Magnesium in PDB 5uza: Adenine Riboswitch Aptamer Domain Labelled with Iodo-Uridine By Position-Selective Labelling of Rna (Plor)

The structure of Adenine Riboswitch Aptamer Domain Labelled with Iodo-Uridine By Position-Selective Labelling of Rna (Plor), PDB code: 5uza was solved by Y.Liu, J.R.Stagno, Y.-X.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.61 / 2.22
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	48.985, 151.575, 24.735, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 25.1

The structure of Adenine Riboswitch Aptamer Domain Labelled with Iodo-Uridine By Position-Selective Labelling of Rna (Plor) also contains other interesting chemical elements:

Iodine

(I)

2 atoms

The binding sites of Magnesium atom in the Adenine Riboswitch Aptamer Domain Labelled with Iodo-Uridine By Position-Selective Labelling of Rna (Plor) (pdb code 5uza). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Adenine Riboswitch Aptamer Domain Labelled with Iodo-Uridine By Position-Selective Labelling of Rna (Plor), PDB code: 5uza:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Adenine Riboswitch Aptamer Domain Labelled with Iodo-Uridine By Position-Selective Labelling of Rna (Plor)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Adenine Riboswitch Aptamer Domain Labelled with Iodo-Uridine By Position-Selective Labelling of Rna (Plor) within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg102 b:49.1 occ:1.00 OP2 X:A23 2.0 43.8 1.0 O X:HOH245 2.1 47.0 1.0 O X:HOH251 2.1 46.1 1.0 O X:HOH250 2.1 46.2 1.0 O X:HOH228 2.2 43.2 1.0 O X:HOH217 2.2 22.7 1.0 P X:A23 3.3 36.8 1.0 H62 X:A21 3.7 29.3 1.0 O3' X:U22 3.7 33.0 1.0 OP1 X:A23 4.2 40.5 1.0 O X:HOH215 4.3 23.1 1.0 N7 X:A21 4.3 24.2 1.0 N6 X:A21 4.4 24.4 1.0 O2' X:U22 4.4 29.1 1.0 O5' X:A23 4.5 34.1 1.0 HN62 X:ADE101 4.5 24.8 1.0 H5' X:A23 4.6 35.9 1.0 H5'' X:A23 4.7 35.9 1.0 H3' X:U22 4.7 37.5 1.0 HO2' X:U22 4.7 35.0 1.0 C3' X:U22 4.7 31.2 1.0 C5' X:A23 4.8 29.9 1.0 H61 X:A21 4.8 29.3 1.0 C5 X:A21 5.0 23.9 1.0

Magnesium binding site 2 out of 3 in the Adenine Riboswitch Aptamer Domain Labelled with Iodo-Uridine By Position-Selective Labelling of Rna (Plor)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Adenine Riboswitch Aptamer Domain Labelled with Iodo-Uridine By Position-Selective Labelling of Rna (Plor) within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg103 b:32.0 occ:1.00 OP1 X:A24 1.9 29.7 1.0 O X:HOH218 2.1 28.2 1.0 O X:HOH241 2.1 32.0 1.0 O X:HOH244 2.1 37.6 1.0 O X:HOH209 2.2 35.2 1.0 O X:HOH236 2.2 26.7 1.0 P X:A24 3.4 22.9 1.0 O X:HOH235 3.7 34.1 1.0 O X:HOH231 3.9 22.2 1.0 O X:HOH212 3.9 18.3 1.0 H8 X:A24 3.9 21.6 1.0 O5' X:A24 4.0 23.2 1.0 O X:HOH240 4.2 31.9 1.0 O X:HOH230 4.3 25.8 1.0 O3' X:A23 4.3 24.9 1.0 N7 X:A24 4.3 18.5 1.0 OP2 X:A24 4.3 18.6 1.0 C8 X:A24 4.4 17.9 1.0 O6 X:G72 4.4 21.0 1.0 H5 X:U71 4.4 31.9 1.0 N7 X:G72 4.5 24.5 1.0 O X:HOH225 4.5 27.5 1.0 C5 X:U71 4.8 26.6 1.0 O4 X:U71 4.9 25.5 1.0

Magnesium binding site 3 out of 3 in the Adenine Riboswitch Aptamer Domain Labelled with Iodo-Uridine By Position-Selective Labelling of Rna (Plor)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Adenine Riboswitch Aptamer Domain Labelled with Iodo-Uridine By Position-Selective Labelling of Rna (Plor) within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg104 b:61.1 occ:1.00 OP2 X:C83 2.1 60.3 1.0 O X:HOH254 2.1 60.3 1.0 P X:C83 3.5 55.6 1.0 H3' X:C82 3.9 60.3 1.0 H5 X:C83 3.9 68.8 1.0 O5' X:C83 4.2 52.8 1.0 OP1 X:C83 4.3 55.6 1.0 O5' X:C82 4.4 47.5 1.0 OP2 X:C82 4.5 46.4 1.0 O3' X:C82 4.5 52.4 1.0 H6 X:C83 4.6 68.3 1.0 C5 X:C83 4.6 57.3 1.0 C3' X:C82 4.6 50.2 1.0 P X:C82 4.8 48.9 1.0 OP1 X:C82 4.8 52.2 1.0 C6 X:C83 5.0 56.9 1.0 H5'' X:C82 5.0 58.0 1.0

Y.Liu, E.Holmstrom, P.Yu, K.Tan, X.Zuo, D.J.Nesbitt, R.Sousa, J.R.Stagno, Y.X.Wang. Incorporation of Isotopic, Fluorescent, and Heavy-Atom-Modified Nucleotides Into Rnas By Position-Selective Labeling of Rna. Nat Protoc V. 13 987 2018.
ISSN: ESSN 1750-2799
PubMed: 29651055
DOI: 10.1038/NPROT.2018.002