Iridium in PDB 9cfn: Crystal Structure of An Exoribonuclease-Resistant Rna From A Tombusvirus-Like Associated Rna

The structure of Crystal Structure of An Exoribonuclease-Resistant Rna From A Tombusvirus-Like Associated Rna, PDB code: 9cfn was solved by J.Gezelle, B.Wimberly, Z.Gong, W.A.Hendrickson, A.L.Steckelberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.06 / 2.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	107.637, 42.392, 84.491, 90, 103.62, 90
R / Rfree (%)	21.7 / 25.8

The structure of Crystal Structure of An Exoribonuclease-Resistant Rna From A Tombusvirus-Like Associated Rna also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Iridium atom in the Crystal Structure of An Exoribonuclease-Resistant Rna From A Tombusvirus-Like Associated Rna (pdb code 9cfn). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 24 binding sites of Iridium where determined in the Crystal Structure of An Exoribonuclease-Resistant Rna From A Tombusvirus-Like Associated Rna, PDB code: 9cfn:
Jump to Iridium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iridium binding site 1 out of 24 in the Crystal Structure of An Exoribonuclease-Resistant Rna From A Tombusvirus-Like Associated Rna


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 An Exoribonuclease-Resistant Rna From A Tombusvirus-Like Associated Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir101 b:94.0 occ:0.35 IR A:IRI101 0.0 94.0 0.3 N5 A:IRI101 2.2 81.2 0.3 N3 A:IRI101 2.2 75.4 0.3 N1 A:IRI101 2.3 66.0 0.3 N6 A:IRI101 2.3 56.5 0.3 N4 A:IRI101 2.3 55.8 0.3 N2 A:IRI101 2.3 63.8 0.3 N5 A:IRI109 3.6 68.4 0.6 OP2 A:G3 3.7 32.9 1.0 N2 A:IRI109 4.4 45.9 0.6 OP2 A:A2 4.6 40.1 1.0 O5' A:A2 4.8 43.9 1.0

Iridium binding site 2 out of 24 in the Crystal Structure of An Exoribonuclease-Resistant Rna From A Tombusvirus-Like Associated Rna


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 An Exoribonuclease-Resistant Rna From A Tombusvirus-Like Associated Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir102 b:104.0 occ:0.28 IR A:IRI102 0.0 104.0 0.3 N2 A:IRI102 2.2 84.0 0.3 N4 A:IRI102 2.3 70.2 0.3 N5 A:IRI102 2.3 78.3 0.3 N3 A:IRI102 2.3 81.3 0.3 N1 A:IRI102 2.3 75.4 0.3 N6 A:IRI102 2.3 78.5 0.3 OP1 A:C8 4.7 55.7 1.0 O3' A:C7 4.8 41.6 1.0

Iridium binding site 3 out of 24 in the Crystal Structure of An Exoribonuclease-Resistant Rna From A Tombusvirus-Like Associated Rna


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 An Exoribonuclease-Resistant Rna From A Tombusvirus-Like Associated Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir103 b:122.8 occ:0.52 IR A:IRI103 0.0 122.8 0.5 N6 A:IRI103 2.3 90.7 0.5 N2 A:IRI103 2.3 91.7 0.5 N4 A:IRI103 2.3 88.9 0.5 N5 A:IRI103 2.3 82.3 0.5 N1 A:IRI103 2.3 97.4 0.5 N3 A:IRI103 2.3 106.1 0.5 OP1 A:C8 3.8 55.7 1.0 OP2 A:C8 4.2 52.0 1.0 P A:C8 4.5 40.5 1.0 OP2 A:U9 5.0 50.6 1.0

Iridium binding site 4 out of 24 in the Crystal Structure of An Exoribonuclease-Resistant Rna From A Tombusvirus-Like Associated Rna


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 4 of Crystal Structure of An Exoribonuclease-Resistant Rna From A Tombusvirus-Like Associated Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir104 b:82.1 occ:0.56 IR A:IRI104 0.0 82.1 0.6 N4 A:IRI104 2.3 55.6 0.6 N2 A:IRI104 2.3 60.6 0.6 N1 A:IRI104 2.3 56.8 0.6 N5 A:IRI104 2.3 75.5 0.6 N6 A:IRI104 2.3 52.1 0.6 N3 A:IRI104 2.3 61.0 0.6 N7 A:G33 3.9 28.8 1.0 O6 A:G34 4.1 36.2 1.0 O6 A:G33 4.1 30.4 1.0 OP1 A:C6 4.2 20.1 1.0 C5 A:G33 4.7 26.5 1.0 C6 A:G33 4.7 27.0 1.0 C8 A:G33 4.9 30.6 1.0 O6 A:G32 4.9 29.1 1.0

Iridium binding site 5 out of 24 in the Crystal Structure of An Exoribonuclease-Resistant Rna From A Tombusvirus-Like Associated Rna


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 5 of Crystal Structure of An Exoribonuclease-Resistant Rna From A Tombusvirus-Like Associated Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir105 b:105.0 occ:0.62 IR A:IRI105 0.0 105.0 0.6 N6 A:IRI105 2.2 80.3 0.6 N4 A:IRI105 2.2 112.1 0.6 N1 A:IRI105 2.3 92.1 0.6 N5 A:IRI105 2.3 87.2 0.6 N2 A:IRI105 2.3 90.2 0.6 N3 A:IRI105 2.3 101.5 0.6 N7 A:G48 3.9 86.2 1.0 O4 A:U49 4.2 101.3 1.0 O4 A:U47 4.3 86.4 1.0 C8 A:G48 4.6 95.0 1.0 C4 A:U47 4.7 85.7 1.0 C5 A:U47 4.8 81.4 1.0 O4 A:U18 4.9 78.2 1.0

Iridium binding site 6 out of 24 in the Crystal Structure of An Exoribonuclease-Resistant Rna From A Tombusvirus-Like Associated Rna


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 6 of Crystal Structure of An Exoribonuclease-Resistant Rna From A Tombusvirus-Like Associated Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir106 b:151.8 occ:1.00 IR A:IRI106 0.0 151.8 1.0 N4 A:IRI106 2.2 111.8 1.0 N5 A:IRI106 2.2 147.3 1.0 N2 A:IRI106 2.3 96.2 1.0 N3 A:IRI106 2.3 140.4 1.0 N6 A:IRI106 2.3 127.8 1.0 N1 A:IRI106 2.3 99.6 1.0 O6 A:G51 5.0 81.8 1.0

Iridium binding site 7 out of 24 in the Crystal Structure of An Exoribonuclease-Resistant Rna From A Tombusvirus-Like Associated Rna


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 7 of Crystal Structure of An Exoribonuclease-Resistant Rna From A Tombusvirus-Like Associated Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir107 b:115.4 occ:0.97 IR A:IRI107 0.0 115.4 1.0 N5 A:IRI107 2.2 139.7 1.0 N2 A:IRI107 2.2 51.5 1.0 N4 A:IRI107 2.2 80.8 1.0 N3 A:IRI107 2.2 100.5 1.0 N6 A:IRI107 2.2 93.8 1.0 N1 A:IRI107 2.3 129.4 1.0 O6 A:G23 4.2 45.2 1.0 N7 A:G23 4.3 50.1 1.0 O6 A:G22 4.6 74.8 1.0 N7 A:G22 4.8 85.8 1.0 C6 A:G23 5.0 45.5 1.0

Iridium binding site 8 out of 24 in the Crystal Structure of An Exoribonuclease-Resistant Rna From A Tombusvirus-Like Associated Rna


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 8 of Crystal Structure of An Exoribonuclease-Resistant Rna From A Tombusvirus-Like Associated Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir108 b:81.0 occ:0.78 IR A:IRI108 0.0 81.0 0.8 N6 A:IRI108 2.2 77.9 0.8 N2 A:IRI108 2.2 90.1 0.8 N5 A:IRI108 2.2 72.7 0.8 N1 A:IRI108 2.2 80.2 0.8 N4 A:IRI108 2.3 90.9 0.8 N3 A:IRI108 2.3 68.0 0.8 N7 A:G55 4.1 84.6 1.0 O6 A:G55 4.5 83.1 1.0

Iridium binding site 9 out of 24 in the Crystal Structure of An Exoribonuclease-Resistant Rna From A Tombusvirus-Like Associated Rna


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 9 of Crystal Structure of An Exoribonuclease-Resistant Rna From A Tombusvirus-Like Associated Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir109 b:56.7 occ:0.62 IR A:IRI109 0.0 56.7 0.6 N3 A:IRI109 2.2 52.0 0.6 N4 A:IRI109 2.2 75.8 0.6 N5 A:IRI109 2.2 68.4 0.6 N6 A:IRI109 2.2 38.9 0.6 N1 A:IRI109 2.3 42.6 0.6 N2 A:IRI109 2.3 45.9 0.6 O6 A:G3 3.6 19.4 1.0 N4 A:IRI101 3.9 55.8 0.3 OP2 A:G35 4.0 32.2 1.0 N6 A:IRI101 4.1 56.5 0.3 O4 A:U4 4.2 16.7 1.0 C6 A:G3 4.6 17.0 1.0 N7 A:G3 4.6 21.7 1.0

Iridium binding site 10 out of 24 in the Crystal Structure of An Exoribonuclease-Resistant Rna From A Tombusvirus-Like Associated Rna


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 10 of Crystal Structure of An Exoribonuclease-Resistant Rna From A Tombusvirus-Like Associated Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir110 b:71.2 occ:0.76 IR A:IRI110 0.0 71.2 0.8 N1 A:IRI110 2.2 70.0 0.8 N6 A:IRI110 2.2 55.9 0.8 N4 A:IRI110 2.2 70.1 0.8 N2 A:IRI110 2.2 46.1 0.8 N5 A:IRI110 2.2 48.5 0.8 N3 A:IRI110 2.3 50.3 0.8 OP1 A:G32 3.4 55.2 1.0 O2 A:U44 4.2 40.2 1.0 O2' A:U44 4.4 33.7 1.0 OP2 A:C45 4.6 45.5 1.0 O2' A:A31 4.6 39.5 1.0 P A:G32 4.8 44.1 1.0 O3' A:U44 4.9 29.5 1.0 OP1 A:G33 5.0 30.1 1.0

J.Gezelle, S.M.Korn, J.Mcdonald, Z.Gong, A.Erickson, C.Huang, M.Cronin, F.Yang, W.A.Hendrickson, B.Wimberly, A.L.Steckelberg. The Structure of A Nuclease-Resistant Infectious Rna Element Reveals Common Molecular Strategies to Evade Host Degradation Machinery To Be Published.