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

Protein crystallography data

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

Other elements in 4p5j:

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

Magnesium Binding Sites:

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 4p5j

Go back to Magnesium Binding Sites List in 4p5j
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 4p5j

Go back to Magnesium Binding Sites List in 4p5j
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

Reference:

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
Page generated: Mon Dec 14 19:19:14 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy