Magnesium 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:

Iridium

(Ir)

12 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium 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 Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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:Mg101 b:31.9 occ:1.00 O A:HOH227 2.0 31.4 1.0 O A:HOH224 2.0 36.4 1.0 O A:HOH236 2.1 20.0 0.6 O A:HOH226 2.1 32.2 1.0 O A:HOH237 2.2 22.1 0.6 O A:HOH229 2.3 32.2 1.0 O A:HOH276 3.9 14.4 0.4 O6 A:G79 4.0 46.4 1.0 O6 A:G78 4.1 31.1 1.0 O4 A:U65 4.1 37.1 1.0 O4' A:U62 4.2 31.2 1.0 O A:HOH240 4.3 27.5 0.8 O2 A:C61 4.3 33.7 1.0 O A:HOH269 4.4 37.8 0.7 O A:HOH253 4.5 30.4 1.0 N7 A:G78 4.5 33.2 1.0 O2 A:U62 4.5 39.2 1.0 O A:HOH265 4.6 25.2 0.6 O A:HOH257 4.6 39.2 1.0 N4 A:C66 4.7 46.7 1.0 C1' A:U62 4.7 31.2 1.0 O A:HOH263 4.7 32.4 0.8 N4 A:C77 4.8 26.9 1.0 C6 A:G78 4.9 35.4 1.0 C2 A:U62 5.0 32.4 1.0

Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg 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:Mg102 b:55.0 occ:1.00 OP2 A:A40 2.0 49.1 1.0 O A:HOH244 2.1 51.4 1.0 O A:HOH273 2.1 48.0 0.7 O A:HOH252 2.2 39.2 0.7 O A:HOH225 2.2 34.4 1.0 O A:HOH228 2.4 52.2 1.0 P A:A40 3.3 50.0 1.0 OP1 A:A40 3.8 47.3 1.0 O5' A:A40 3.9 52.1 1.0 OP2 A:C3 4.1 57.3 1.0 O A:HOH297 4.1 34.3 0.9 N2 A:IRI114 4.1 43.4 0.3 N7 A:A41 4.5 38.7 1.0 O3' A:U39 4.5 53.1 1.0 OP2 A:A41 4.9 44.9 1.0 N6 A:A41 4.9 35.2 1.0 O A:HOH301 4.9 47.1 1.0 O2' A:G2 4.9 61.5 1.0 O A:HOH315 5.0 45.4 0.7 C8 A:A40 5.0 51.8 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