PDBsum entry 310d

RNA

PDB id: 310d

Contents

Ligands

OMC-OMG-OMC-OMG-OMC-OMG ×2

Metals

_MG ×2

Waters ×44

References listed in PDB file

Key reference

• Title: Crystal structure of 2'-O-Me(cgcgcg)2, An RNA duplex at 1.30 a resolution. Hydration pattern of 2'-O-Methylated RNA.
• Authors: D.A.Adamiak, J.Milecki, M.Popenda, R.W.Adamiak, Z.Dauter, W.R.Rypniewski.
• Ref.: Nucleic Acids Res, 1997, 25, 4599-4607.
• PubMed id: 9358171

Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a percentage match of 96%.

Abstract

The molecular and crystal structure of 2'-O-Me (CGCGCG)2 has been determined using synchrotron radiation at near-atomic resolution (1.30 A), the highest resolution to date in the RNA field. The crystal structure is a half-turn A-type helix with some helical parameters deviating from canonical A-RNA, such as low base pair rise, elevated helical twist and inclination angles. In CG steps, inter-strand guanines are parallel while cytosines are not parallel. In steps GC this motif is reversed. This type of regularity is not seen in other RNA crystal structures. The structure includes 44 water molecules and two hydrated Mg2+ions one of which lies exactly on the crystallographic 2-fold axis. There are distinct patterns of hydration in the major and the minor grooves. The major groove is stabilised by water clusters consisting of fused five- and six-membered rings. Minor groove contains only a single row of water molecules; each water bridges either two self-parallel cytosines or two self-parallel guanines by a pair of hydrogen bonds. The structure provides the first view of the hydration scheme of 2'-O-methylated RNA duplex.

Secondary reference #1

• Title: Low salt nmr study of r(cgcgcg) and 2'-O-Me(cgcgcg) reveals structure of RNA duplexes containing consecutive cg base pairs
• Authors: M.Popenda, E.Biala, J.Milecki, R.W.Adamiak.
• Ref.: TO BE PUBLISHED ...