Iridium in PDB 9dib: Rous Sarcoma Virus Frameshifting Pseudoknot Rna

The structure of Rous Sarcoma Virus Frameshifting Pseudoknot Rna, PDB code: 9dib was solved by C.P.Jones, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.82 / 2.68
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.763, 68.246, 209.563, 90, 90, 90
R / Rfree (%)	20.6 / 26.8

The structure of Rous Sarcoma Virus Frameshifting Pseudoknot Rna also contains other interesting chemical elements:

Potassium	(K)	5 atoms
Magnesium	(Mg)	4 atoms

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>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Iridium atom in the Rous Sarcoma Virus Frameshifting Pseudoknot Rna (pdb code 9dib). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 18 binding sites of Iridium where determined in the Rous Sarcoma Virus Frameshifting Pseudoknot Rna, PDB code: 9dib:
Jump to Iridium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iridium binding site 1 out of 18 in the Rous Sarcoma Virus Frameshifting Pseudoknot Rna


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 1 of Rous Sarcoma Virus Frameshifting Pseudoknot Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir201 b:162.2 occ:1.00 IR A:IRI201 0.0 162.2 1.0 N3 A:IRI201 2.2 96.4 1.0 N4 A:IRI201 2.2 102.1 1.0 N6 A:IRI201 2.2 110.9 1.0 N2 A:IRI201 2.2 132.6 1.0 N5 A:IRI201 2.2 108.8 1.0 N1 A:IRI201 2.3 133.9 1.0 O6 A:G32 3.6 83.7 1.0 O6 A:G33 4.1 72.9 1.0 N7 A:G32 4.2 66.3 1.0 C6 A:G32 4.3 60.0 1.0 C5 A:G32 4.6 56.2 1.0 O6 A:G50 4.9 63.3 1.0

Iridium binding site 2 out of 18 in the Rous Sarcoma Virus Frameshifting Pseudoknot Rna


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 2 of Rous Sarcoma Virus Frameshifting Pseudoknot Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir202 b:169.4 occ:1.00 IR A:IRI202 0.0 169.4 1.0 N2 A:IRI202 2.2 99.1 1.0 N6 A:IRI202 2.3 100.1 1.0 N1 A:IRI202 2.3 102.2 1.0 N3 A:IRI202 2.3 121.1 1.0 N4 A:IRI202 2.3 126.6 1.0 N5 A:IRI202 2.3 122.3 1.0 N7 A:G54 4.0 69.4 1.0 OP1 A:C102 4.2 105.6 1.0 OP2 A:A53 4.4 88.1 1.0 OP1 A:U103 4.5 73.8 1.0 C8 A:G54 4.6 63.5 1.0 OP2 A:U103 4.7 71.4 1.0 OP2 A:C102 4.8 93.6 1.0 OP2 A:G54 4.8 80.2 1.0 P A:C102 5.0 98.8 1.0

Iridium binding site 3 out of 18 in the Rous Sarcoma Virus Frameshifting Pseudoknot Rna


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 3 of Rous Sarcoma Virus Frameshifting Pseudoknot Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir203 b:179.9 occ:1.00 IR A:IRI203 0.0 179.9 1.0 N1 A:IRI203 2.2 124.3 1.0 N4 A:IRI203 2.2 150.4 1.0 N6 A:IRI203 2.3 153.6 1.0 N3 A:IRI203 2.3 148.9 1.0 N5 A:IRI203 2.3 119.5 1.0 N2 A:IRI203 2.3 116.5 1.0 O6 A:G62 4.0 103.7 1.0 N7 A:G62 4.2 75.5 1.0 C6 A:G62 4.5 96.1 1.0 C5 A:G62 4.5 86.7 1.0 OP1 A:A64 4.5 70.2 1.0 OP2 A:A64 4.9 73.7 1.0

Iridium binding site 4 out of 18 in the Rous Sarcoma Virus Frameshifting Pseudoknot Rna


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 4 of Rous Sarcoma Virus Frameshifting Pseudoknot Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir204 b:143.3 occ:1.00 IR A:IRI204 0.0 143.3 1.0 N5 A:IRI204 2.3 99.5 1.0 N1 A:IRI204 2.3 112.3 1.0 N6 A:IRI204 2.3 133.9 1.0 N3 A:IRI204 2.3 101.5 1.0 N4 A:IRI204 2.3 124.3 1.0 N2 A:IRI204 2.3 115.8 1.0 O6 A:G46 3.9 87.5 1.0 O4 A:U38 4.0 81.2 1.0 O4 A:U37 4.5 99.0 0.5 O4 A:U37 4.6 98.9 0.5 N7 A:G46 4.6 71.3 1.0 O6 A:G47 4.8 77.0 1.0 C6 A:G46 4.8 67.4 1.0

Iridium binding site 5 out of 18 in the Rous Sarcoma Virus Frameshifting Pseudoknot Rna


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 5 of Rous Sarcoma Virus Frameshifting Pseudoknot Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir205 b:176.1 occ:1.00 IR A:IRI205 0.0 176.1 1.0 N1 A:IRI205 2.2 121.0 1.0 N5 A:IRI205 2.3 145.7 1.0 N6 A:IRI205 2.3 127.2 1.0 N4 A:IRI205 2.3 131.5 1.0 N3 A:IRI205 2.3 157.5 1.0 N2 A:IRI205 2.3 125.5 1.0 OP2 A:G66 4.1 83.3 1.0 N7 A:G66 4.6 77.0 1.0

Iridium binding site 6 out of 18 in the Rous Sarcoma Virus Frameshifting Pseudoknot Rna


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 6 of Rous Sarcoma Virus Frameshifting Pseudoknot Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir206 b:229.9 occ:1.00 IR A:IRI206 0.0 229.9 1.0 N4 A:IRI206 2.2 142.2 1.0 N3 A:IRI206 2.2 163.9 1.0 N2 A:IRI206 2.2 157.1 1.0 N6 A:IRI206 2.3 150.5 1.0 N5 A:IRI206 2.3 162.4 1.0 N1 A:IRI206 2.3 140.5 1.0 O4 A:U13 3.3 149.0 1.0 O4 A:U74 4.3 111.6 1.0 C4 A:U13 4.3 148.7 1.0 O4 A:U73 4.5 97.0 1.0 OP2 A:G71 4.5 92.7 1.0 OP1 A:G71 4.7 133.7 1.0 OP2 A:A72 4.8 108.9 1.0

Iridium binding site 7 out of 18 in the Rous Sarcoma Virus Frameshifting Pseudoknot Rna


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 7 of Rous Sarcoma Virus Frameshifting Pseudoknot Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir207 b:211.4 occ:1.00 IR A:IRI207 0.0 211.4 1.0 N6 A:IRI207 2.2 125.7 1.0 N1 A:IRI207 2.2 125.2 1.0 N4 A:IRI207 2.2 175.7 1.0 N5 A:IRI207 2.2 161.3 1.0 N3 A:IRI207 2.2 166.7 1.0 N2 A:IRI207 2.2 127.1 1.0 N7 A:G70 4.4 91.0 1.0 O6 A:G71 4.5 77.1 1.0 O6 A:G70 4.5 76.7 1.0 N7 A:G71 4.9 79.3 1.0

Iridium binding site 8 out of 18 in the Rous Sarcoma Virus Frameshifting Pseudoknot Rna


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 8 of Rous Sarcoma Virus Frameshifting Pseudoknot Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir208 b:191.1 occ:1.00 IR A:IRI208 0.0 191.1 1.0 N6 A:IRI208 2.2 104.9 1.0 N5 A:IRI208 2.2 144.7 1.0 N3 A:IRI208 2.2 133.9 1.0 N1 A:IRI208 2.2 151.5 1.0 N2 A:IRI208 2.3 155.8 1.0 N4 A:IRI208 2.3 106.3 1.0 N7 A:G1 3.9 76.9 1.0 O6 A:G1 4.2 80.6 1.0 O6 B:G21 4.6 57.9 1.0 C5 A:G1 4.8 76.4 1.0 C6 A:G1 4.9 78.1 1.0 C8 A:G1 4.9 75.3 1.0

Iridium binding site 9 out of 18 in the Rous Sarcoma Virus Frameshifting Pseudoknot Rna


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 9 of Rous Sarcoma Virus Frameshifting Pseudoknot Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir209 b:205.6 occ:1.00 IR A:IRI209 0.0 205.6 1.0 N4 A:IRI209 2.2 144.2 1.0 N3 A:IRI209 2.2 134.0 1.0 N6 A:IRI209 2.2 116.2 1.0 N5 A:IRI209 2.2 113.5 1.0 N2 A:IRI209 2.2 135.3 1.0 N1 A:IRI209 2.3 113.7 1.0 O2' A:C102 3.8 83.0 1.0 OP1 A:U104 4.2 90.2 1.0 OP2 A:U104 4.5 74.2 1.0 P A:U104 4.7 73.9 1.0 O2 A:C102 4.8 87.4 1.0 O2' A:U19 4.8 68.7 1.0 C2' A:C102 4.8 83.4 1.0

Iridium binding site 10 out of 18 in the Rous Sarcoma Virus Frameshifting Pseudoknot Rna


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 10 of Rous Sarcoma Virus Frameshifting Pseudoknot Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Ir201 b:179.6 occ:1.00 IR B:IRI201 0.0 179.6 1.0 N4 B:IRI201 2.2 124.0 1.0 N6 B:IRI201 2.2 135.2 1.0 N3 B:IRI201 2.2 126.1 1.0 N1 B:IRI201 2.3 143.5 1.0 N2 B:IRI201 2.3 152.1 1.0 N5 B:IRI201 2.3 151.2 1.0 O4 B:U38 3.7 93.8 1.0 O4 B:U37 4.0 94.7 1.0 O6 B:G46 4.1 112.9 1.0 N7 B:G46 4.8 141.9 1.0 O6 B:G47 4.8 108.2 1.0 C4 B:U37 4.9 77.4 1.0 C6 B:G46 4.9 127.8 1.0 C4 B:U38 5.0 95.8 1.0

C.P.Jones, A.R.Ferre-D'amare. Structural Switching Dynamically Controls the Doubly Pseudoknotted Rous Sarcoma Virus Programmed Ribosomal Frameshifting Element Proc.Natl.Acad.Sci.Usa 2025.
ISSN: ESSN 1091-6490