Iridium in PDB 4p5j: Crystal Structure of the Trna-Like Structure From Turnip Yellow Mosaic Virus (Tymv), A Trna Mimicking Rna

The structure of Crystal Structure of the Trna-Like Structure From Turnip Yellow Mosaic Virus (Tymv), A Trna Mimicking Rna, PDB code: 4p5j was solved by T.M.Colussi, D.A.Costantino, J.A.Hammond, G.M.Ruehle, J.C.Nix, J.S.Kieft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.87 / 1.99
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	55.270, 101.570, 111.610, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 24

The structure of Crystal Structure of the Trna-Like Structure From Turnip Yellow Mosaic Virus (Tymv), A Trna Mimicking Rna also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iridium atom in the Crystal Structure of the Trna-Like Structure From Turnip Yellow Mosaic Virus (Tymv), A Trna Mimicking Rna (pdb code 4p5j). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 12 binding sites of Iridium where determined in the Crystal Structure of the Trna-Like Structure From Turnip Yellow Mosaic Virus (Tymv), A Trna Mimicking Rna, PDB code: 4p5j:
Jump to Iridium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iridium binding site 1 out of 12 in the Crystal Structure of the Trna-Like Structure From Turnip Yellow Mosaic Virus (Tymv), A Trna Mimicking 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 the Trna-Like Structure From Turnip Yellow Mosaic Virus (Tymv), A Trna Mimicking Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir103 b:37.1 occ:0.49 IR A:IRI103 0.0 37.1 0.5 N1 A:IRI103 2.2 29.8 0.5 N5 A:IRI103 2.2 32.3 0.5 N6 A:IRI103 2.2 30.4 0.5 N2 A:IRI103 2.2 27.3 0.5 N3 A:IRI103 2.2 37.1 0.5 N4 A:IRI103 2.2 42.5 0.5 O A:HOH258 3.6 42.8 0.8 O A:HOH287 3.6 37.9 0.8 O A:HOH286 3.7 25.6 0.7 O A:HOH284 3.9 34.2 0.6 O A:HOH325 4.0 53.5 1.0 O2' A:A51 4.1 24.9 1.0 O6 A:G45 4.2 27.9 1.0 N7 A:G45 4.2 33.5 1.0 O A:HOH275 4.4 36.9 0.7 O6 A:G46 4.7 25.1 1.0 C6 A:G45 4.9 31.6 1.0 C5 A:G45 4.9 30.2 1.0

Iridium binding site 2 out of 12 in the Crystal Structure of the Trna-Like Structure From Turnip Yellow Mosaic Virus (Tymv), A Trna Mimicking 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 the Trna-Like Structure From Turnip Yellow Mosaic Virus (Tymv), A Trna Mimicking Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir104 b:92.0 occ:0.25 IR A:IRI104 0.0 92.0 0.2 N2 A:IRI104 2.2 85.0 0.2 N3 A:IRI104 2.2 74.4 0.2 N6 A:IRI104 2.2 78.6 0.2 N4 A:IRI104 2.2 67.6 0.2 N1 A:IRI104 2.3 73.8 0.2 N5 A:IRI104 2.3 74.8 0.2 O A:HOH311 3.5 66.1 1.0 O2 A:U26 3.7 62.3 1.0 O A:HOH319 4.1 49.5 0.9 O2' A:U26 4.5 58.9 1.0 OP2 A:C30 4.8 93.6 1.0 C2 A:U26 4.9 60.9 1.0

Iridium binding site 3 out of 12 in the Crystal Structure of the Trna-Like Structure From Turnip Yellow Mosaic Virus (Tymv), A Trna Mimicking 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 the Trna-Like Structure From Turnip Yellow Mosaic Virus (Tymv), A Trna Mimicking Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir105 b:65.5 occ:0.25 IR A:IRI105 0.0 65.5 0.2 N3 A:IRI105 2.2 33.9 0.2 N1 A:IRI105 2.2 33.6 0.2 N4 A:IRI105 2.2 27.0 0.2 N2 A:IRI105 2.2 39.2 0.2 N6 A:IRI105 2.3 30.6 0.2 N5 A:IRI105 2.3 32.3 0.2 O A:HOH310 3.4 41.4 0.9 O A:HOH291 3.8 39.7 0.9 O6 A:G71 4.0 30.4 1.0 O A:HOH248 4.1 35.3 1.0 O6 A:G72 4.1 29.3 1.0 N7 A:G71 4.3 32.2 1.0 O A:HOH290 4.6 35.7 0.5 O A:HOH262 4.6 46.7 1.0 O A:HOH249 4.6 24.9 0.6 O6 A:G57 4.7 29.8 1.0 C6 A:G71 4.7 27.1 1.0 C5 A:G71 4.8 30.3 1.0 N4 A:C58 4.8 35.2 1.0 O A:HOH255 4.9 30.1 1.0

Iridium binding site 4 out of 12 in the Crystal Structure of the Trna-Like Structure From Turnip Yellow Mosaic Virus (Tymv), A Trna Mimicking 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 the Trna-Like Structure From Turnip Yellow Mosaic Virus (Tymv), A Trna Mimicking Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir106 b:47.5 occ:0.35 IR A:IRI106 0.0 47.5 0.3 N2 A:IRI106 2.2 43.1 0.3 N6 A:IRI106 2.2 38.7 0.3 N4 A:IRI106 2.2 40.8 0.3 N1 A:IRI106 2.2 41.0 0.3 N5 A:IRI106 2.2 40.6 0.3 N3 A:IRI106 2.3 39.4 0.3 OP2 A:G79 4.1 47.8 1.0 O1C A:A2384 4.2 48.7 1.0 O A:HOH309 4.3 54.2 1.0 O A:HOH269 4.5 37.8 0.7 OP2 A:G78 4.9 36.8 1.0

Iridium binding site 5 out of 12 in the Crystal Structure of the Trna-Like Structure From Turnip Yellow Mosaic Virus (Tymv), A Trna Mimicking 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 the Trna-Like Structure From Turnip Yellow Mosaic Virus (Tymv), A Trna Mimicking Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir107 b:93.1 occ:0.41 IR A:IRI107 0.0 93.1 0.4 N4 A:IRI107 2.2 25.1 0.4 N6 A:IRI107 2.2 46.2 0.4 N2 A:IRI107 2.3 56.4 0.4 N1 A:IRI107 2.3 50.8 0.4 N3 A:IRI107 2.3 51.4 0.4 N5 A:IRI107 2.3 52.3 0.4 O4 A:U62 4.4 46.5 1.0

Iridium binding site 6 out of 12 in the Crystal Structure of the Trna-Like Structure From Turnip Yellow Mosaic Virus (Tymv), A Trna Mimicking 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 the Trna-Like Structure From Turnip Yellow Mosaic Virus (Tymv), A Trna Mimicking Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir108 b:75.7 occ:0.28 IR A:IRI108 0.0 75.7 0.3 N6 A:IRI108 2.2 53.6 0.3 N3 A:IRI108 2.2 35.2 0.3 N4 A:IRI108 2.3 48.9 0.3 N2 A:IRI108 2.3 47.4 0.3 N1 A:IRI108 2.3 53.5 0.3 N5 A:IRI108 2.3 38.5 0.3 O6 A:G48 3.9 25.9 1.0 N7 A:G48 4.2 24.2 1.0 O A:HOH203 4.2 27.4 0.7 O A:HOH268 4.5 33.5 0.8 OP2 A:U47 4.5 31.0 1.0 OP1 A:A50 4.7 24.6 1.0 C6 A:G48 4.7 22.0 1.0 C5 A:G48 4.8 24.1 1.0

Iridium binding site 7 out of 12 in the Crystal Structure of the Trna-Like Structure From Turnip Yellow Mosaic Virus (Tymv), A Trna Mimicking 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 the Trna-Like Structure From Turnip Yellow Mosaic Virus (Tymv), A Trna Mimicking Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir109 b:54.5 occ:0.18 IR A:IRI109 0.0 54.5 0.2 N4 A:IRI109 2.3 45.6 0.2 N3 A:IRI109 2.3 46.4 0.2 N5 A:IRI109 2.3 38.6 0.2 N2 A:IRI109 2.3 42.0 0.2 N6 A:IRI109 2.3 43.9 0.2 N1 A:IRI109 2.3 40.1 0.2 O A:HOH303 3.1 43.1 0.5 O4 A:U39 3.5 42.4 1.0 O A:HOH282 3.7 44.6 0.7 OP2 A:A17 3.8 30.1 1.0 N7 A:A17 4.6 31.9 1.0 C4 A:U39 4.7 42.6 1.0

Iridium binding site 8 out of 12 in the Crystal Structure of the Trna-Like Structure From Turnip Yellow Mosaic Virus (Tymv), A Trna Mimicking 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 the Trna-Like Structure From Turnip Yellow Mosaic Virus (Tymv), A Trna Mimicking Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir110 b:60.5 occ:0.25 IR A:IRI110 0.0 60.5 0.2 N2 A:IRI110 2.2 46.1 0.2 N1 A:IRI110 2.2 48.6 0.2 N4 A:IRI110 2.2 49.1 0.2 N3 A:IRI110 2.3 52.6 0.2 N6 A:IRI110 2.3 51.7 0.2 N5 A:IRI110 2.3 36.2 0.2 OP1 A:C61 3.8 43.7 1.0 O3' A:C60 4.7 45.5 1.0 OP2 A:A75 4.9 47.8 1.0

Iridium binding site 9 out of 12 in the Crystal Structure of the Trna-Like Structure From Turnip Yellow Mosaic Virus (Tymv), A Trna Mimicking 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 the Trna-Like Structure From Turnip Yellow Mosaic Virus (Tymv), A Trna Mimicking Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir111 b:43.1 occ:0.22 IR A:IRI111 0.0 43.1 0.2 N2 A:IRI111 2.2 36.6 0.2 N1 A:IRI111 2.2 34.4 0.2 N5 A:IRI111 2.2 42.4 0.2 N4 A:IRI111 2.3 38.0 0.2 N6 A:IRI111 2.3 36.9 0.2 N3 A:IRI111 2.3 38.2 0.2 O2 A:C43 4.2 36.5 1.0 O2' A:C58 4.2 43.1 1.0 O2 A:C58 4.3 37.2 1.0 O2' A:C43 4.5 35.3 1.0 O4 A:U73 4.6 40.7 1.0 N2 A:G57 4.7 32.5 1.0 O4' A:G44 4.9 31.9 1.0 C1' A:C58 5.0 41.8 1.0

Iridium binding site 10 out of 12 in the Crystal Structure of the Trna-Like Structure From Turnip Yellow Mosaic Virus (Tymv), A Trna Mimicking 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 the Trna-Like Structure From Turnip Yellow Mosaic Virus (Tymv), A Trna Mimicking Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir112 b:0.1 occ:0.37 IR A:IRI112 0.0 0.1 0.4 N3 A:IRI112 2.2 94.1 0.4 N6 A:IRI112 2.3 90.3 0.4 N1 A:IRI112 2.3 84.6 0.4 N4 A:IRI112 2.3 81.5 0.4 N2 A:IRI112 2.3 97.7 0.4 N5 A:IRI112 2.3 91.0 0.4 OP1 A:U22 4.2 73.7 1.0

T.M.Colussi, D.A.Costantino, J.A.Hammond, G.M.Ruehle, J.C.Nix, J.S.Kieft. The Structural Basis of Transfer Rna Mimicry and Conformational Plasticity By A Viral Rna. Nature V. 511 366 2014.
ISSN: ESSN 1476-4687
PubMed: 24909993
DOI: 10.1038/NATURE13378