7 A:G84 4.7 23.1 1.0 C4 A:G83 4.7 22.1 1.0 O A:HOH346 4.8 23.9 1.0 C4 A:A82 4.8 22.7 1.0 N9 A:G83 4.9 22.9 1.0 N1 A:A82 4.9 23.4 1.0

Thallium binding site 6 out of 11 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 6 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Tl255 b:35.3 occ:0.20 TL A:TL255 0.0 35.3 0.2 N7 A:G123 2.6 24.8 1.0 TL A:TL255 2.9 46.1 0.3 O6 A:G123 2.9 25.2 1.0 O6 A:G122 3.4 26.6 1.0 C5 A:G123 3.4 25.4 1.0 C6 A:G123 3.5 25.3 1.0 C6 A:G122 3.5 26.8 1.0 C5 A:G122 3.6 26.6 1.0 N7 A:G122 3.6 26.0 1.0 C8 A:G123 3.8 25.2 1.0 N1 A:G122 4.4 26.8 1.0 C8 A:G122 4.5 26.5 1.0 C4 A:G122 4.5 26.8 1.0 C4 A:G123 4.7 25.5 1.0 N7 A:G124 4.8 26.8 1.0 O6 A:G124 4.8 27.2 1.0 N1 A:G123 4.9 25.2 1.0 N9 A:G123 4.9 25.6 1.0 N9 A:G122 5.0 26.9 1.0

Thallium binding site 7 out of 11 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 7 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Tl255 b:46.1 occ:0.30 TL A:TL255 0.0 46.1 0.3 N7 A:G124 2.7 26.8 1.0 O6 A:G125 2.8 23.7 1.0 TL A:TL255 2.9 35.3 0.2 C6 A:G125 3.3 23.7 1.0 N7 A:G123 3.4 24.8 1.0 O6 A:G124 3.6 27.2 1.0 C8 A:G124 3.7 26.4 1.0 C5 A:G124 3.7 26.9 1.0 C5 A:G123 3.7 25.4 1.0 O6 A:G123 3.8 25.2 1.0 C6 A:G123 3.9 25.3 1.0 C5 A:G125 3.9 23.6 1.0 C6 A:G124 4.0 27.1 1.0 C8 A:G123 4.1 25.2 1.0 N7 A:G125 4.1 23.2 1.0 N1 A:G125 4.2 23.7 1.0 C4 A:G123 4.5 25.5 1.0 N9 A:G123 4.8 25.6 1.0 N1 A:G123 4.8 25.2 1.0 N9 A:G124 4.9 26.9 1.0 C4 A:G124 4.9 26.7 1.0

Thallium binding site 8 out of 11 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 8 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Tl256 b:44.7 occ:0.20 O6 A:G141 2.6 25.4 1.0 O6 A:G161 2.7 24.5 1.0 O4 A:U142 2.8 20.6 1.0 O6 A:G160 2.8 26.9 1.0 O A:HOH341 3.0 25.5 1.0 C6 A:G160 3.5 27.0 1.0 C4 A:U142 3.6 20.6 1.0 N3 A:U142 3.7 20.7 1.0 N6 A:A162 3.7 25.4 1.0 C6 A:G141 3.8 25.7 1.0 C6 A:G161 3.8 24.5 1.0 C5 A:G160 4.2 27.2 1.0 N7 A:G161 4.3 24.2 1.0 N1 A:G160 4.4 26.8 1.0 C5 A:G161 4.4 24.6 1.0 N7 A:G160 4.5 27.2 1.0 O4 A:U140 4.5 27.7 1.0 N1 A:G141 4.6 25.5 1.0 C6 A:A162 4.6 25.6 1.0 N4 A:C143 4.7 21.9 1.0 C5 A:G141 4.7 25.8 1.0 N1 A:A162 4.8 25.7 1.0 C2 A:U142 4.9 20.8 1.0 C5 A:U142 4.9 19.9 1.0 N1 A:G161 5.0 24.6 1.0

Thallium binding site 9 out of 11 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 9 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Tl257 b:42.8 occ:0.20 N7 A:G172 2.9 26.6 1.0 O6 A:G172 2.9 26.7 1.0 O4 A:U173 3.1 31.1 1.0 C5 A:G172 3.5 26.8 1.0 C6 A:G172 3.5 26.8 1.0 C4 A:U173 3.8 30.8 1.0 N7 A:G171 3.8 25.3 1.0 O6 A:G171 4.0 25.4 1.0 C8 A:G172 4.0 26.8 1.0 C5 A:G171 4.1 25.0 1.0 C6 A:G171 4.2 25.2 1.0 C5 A:U173 4.5 30.8 1.0 N3 A:U173 4.6 30.8 1.0 C8 A:G171 4.6 25.3 1.0 C4 A:G172 4.9 26.9 1.0 N1 A:G172 4.9 26.9 1.0

Thallium binding site 10 out of 11 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 10 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Tl+ Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Tl258 b:24.7 occ:0.20 O A:HOH328 2.3 11.9 1.0 O A:HOH345 2.7 19.0 1.0 O6 A:G69 2.7 23.1 1.0 N7 A:G68 2.8 23.0 1.0 C6 A:G69 3.4 23.1 1.0 C8 A:G68 3.6 23.1 1.0 N2 A:G25 3.7 21.4 1.0 N7 A:G69 3.8 22.4 1.0 N7 A:A67 3.8 24.0 1.0 C5 A:G69 3.9 22.9 1.0 C5 A:G68 3.9 23.1 1.0 O6 A:G68 4.1 22.9 1.0 C8 A:A67 4.1 24.2 1.0 OP2 A:G68 4.4 25.4 1.0 C6 A:G68 4.4 23.1 1.0 C2 A:G25 4.4 21.3 1.0 C5 A:A67 4.5 24.1 1.0 N1 A:G69 4.5 23.0 1.0 O4 A:U24 4.5 18.4 1.0 N6 A:A23 4.6 17.0 1.0 OP2 A:A67 4.6 28.0 1.0 N3 A:G25 4.6 21.7 1.0 N3 A:U24 4.6 19.6 1.0 C8 A:G69 4.9 22.6 1.0 N9 A:G68 4.9 23.4 1.0 N9 A:A67 5.0 24.2 1.0 O A:HOH311 5.0 11.9 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