Magnesium in PDB 1yrj: Crystal Structure of Apramycin Bound to A Ribosomal Rna A Site Oligonucleotide

The structure of Crystal Structure of Apramycin Bound to A Ribosomal Rna A Site Oligonucleotide, PDB code: 1yrj was solved by Q.Han, Q.Zhao, S.Fish, K.B.Simonsen, D.Vourloumis, J.M.Froelich, D.Wall, T.Hermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	92.250, 30.900, 45.810, 90.00, 90.00, 90.00
R / Rfree (%)	24.6 / 30.7

The structure of Crystal Structure of Apramycin Bound to A Ribosomal Rna A Site Oligonucleotide also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Apramycin Bound to A Ribosomal Rna A Site Oligonucleotide (pdb code 1yrj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Apramycin Bound to A Ribosomal Rna A Site Oligonucleotide, PDB code: 1yrj:

Magnesium binding site 1 out of 1 in the Crystal Structure of Apramycin Bound to A Ribosomal Rna A Site Oligonucleotide


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 Apramycin Bound to A Ribosomal Rna A Site Oligonucleotide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:25.0 occ:1.00 O6 A:G16 2.5 12.5 1.0 O4 A:U15 2.9 35.6 1.0 O A:HOH158 3.3 25.4 1.0 C6 A:G16 3.6 14.6 1.0 C4 A:U15 3.6 36.6 1.0 O B:HOH166 3.9 28.2 1.0 C5 A:U15 4.0 36.3 1.0 N7 A:G16 4.1 14.6 1.0 C5 A:G16 4.2 15.4 1.0 N4 B:C32 4.3 32.1 1.0 N6 B:A33 4.3 24.3 1.0 N3 A:U15 4.7 35.2 1.0 N1 A:G16 4.7 16.0 1.0 N6 B:A31 4.8 53.5 1.0 N1 B:A33 4.8 23.0 1.0 C6 B:A33 4.9 23.7 1.0

Q.Han, Q.Zhao, S.Fish, K.B.Simonsen, D.Vourloumis, J.M.Froelich, D.Wall, T.Hermann. Molecular Recognition By Glycoside Pseudo Base Pairs and Triples in An Apramycin-Rna Complex. Angew.Chem.Int.Ed.Engl. V. 44 2694 2005.
ISSN: ISSN 1433-7851
PubMed: 15849690
DOI: 10.1002/ANIE.200500028