Iridium in PDB 8xze: Crystal Structure of Thf-II Riboswitch with Thf and Soaked with Ir

The structure of Crystal Structure of Thf-II Riboswitch with Thf and Soaked with Ir, PDB code: 8xze was solved by C.Y.Li, A.M.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.07 / 2.34
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.276, 58.127, 62.096, 90, 90, 90
R / Rfree (%)	19.7 / 24.5

The structure of Crystal Structure of Thf-II Riboswitch with Thf and Soaked with Ir also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Iridium atom in the Crystal Structure of Thf-II Riboswitch with Thf and Soaked with Ir (pdb code 8xze). 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 Thf-II Riboswitch with Thf and Soaked with Ir, PDB code: 8xze:
Jump to Iridium binding site number: 1; 2; 3;

Iridium binding site 1 out of 3 in the Crystal Structure of Thf-II Riboswitch with Thf and Soaked with Ir


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 Thf-II Riboswitch with Thf and Soaked with Ir within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir107 b:148.2 occ:1.00 O4 A:U4 3.8 44.1 1.0 O6 A:G3 4.5 50.3 1.0 O A:HOH215 4.5 48.4 1.0 O1A A:GTP1 4.6 105.5 1.0 N7 A:G2 4.8 67.0 1.0 C4 A:U4 4.9 47.9 1.0 N7 A:G3 4.9 49.9 1.0

Iridium binding site 2 out of 3 in the Crystal Structure of Thf-II Riboswitch with Thf and Soaked with Ir


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 Thf-II Riboswitch with Thf and Soaked with Ir within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir108 b:86.2 occ:1.00 O A:HOH211 3.5 55.6 1.0 O6 A:G7 3.7 37.8 1.0 OP2 A:G46 4.0 43.9 1.0 O A:HOH215 4.1 48.4 1.0 O4 A:U6 4.4 38.0 1.0 OP1 A:G45 4.6 51.9 1.0 C6 A:G7 4.6 39.9 1.0 N1 A:G7 4.9 44.7 1.0

Iridium binding site 3 out of 3 in the Crystal Structure of Thf-II Riboswitch with Thf and Soaked with Ir


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 Thf-II Riboswitch with Thf and Soaked with Ir within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir109 b:96.3 occ:1.00 O6 A:G37 3.8 59.4 1.0 O6 A:G38 4.3 49.8 1.0 N7 A:G37 4.4 48.1 1.0 O A:HOH207 4.4 40.5 1.0 C6 A:G37 4.7 51.1 1.0 O4 A:U22 4.8 43.5 1.0 C5 A:G37 4.9 50.4 1.0 N4 A:C23 4.9 38.2 1.0

C.Li, X.Xu, Z.Geng, L.Zheng, Q.Song, X.Shen, J.Wu, J.Zhao, H.Li, M.He, X.Tai, L.Zhang, J.Ma, Y.Dong, A.Ren. Structure-Based Characterization and Compound Identification of the Wild-Type Thf Class-II Riboswitch. Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
PubMed: 38769061
DOI: 10.1093/NAR/GKAE377