Iridium in PDB 8hzk: A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak

The structure of A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak, PDB code: 8hzk was solved by K.Y.Huang, A.M.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.11 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	74.893, 44.022, 58.304, 90, 112.94, 90
R / Rfree (%)	20.3 / 24

The structure of A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak also contains other interesting chemical elements:

Magnesium

(Mg)

8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Iridium atom in the A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak (pdb code 8hzk). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 14 binding sites of Iridium where determined in the A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak, PDB code: 8hzk:
Jump to Iridium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iridium binding site 1 out of 14 in the A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 1 of A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir101 b:28.6 occ:1.00 IR A:IRI101 0.0 28.6 1.0 N2 A:IRI101 2.2 18.7 1.0 N1 A:IRI101 2.2 27.7 1.0 N6 A:IRI101 2.2 19.4 1.0 N5 A:IRI101 2.2 18.7 1.0 N4 A:IRI101 2.2 25.1 1.0 N3 A:IRI101 2.2 21.2 1.0 O A:HOH207 3.2 29.4 1.0 O A:HOH219 3.8 22.7 1.0 O A:HOH227 3.9 23.1 1.0 O A:HOH231 4.1 25.6 1.0 O A:HOH243 4.6 23.9 1.0

Iridium binding site 2 out of 14 in the A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 2 of A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir102 b:33.4 occ:1.00 IR A:IRI102 0.0 33.4 1.0 N5 A:IRI102 2.2 24.4 1.0 N6 A:IRI102 2.2 31.1 1.0 N1 A:IRI102 2.2 17.1 1.0 N4 A:IRI102 2.2 23.5 1.0 N2 A:IRI102 2.3 22.8 1.0 N3 A:IRI102 2.3 20.7 1.0 OP2 A:A4 4.0 22.6 1.0 OP2 A:U7 4.0 20.1 1.0 OP2 A:G5 4.1 20.4 1.0 O2' A:A6 4.1 18.4 1.0 O3' A:A6 4.5 19.5 1.0 OP1 A:A4 4.6 29.9 1.0 P A:A4 4.7 28.6 1.0 O A:HOH220 4.9 26.8 1.0 P A:U7 4.9 23.1 1.0

Iridium binding site 3 out of 14 in the A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 3 of A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir103 b:26.9 occ:1.00 IR A:IRI103 0.0 26.9 1.0 N2 A:IRI103 2.2 14.4 1.0 N1 A:IRI103 2.2 15.4 1.0 N4 A:IRI103 2.2 19.6 1.0 N6 A:IRI103 2.2 18.5 1.0 N3 A:IRI103 2.2 18.2 1.0 N5 A:IRI103 2.2 15.5 1.0 O A:HOH236 3.7 26.9 1.0 OP1 A:A27 3.8 19.2 1.0 OP2 A:U8 3.9 31.7 1.0 O A:HOH225 4.1 24.9 1.0 OP1 B:A21 4.1 18.3 1.0 O2' A:U7 4.2 21.0 1.0 N7 B:A21 4.3 23.3 1.0 O3' A:U7 4.4 20.8 1.0 O A:HOH239 4.5 19.3 1.0 C8 B:A21 4.7 23.7 1.0 P A:U8 4.7 23.2 1.0 O3' B:G20 4.8 23.0 1.0 O A:HOH215 4.9 24.8 1.0 P A:A27 4.9 20.5 1.0

Iridium binding site 4 out of 14 in the A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 4 of A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir104 b:26.7 occ:1.00 IR A:IRI104 0.0 26.7 1.0 N2 A:IRI104 2.2 22.8 1.0 N6 A:IRI104 2.2 12.3 1.0 N4 A:IRI104 2.2 21.3 1.0 N5 A:IRI104 2.2 14.1 1.0 N1 A:IRI104 2.2 19.8 1.0 N3 A:IRI104 2.2 22.9 1.0 O2 A:C30 4.0 19.6 1.0 O A:HOH228 4.0 17.7 1.0 O A:HOH245 4.3 33.1 1.0 N3 A:C30 4.3 18.2 1.0 C2 A:C30 4.6 17.5 1.0 O15 A:NI4116 4.7 19.9 1.0

Iridium binding site 5 out of 14 in the A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 5 of A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir105 b:83.3 occ:1.00 IR A:IRI105 0.0 83.3 1.0 N1 A:IRI105 2.3 62.1 1.0 N5 A:IRI105 2.3 43.0 1.0 N4 A:IRI105 2.3 61.6 1.0 N6 A:IRI105 2.3 36.9 1.0 N2 A:IRI105 2.3 37.6 1.0 N3 A:IRI105 2.3 32.8 1.0 MG A:MG114 3.3 25.9 1.0 O3' A:A15 4.8 24.4 1.0

Iridium binding site 6 out of 14 in the A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 6 of A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir106 b:88.7 occ:1.00 IR A:IRI106 0.0 88.7 1.0 N3 A:IRI106 2.2 43.5 1.0 N4 A:IRI106 2.3 39.0 1.0 N2 A:IRI106 2.3 60.0 1.0 N6 A:IRI106 2.3 47.9 1.0 N1 A:IRI106 2.3 43.7 1.0 N5 A:IRI106 2.3 43.8 1.0 O A:HOH205 2.8 29.9 1.0 O A:HOH212 3.9 38.6 1.0 O A:HOH221 3.9 29.2 1.0 O6 A:G2 4.3 26.9 1.0 O A:HOH213 4.3 26.8 1.0 N7 A:G1 4.5 29.1 1.0 O6 A:G1 4.5 25.2 1.0 N7 A:G2 4.8 24.3 1.0 C5 A:G1 5.0 22.7 1.0 C6 A:G1 5.0 19.8 1.0

Iridium binding site 7 out of 14 in the A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 7 of A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir107 b:48.0 occ:1.00 IR A:IRI107 0.0 48.0 1.0 N6 A:IRI107 2.2 36.6 1.0 N2 A:IRI107 2.3 30.9 1.0 N4 A:IRI107 2.3 38.9 1.0 N5 A:IRI107 2.3 38.5 1.0 N1 A:IRI107 2.3 36.6 1.0 N3 A:IRI107 2.3 29.4 1.0 OP2 A:A31 3.8 26.7 1.0 OP2 A:C30 4.3 27.6 1.0 OP1 A:A31 4.7 32.0 1.0 P A:A31 4.8 27.3 1.0

Iridium binding site 8 out of 14 in the A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 8 of A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir108 b:66.7 occ:1.00 IR A:IRI108 0.0 66.7 1.0 N5 A:IRI108 2.3 22.7 1.0 N6 A:IRI108 2.3 40.7 1.0 N3 A:IRI108 2.3 49.0 1.0 N4 A:IRI108 2.3 30.4 1.0 N2 A:IRI108 2.3 48.2 1.0 N1 A:IRI108 2.3 26.3 1.0 O2 A:U7 3.6 24.7 1.0 O A:HOH239 4.0 19.3 1.0 C2 A:U7 4.8 19.1 1.0

Iridium binding site 9 out of 14 in the A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 9 of A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir109 b:58.1 occ:1.00 IR A:IRI109 0.0 58.1 1.0 N5 A:IRI109 2.3 52.5 1.0 N4 A:IRI109 2.3 48.9 1.0 N1 A:IRI109 2.3 51.2 1.0 N6 A:IRI109 2.3 43.1 1.0 N3 A:IRI109 2.3 30.2 1.0 N2 A:IRI109 2.3 48.9 1.0 O A:HOH208 3.2 41.7 1.0 N7 A:G20 4.1 25.6 1.0 OP1 A:A22 4.3 30.0 1.0 O A:HOH241 4.3 32.5 1.0 O6 A:G20 4.6 28.9 1.0 O A:HOH234 4.8 29.1 1.0 C5 A:G20 4.9 21.2 1.0 C8 A:G20 4.9 24.0 1.0

Iridium binding site 10 out of 14 in the A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 10 of A New Fluorescent Rna Aptamer Bound with N, Iridium Hexammine Soak within 5.0Å range: probe atom residue distance (Å) B Occ B:Ir101 b:85.8 occ:1.00 IR B:IRI101 0.0 85.8 1.0 N3 B:IRI101 2.3 46.1 1.0 N6 B:IRI101 2.3 47.3 1.0 N2 B:IRI101 2.3 54.4 1.0 N4 B:IRI101 2.3 46.5 1.0 N5 B:IRI101 2.3 37.2 1.0 N1 B:IRI101 2.3 28.4 1.0 O B:HOH203 3.0 43.7 1.0 OP1 A:A21 3.5 40.1 1.0 O B:HOH202 3.9 44.9 1.0 OP2 B:U8 3.9 47.4 1.0 OP1 B:A27 4.1 37.2 1.0 O A:HOH230 4.5 28.1 1.0 OP2 B:G28 4.5 24.9 1.0 P A:A21 4.9 37.6 1.0

K.Huang, Q.Song, M.Fang, D.Yao, X.Shen, X.Xu, X.Chen, L.Zhu, Y.Yang, A.Ren. Structural Basis of A Small Monomeric Clivia Fluorogenic Rna with A Large Stokes Shift. Nat.Chem.Biol. 2024.
ISSN: ESSN 1552-4469
PubMed: 38816645
DOI: 10.1038/S41589-024-01633-1