Iridium 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
Sodium	(Na)	14 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Iridium 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 Iridium atom.
In total 18 binding sites of Iridium where determined in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, Iridium Hexamine Soak, PDB code: 3dio:
Jump to Iridium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iridium binding site 1 out of 18 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 Iridium with other atoms in the Ir 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:Ir250 b:53.7 occ:1.00 IR X:IRI250 0.0 53.7 1.0 N1 X:IRI250 2.0 53.8 1.0 N5 X:IRI250 2.0 53.4 1.0 N6 X:IRI250 2.0 53.6 1.0 N3 X:IRI250 2.0 53.9 1.0 N4 X:IRI250 2.0 54.0 1.0 N2 X:IRI250 2.0 54.0 1.0 O4 X:U173 3.9 32.4 1.0 O X:HOH321 3.9 15.9 1.0 O X:HOH320 3.9 24.3 1.0 O X:HOH558 4.0 29.1 1.0 O6 X:G172 4.1 24.8 1.0 O6 X:G1 4.1 35.1 1.0 O X:HOH555 4.2 30.7 1.0 C4 X:U173 4.9 31.9 1.0 O6 X:G2 5.0 26.2 1.0

Iridium binding site 2 out of 18 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 Iridium with other atoms in the Ir 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:Ir251 b:52.9 occ:0.30 IR X:IRI251 0.0 52.9 0.3 N2 X:IRI251 2.0 52.8 0.3 N1 X:IRI251 2.0 52.8 0.3 N3 X:IRI251 2.0 52.8 0.3 N6 X:IRI251 2.0 52.7 0.3 N4 X:IRI251 2.0 52.7 0.3 N5 X:IRI251 2.0 52.7 0.3 OP2 X:G110 3.9 28.6 1.0 OP1 X:U109 3.9 24.5 1.0 O X:HOH366 4.7 31.1 1.0 P X:U109 4.8 22.8 1.0 OP2 X:U109 4.8 22.9 1.0

Iridium binding site 3 out of 18 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 Iridium with other atoms in the Ir 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:Ir252 b:57.5 occ:0.20 IR X:IRI252 0.0 57.5 0.2 N2 X:IRI252 2.0 57.3 0.2 N5 X:IRI252 2.0 57.3 0.2 N6 X:IRI252 2.0 57.3 0.2 N4 X:IRI252 2.0 57.3 0.2 N3 X:IRI252 2.0 57.2 0.2 N1 X:IRI252 2.0 57.3 0.2 O6 X:G125 3.8 13.1 1.0 N7 X:G123 4.2 15.7 1.0 O6 X:G123 4.3 16.0 1.0 O X:HOH489 4.4 19.3 1.0 C6 X:G125 4.6 12.8 1.0 O6 X:G124 4.8 11.3 1.0 N1 X:G125 4.9 12.3 1.0 C5 X:G123 4.9 15.2 1.0 C6 X:G123 4.9 14.6 1.0

Iridium binding site 4 out of 18 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 Iridium with other atoms in the Ir 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:Ir253 b:56.7 occ:0.10 IR X:IRI253 0.0 56.7 0.1 N4 X:IRI253 2.0 56.7 0.1 N3 X:IRI253 2.0 56.7 0.1 N1 X:IRI253 2.0 56.7 0.1 N5 X:IRI253 2.0 56.7 0.1 N6 X:IRI253 2.0 56.7 0.1 N2 X:IRI253 2.0 56.7 0.1 N3 X:IRI253 2.1 59.5 0.1 O6 X:G57 3.5 64.5 1.0 O6 X:G56 3.9 54.4 1.0 N2 X:IRI253 3.9 59.5 0.1 IR X:IRI253 3.9 59.5 0.1 N6 X:IRI253 4.1 59.5 0.1 N7 X:G56 4.3 54.0 1.0 C6 X:G57 4.5 64.5 1.0 C6 X:G56 4.7 54.2 1.0 N5 X:IRI253 4.7 59.5 0.1 N4 X:IRI253 4.9 59.5 0.1 C5 X:G56 4.9 54.2 1.0

Iridium binding site 5 out of 18 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 Iridium with other atoms in the Ir 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:Ir253 b:59.5 occ:0.10 IR X:IRI253 0.0 59.5 0.1 N6 X:IRI253 2.0 59.5 0.1 N2 X:IRI253 2.0 59.5 0.1 N3 X:IRI253 2.0 59.5 0.1 N5 X:IRI253 2.0 59.5 0.1 N1 X:IRI253 2.0 59.5 0.1 N4 X:IRI253 2.0 59.5 0.1 N4 X:IRI253 2.8 56.7 0.1 N1 X:IRI253 3.0 56.7 0.1 IR X:IRI253 3.9 56.7 0.1 N5 X:IRI253 4.0 56.7 0.1 N7 X:G55 4.3 55.4 1.0 O6 X:G55 4.4 55.6 1.0 OP2 X:G54 4.6 56.4 1.0 N6 X:IRI253 4.8 56.7 0.1

Iridium binding site 6 out of 18 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 Iridium with other atoms in the Ir 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:Ir254 b:58.3 occ:0.40 IR X:IRI254 0.0 58.3 0.4 N3 X:IRI254 2.0 58.0 0.4 N4 X:IRI254 2.0 58.0 0.4 N6 X:IRI254 2.0 57.9 0.4 N2 X:IRI254 2.0 58.0 0.4 N5 X:IRI254 2.0 58.0 0.4 N1 X:IRI254 2.0 57.9 0.4 O X:HOH556 3.5 34.0 1.0 O4 X:U109 3.8 16.0 1.0 O X:HOH515 3.8 20.7 1.0 N7 X:G83 4.3 10.3 1.0 O X:HOH549 4.4 26.1 1.0 O X:HOH554 4.4 22.0 1.0 O X:HOH368 4.5 27.2 1.0 O6 X:G84 4.6 12.6 1.0 N7 X:G84 4.6 10.5 1.0 O6 X:G83 4.6 10.4 1.0 C4 X:U109 4.9 15.2 1.0

Iridium binding site 7 out of 18 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 Iridium with other atoms in the Ir 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:Ir255 b:45.5 occ:1.00 IR X:IRI255 0.0 45.5 1.0 N6 X:IRI255 2.0 45.2 1.0 N1 X:IRI255 2.0 45.0 1.0 N4 X:IRI255 2.0 45.2 1.0 N3 X:IRI255 2.0 45.1 1.0 N2 X:IRI255 2.0 45.2 1.0 N5 X:IRI255 2.0 45.1 1.0 OP1 X:G117 3.9 13.3 1.0 O X:HOH312 4.0 3.0 1.0 O2 X:C13 4.2 16.6 1.0 OP1 X:C15 4.2 10.2 1.0 O X:HOH383 4.2 12.0 1.0 OP1 X:C131 4.3 18.7 1.0 O3' X:G116 4.8 13.2 1.0 C2 X:C13 5.0 17.2 1.0

Iridium binding site 8 out of 18 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 Iridium with other atoms in the Ir 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:Ir256 b:61.2 occ:0.25 IR X:IRI256 0.0 61.2 0.2 N3 X:IRI256 2.0 61.1 0.2 N5 X:IRI256 2.0 61.0 0.2 N4 X:IRI256 2.0 61.1 0.2 N2 X:IRI256 2.0 61.0 0.2 N6 X:IRI256 2.0 61.0 0.2 N1 X:IRI256 2.0 61.0 0.2 O X:HOH471 3.8 40.0 1.0 OP2 X:G146 4.3 28.0 1.0 O X:HOH470 4.3 20.6 1.0 O X:HOH472 4.5 30.6 1.0 OP2 X:G147 4.5 31.6 1.0

Iridium binding site 9 out of 18 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 Iridium with other atoms in the Ir 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:Ir257 b:55.3 occ:0.80 IR X:IRI257 0.0 55.3 0.8 N4 X:IRI257 2.0 55.0 0.8 N6 X:IRI257 2.0 55.2 0.8 N5 X:IRI257 2.0 55.2 0.8 N1 X:IRI257 2.0 55.4 0.8 N3 X:IRI257 2.0 55.5 0.8 N2 X:IRI257 2.0 55.0 0.8 O6 X:G150 4.2 44.6 1.0 O6 X:G149 4.2 24.8 1.0 N7 X:G149 4.2 23.7 1.0 O X:HOH517 4.7 29.0 1.0 C6 X:G149 4.9 23.3 1.0 C5 X:G149 4.9 23.5 1.0

Iridium binding site 10 out of 18 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 Iridium with other atoms in the Ir 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:Ir258 b:56.7 occ:0.70 IR X:IRI258 0.0 56.7 0.7 N5 X:IRI258 2.0 56.3 0.7 N4 X:IRI258 2.0 56.3 0.7 N1 X:IRI258 2.0 56.2 0.7 N6 X:IRI258 2.0 56.5 0.7 N3 X:IRI258 2.0 56.2 0.7 N2 X:IRI258 2.0 56.4 0.7 OP1 X:G114 4.0 13.8 1.0 O X:HOH387 4.0 18.6 1.0 N7 X:G115 4.1 8.4 1.0 O3' X:U113 4.3 13.7 1.0 OP2 X:G115 4.4 11.2 1.0 O2' X:U113 4.6 11.9 1.0 O6 X:G115 4.7 9.1 1.0 P X:G114 4.8 13.1 1.0 C8 X:G115 5.0 8.2 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