310D

Crystal structure of 2'-O-Me(CGCGCG)2: an RNA duplex at 1.3 A resolution. Hydration pattern of 2'-O-methylated RNA

Summary for 310D

• Entry DOI: 10.2210/pdb310d/pdb
• Descriptor: RNA (5'-R(*(OMC)P*(OMG)P*(OMC)P*(OMG)P*(OMC)P*(OMG))-3'), MAGNESIUM ION (3 entities in total)
• Functional Keywords: a-rna, double helix, modified, rna
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 4029.33

Authors

Adamiak, D.A.,Milecki, J.,Adamiak, R.W.,Dauter, Z.,Rypniewski, W.R. (deposition date: 1996-05-25, release date: 1997-06-24, Last modification date: 2024-04-03)

Primary citation

Adamiak, D.A.,Milecki, J.,Popenda, M.,Adamiak, R.W.,Dauter, Z.,Rypniewski, W.R.
Crystal structure of 2'-O-Me(CGCGCG)2, an RNA duplex at 1.30 A resolution. Hydration pattern of 2'-O-methylated RNA.
Nucleic Acids Res., 25:4599-4607, 1997

PubMed 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.

PubMed: 9358171
DOI: 10.1093/nar/25.22.4599

Experimental method

X-RAY DIFFRACTION (1.3 Å)