Iridium in PDB 3sd3: The Structure of the Tetrahydrofolate Riboswitch Containing A U25C Mutation

The structure of The Structure of the Tetrahydrofolate Riboswitch Containing A U25C Mutation, PDB code: 3sd3 was solved by F.E.Reyes, J.J.Trausch, P.Ceres, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.90 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	27.520, 68.590, 158.080, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 24.3

The binding sites of Iridium atom in the The Structure of the Tetrahydrofolate Riboswitch Containing A U25C Mutation (pdb code 3sd3). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 5 binding sites of Iridium where determined in the The Structure of the Tetrahydrofolate Riboswitch Containing A U25C Mutation, PDB code: 3sd3:
Jump to Iridium binding site number: 1; 2; 3; 4; 5;

Iridium binding site 1 out of 5 in the The Structure of the Tetrahydrofolate Riboswitch Containing A U25C Mutation


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 1 of The Structure of the Tetrahydrofolate Riboswitch Containing A U25C Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir90 b:0.2 occ:0.60 IR A:IRI90 0.0 0.2 0.6 N5 A:IRI90 2.5 64.1 0.0 N3 A:IRI90 2.5 92.2 0.5 N1 A:IRI90 2.5 49.0 0.0 N6 A:IRI90 2.5 86.5 0.7 N2 A:IRI90 2.5 0.7 0.0 N4 A:IRI90 2.5 44.7 0.6 O6 A:G61 3.5 34.3 1.0 O2' A:G59 4.1 26.9 1.0 O A:HOH186 4.2 44.7 1.0 C6 A:G61 4.7 32.7 1.0

Iridium binding site 2 out of 5 in the The Structure of the Tetrahydrofolate Riboswitch Containing A U25C Mutation


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 2 of The Structure of the Tetrahydrofolate Riboswitch Containing A U25C Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir91 b:41.7 occ:0.13 IR A:IRI91 0.0 41.7 0.1 N3 A:IRI91 2.5 81.4 1.0 N4 A:IRI91 2.5 0.4 1.0 N5 A:IRI91 2.5 0.6 1.0 N6 A:IRI91 2.5 0.9 1.0 N2 A:IRI91 2.5 80.2 1.0 N1 A:IRI91 2.5 86.1 1.0 OP2 A:G9 4.4 33.9 1.0 O A:HOH101 4.5 43.0 1.0 O A:HOH134 4.7 31.6 1.0 O A:HOH120 4.7 33.5 1.0

Iridium binding site 3 out of 5 in the The Structure of the Tetrahydrofolate Riboswitch Containing A U25C Mutation


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 3 of The Structure of the Tetrahydrofolate Riboswitch Containing A U25C Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir92 b:47.3 occ:0.37 IR A:IRI92 0.0 47.3 0.4 N6 A:IRI92 2.5 88.7 1.0 N2 A:IRI92 2.5 87.8 1.0 N3 A:IRI92 2.5 41.2 1.0 N4 A:IRI92 2.5 53.8 1.0 N1 A:IRI92 2.5 43.6 1.0 N5 A:IRI92 2.5 89.3 1.0 O A:HOH166 3.2 46.0 1.0 O6 A:G78 4.0 36.8 1.0 O4 A:U77 4.0 35.1 1.0 O A:HOH125 4.1 40.8 1.0 O A:HOH104 4.3 27.8 1.0 O A:HOH120 4.8 33.5 1.0 C6 A:G78 4.8 35.3 1.0

Iridium binding site 4 out of 5 in the The Structure of the Tetrahydrofolate Riboswitch Containing A U25C Mutation


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 4 of The Structure of the Tetrahydrofolate Riboswitch Containing A U25C Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir93 b:0.7 occ:0.88 IR A:IRI93 0.0 0.7 0.9 N1 A:IRI93 2.5 56.6 0.0 N6 A:IRI93 2.5 63.3 1.0 N5 A:IRI93 2.5 51.9 0.4 N3 A:IRI93 2.5 50.5 0.8 N4 A:IRI93 2.5 71.3 0.0 N2 A:IRI93 2.5 38.7 0.5 O A:HOH163 4.1 28.3 1.0 O A:HOH123 4.1 27.6 1.0 O A:HOH188 4.2 50.9 1.0 O A:HOH131 4.6 26.4 1.0 O6 A:G32 4.7 26.2 1.0 N6 A:A33 4.8 27.8 1.0 N7 A:G32 4.9 29.6 1.0

Iridium binding site 5 out of 5 in the The Structure of the Tetrahydrofolate Riboswitch Containing A U25C Mutation


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 5 of The Structure of the Tetrahydrofolate Riboswitch Containing A U25C Mutation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir94 b:0.6 occ:0.67 IR A:IRI94 0.0 0.6 0.7 N6 A:IRI94 2.5 94.3 0.6 N3 A:IRI94 2.5 72.7 0.9 N1 A:IRI94 2.5 55.0 0.5 N4 A:IRI94 2.5 83.9 0.0 N5 A:IRI94 2.5 80.4 0.6 N2 A:IRI94 2.5 77.7 1.0 O A:HOH188 3.7 50.9 1.0 O A:HOH169 4.7 40.8 1.0 N7 A:G30 4.9 30.9 1.0

J.J.Trausch, P.Ceres, F.E.Reyes, R.T.Batey. The Structure of A Tetrahydrofolate-Sensing Riboswitch Reveals Two Ligand Binding Sites in A Single Aptamer. Structure V. 19 1413 2011.
ISSN: ISSN 0969-2126
PubMed: 21906956
DOI: 10.1016/J.STR.2011.06.019