Iridium in PDB 3d0u: Crystal Structure of Lysine Riboswitch Bound to Lysine

The structure of Crystal Structure of Lysine Riboswitch Bound to Lysine, PDB code: 3d0u was solved by A.D.Garst, A.Heroux, R.P.Rambo, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.62 / 2.80
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	119.823, 119.823, 58.744, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 20.9

The binding sites of Iridium atom in the Crystal Structure of Lysine Riboswitch Bound to Lysine (pdb code 3d0u). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 3 binding sites of Iridium where determined in the Crystal Structure of Lysine Riboswitch Bound to Lysine, PDB code: 3d0u:
Jump to Iridium binding site number: 1; 2; 3;

Iridium binding site 1 out of 3 in the Crystal Structure of Lysine Riboswitch Bound to Lysine


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 1 of Crystal Structure of Lysine Riboswitch Bound to Lysine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir202 b:56.3 occ:1.00 IR A:IRI202 0.0 56.3 1.0 N2 A:IRI202 2.2 50.2 1.0 N6 A:IRI202 2.2 41.5 1.0 N5 A:IRI202 2.2 61.2 1.0 N3 A:IRI202 2.3 45.9 1.0 N1 A:IRI202 2.3 50.8 1.0 N4 A:IRI202 2.3 50.2 1.0 O6 A:G149 3.6 38.8 1.0 N7 A:G149 4.3 38.6 1.0 O4 A:U139 4.4 38.5 1.0 C6 A:G149 4.4 38.9 1.0 O A:HOH212 4.6 37.6 1.0 O6 A:G138 4.6 38.9 1.0 C5 A:G149 4.7 37.6 1.0 O6 A:G150 4.7 41.1 1.0 O4 A:U137 4.8 41.4 1.0

Iridium binding site 2 out of 3 in the Crystal Structure of Lysine Riboswitch Bound to Lysine


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 2 of Crystal Structure of Lysine Riboswitch Bound to Lysine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir203 b:0.9 occ:1.00 IR A:IRI203 0.0 0.9 1.0 N2 A:IRI203 2.2 89.7 1.0 N6 A:IRI203 2.2 76.7 1.0 N5 A:IRI203 2.3 0.9 1.0 N1 A:IRI203 2.3 0.8 1.0 N3 A:IRI203 2.3 88.2 1.0 N4 A:IRI203 2.3 0.4 1.0 O6 A:G122 4.1 65.9 1.0 N7 A:G120 4.4 56.0 1.0 O6 A:G120 4.9 51.5 1.0

Iridium binding site 3 out of 3 in the Crystal Structure of Lysine Riboswitch Bound to Lysine


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 3 of Crystal Structure of Lysine Riboswitch Bound to Lysine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir204 b:0.3 occ:1.00 IR A:IRI204 0.0 0.3 1.0 N2 A:IRI204 2.2 66.2 1.0 N6 A:IRI204 2.2 79.3 1.0 N5 A:IRI204 2.3 73.1 1.0 N1 A:IRI204 2.3 57.6 1.0 N3 A:IRI204 2.3 93.0 1.0 N4 A:IRI204 2.3 85.6 1.0 C5 A:C81 4.0 41.6 1.0 N4 A:C81 4.5 39.9 1.0 O4 A:U106 4.6 41.4 1.0 C4 A:C81 4.8 40.8 1.0 N7 A:G80 5.0 37.2 1.0 C6 A:C81 5.0 37.9 1.0

A.D.Garst, A.Heroux, R.P.Rambo, R.T.Batey. Crystal Structure of the Lysine Riboswitch Regulatory Mrna Element. J.Biol.Chem. V. 283 22347 2008.
ISSN: ISSN 0021-9258
PubMed: 18593706
DOI: 10.1074/JBC.C800120200