Iridium in PDB 4qka: C-Di-Amp Riboswitch From Thermoanaerobacter Pseudethanolicus, Iridium Hexamine Soak

The structure of C-Di-Amp Riboswitch From Thermoanaerobacter Pseudethanolicus, Iridium Hexamine Soak, PDB code: 4qka was solved by A.Gao, A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.01 / 3.20
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.035, 116.035, 114.098, 90.00, 90.00, 120.00
R / Rfree (%)	17.1 / 19.7

The structure of C-Di-Amp Riboswitch From Thermoanaerobacter Pseudethanolicus, Iridium Hexamine Soak also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Potassium	(K)	1 atom

The binding sites of Iridium atom in the C-Di-Amp Riboswitch From Thermoanaerobacter Pseudethanolicus, Iridium Hexamine Soak (pdb code 4qka). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 5 binding sites of Iridium where determined in the C-Di-Amp Riboswitch From Thermoanaerobacter Pseudethanolicus, Iridium Hexamine Soak, PDB code: 4qka:
Jump to Iridium binding site number: 1; 2; 3; 4; 5;

Iridium binding site 1 out of 5 in the C-Di-Amp Riboswitch From Thermoanaerobacter Pseudethanolicus, 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 C-Di-Amp Riboswitch From Thermoanaerobacter Pseudethanolicus, Iridium Hexamine Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir206 b:0.3 occ:0.67 IR A:IRI206 0.0 0.3 0.7 N5 A:IRI206 2.2 0.3 0.7 N6 A:IRI206 2.2 0.1 0.7 N4 A:IRI206 2.3 0.4 0.7 N2 A:IRI206 2.3 1.0 0.7 N1 A:IRI206 2.3 0.8 0.7 N3 A:IRI206 2.3 0.6 0.7 O6 A:G120 4.3 99.5 1.0 O6 A:G119 4.4 94.8 1.0 N7 A:G119 4.6 96.5 1.0 N7 A:G120 5.0 93.6 1.0

Iridium binding site 2 out of 5 in the C-Di-Amp Riboswitch From Thermoanaerobacter Pseudethanolicus, 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 C-Di-Amp Riboswitch From Thermoanaerobacter Pseudethanolicus, Iridium Hexamine Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir207 b:0.0 occ:0.42 IR A:IRI207 0.0 0.0 0.4 N4 A:IRI207 2.3 0.0 0.4 N6 A:IRI207 2.3 0.1 0.4 N5 A:IRI207 2.3 0.4 0.4 N3 A:IRI207 2.3 0.4 0.4 N2 A:IRI207 2.3 0.6 0.4 N1 A:IRI207 2.3 98.9 0.4 N7 A:G19 4.5 0.6 1.0 O4 A:U20 4.5 84.2 1.0 O6 A:G19 4.9 95.1 1.0

Iridium binding site 3 out of 5 in the C-Di-Amp Riboswitch From Thermoanaerobacter Pseudethanolicus, 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 C-Di-Amp Riboswitch From Thermoanaerobacter Pseudethanolicus, Iridium Hexamine Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir208 b:0.9 occ:0.38 IR A:IRI208 0.0 0.9 0.4 N3 A:IRI208 2.2 90.7 0.4 N5 A:IRI208 2.3 0.6 0.4 N6 A:IRI208 2.3 84.1 0.4 N4 A:IRI208 2.3 0.5 0.4 N1 A:IRI208 2.3 0.1 0.4 N2 A:IRI208 2.3 96.3 0.4 O6 A:G42 4.2 74.6 1.0 N7 A:G42 4.5 70.2 1.0 O4 A:U43 4.6 77.6 1.0

Iridium binding site 4 out of 5 in the C-Di-Amp Riboswitch From Thermoanaerobacter Pseudethanolicus, 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 C-Di-Amp Riboswitch From Thermoanaerobacter Pseudethanolicus, Iridium Hexamine Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir209 b:98.1 occ:0.80 IR A:IRI209 0.0 98.1 0.8 N5 A:IRI209 2.3 79.9 0.8 N6 A:IRI209 2.3 79.8 0.8 N2 A:IRI209 2.3 82.5 0.8 N4 A:IRI209 2.3 86.0 0.8 N3 A:IRI209 2.3 95.3 0.8 N1 A:IRI209 2.3 90.0 0.8 OP1 A:C95 3.6 84.6 1.0 OP2 A:U96 3.7 87.0 1.0 OP2 A:G26 4.0 75.7 1.0 OP1 A:A25 4.3 76.9 1.0 OP2 A:A25 4.4 70.5 1.0 P A:A25 4.7 71.0 1.0 P A:C95 4.8 91.1 1.0 P A:U96 4.9 89.9 1.0 O5' A:A25 5.0 69.4 1.0

Iridium binding site 5 out of 5 in the C-Di-Amp Riboswitch From Thermoanaerobacter Pseudethanolicus, 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 C-Di-Amp Riboswitch From Thermoanaerobacter Pseudethanolicus, Iridium Hexamine Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir210 b:0.3 occ:0.60 IR A:IRI210 0.0 0.3 0.6 N5 A:IRI210 2.3 0.8 0.6 N3 A:IRI210 2.3 0.2 0.6 N2 A:IRI210 2.3 0.6 0.6 N6 A:IRI210 2.3 0.3 0.6 N4 A:IRI210 2.3 0.8 0.6 N1 A:IRI210 2.3 0.9 0.6 O4 A:U65 4.7 0.7 1.0

A.Gao, A.Serganov. Structural Insights Into Recognition of C-Di-Amp By the Ydao Riboswitch. Nat.Chem.Biol. V. 10 787 2014.
ISSN: ISSN 1552-4450
PubMed: 25086507
DOI: 10.1038/NCHEMBIO.1607