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Iridium in PDB 7lyj: Sars-Cov-2 Frameshifting Pseudoknot Rna

Protein crystallography data

The structure of Sars-Cov-2 Frameshifting Pseudoknot Rna, PDB code: 7lyj 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) 57.09 / 2.11
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 115.465, 39.477, 39.398, 90, 98.53, 90
R / Rfree (%) 21 / 25.1

Other elements in 7lyj:

The structure of Sars-Cov-2 Frameshifting Pseudoknot Rna also contains other interesting chemical elements:

Potassium (K) 2 atoms
Magnesium (Mg) 12 atoms

Iridium Binding Sites:

The binding sites of Iridium atom in the Sars-Cov-2 Frameshifting Pseudoknot Rna (pdb code 7lyj). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 2 binding sites of Iridium where determined in the Sars-Cov-2 Frameshifting Pseudoknot Rna, PDB code: 7lyj:
Jump to Iridium binding site number: 1; 2;

Iridium binding site 1 out of 2 in 7lyj

Go back to Iridium Binding Sites List in 7lyj
Iridium binding site 1 out of 2 in the Sars-Cov-2 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 Sars-Cov-2 Frameshifting Pseudoknot Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir101

b:45.1
occ:1.00
IR A:IRI101 0.0 45.1 1.0
N5 A:IRI101 2.2 49.0 1.0
N2 A:IRI101 2.2 58.0 1.0
N4 A:IRI101 2.3 50.7 1.0
N6 A:IRI101 2.3 29.2 1.0
N1 A:IRI101 2.3 33.6 1.0
N3 A:IRI101 2.3 28.4 1.0
OP2 A:C17 4.0 48.1 1.0
O6 A:G9 4.1 45.3 1.0
N7 A:G9 4.2 47.0 1.0
N7 A:G18 4.2 46.2 1.0
O A:HOH231 4.2 43.1 1.0
OP2 A:G18 4.6 50.0 1.0
O6 A:G18 4.7 50.0 1.0
C6 A:G9 4.8 46.6 1.0
C5 A:G9 4.9 48.5 1.0
P A:C17 5.0 46.3 1.0

Iridium binding site 2 out of 2 in 7lyj

Go back to Iridium Binding Sites List in 7lyj
Iridium binding site 2 out of 2 in the Sars-Cov-2 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 Sars-Cov-2 Frameshifting Pseudoknot Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ir102

b:117.8
occ:0.63
IR A:IRI102 0.0 117.8 0.6
N4 A:IRI102 2.2 100.8 0.6
N3 A:IRI102 2.2 82.7 0.6
N6 A:IRI102 2.2 53.1 0.6
N5 A:IRI102 2.2 49.7 0.6
N2 A:IRI102 2.3 30.6 0.6
N1 A:IRI102 2.3 134.6 0.6
O6 A:G64 4.0 56.0 1.0
N7 A:G64 4.4 51.2 1.0
N7 A:G63 4.7 52.0 1.0
O6 A:G63 4.8 53.2 1.0
C6 A:G64 4.8 53.6 1.0

Reference:

C.P.Jones, A.R.Ferre-D'amare. Sars-Cov-2 Frameshifting Pseudoknot Rna To Be Published.
Page generated: Sat Jul 10 16:18:01 2021

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