RNA double-helical fragments at atomic resolution

II. The crystal structure of sodium guanylyl-3′,5′-cytidine nonahydrate

John M. Rosenberg, Nadrian Seeman, Roberta O. Day, Alexander Rich

Research output: Contribution to journalArticle

Abstract

The crystal structure of sodium guanylyl-3′,5′-cytidine (GpC) nonahydrate has been determined by X-ray diffraction procedures and refined to an R value of 0.054. GpC crystallizes with four molecules per monoclinic unit cell, space group C2, with cell dimensions: a = 21.460, b = 16.297, c = 9.332 A ̊ and β = 90.54 °. Two molecules of GpC related by the 2-fold axis of the crystal form a small segment of right-handed, anti-parallel double-helical RNA in the crystal. Guanine is paired to cytosine through three hydrogen bonds of lengths 2.91, 2.95 and 2.86 Å. The bases along each strand are heavily stacked at a distance of about 3.4 Å. The fragments form skewed flattened rods within the lattice by the inter-molecular stacking of guanines with each other and the stacking of cytosine with the guanosine Ol′atom. The sodium cations are bound only to the ionized phosphate groups in this structure and exhibit face-sharing octahedral co-ordination. The sodium cations serve to bridge the rods of GpC fragments and organize them into sheets within the crystal. There are 18 water molecules per double-helical fragment which are all part of the first co-ordination shell of nitrogen, oxygen or sodium atoms.

Original languageEnglish (US)
Pages (from-to)145-167
Number of pages23
JournalJournal of Molecular Biology
Volume104
Issue number1
DOIs
StatePublished - Jun 14 1976

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Cytidine
Sodium
RNA
Cytosine
Guanine
Cations
Guanosine
X-Ray Diffraction
Hydrogen
Nitrogen
Phosphates
Oxygen
Water

ASJC Scopus subject areas

  • Virology

Cite this

RNA double-helical fragments at atomic resolution : II. The crystal structure of sodium guanylyl-3′,5′-cytidine nonahydrate. / Rosenberg, John M.; Seeman, Nadrian; Day, Roberta O.; Rich, Alexander.

In: Journal of Molecular Biology, Vol. 104, No. 1, 14.06.1976, p. 145-167.

Research output: Contribution to journalArticle

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abstract = "The crystal structure of sodium guanylyl-3′,5′-cytidine (GpC) nonahydrate has been determined by X-ray diffraction procedures and refined to an R value of 0.054. GpC crystallizes with four molecules per monoclinic unit cell, space group C2, with cell dimensions: a = 21.460, b = 16.297, c = 9.332 A ̊ and β = 90.54 °. Two molecules of GpC related by the 2-fold axis of the crystal form a small segment of right-handed, anti-parallel double-helical RNA in the crystal. Guanine is paired to cytosine through three hydrogen bonds of lengths 2.91, 2.95 and 2.86 {\AA}. The bases along each strand are heavily stacked at a distance of about 3.4 {\AA}. The fragments form skewed flattened rods within the lattice by the inter-molecular stacking of guanines with each other and the stacking of cytosine with the guanosine Ol′atom. The sodium cations are bound only to the ionized phosphate groups in this structure and exhibit face-sharing octahedral co-ordination. The sodium cations serve to bridge the rods of GpC fragments and organize them into sheets within the crystal. There are 18 water molecules per double-helical fragment which are all part of the first co-ordination shell of nitrogen, oxygen or sodium atoms.",
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AB - The crystal structure of sodium guanylyl-3′,5′-cytidine (GpC) nonahydrate has been determined by X-ray diffraction procedures and refined to an R value of 0.054. GpC crystallizes with four molecules per monoclinic unit cell, space group C2, with cell dimensions: a = 21.460, b = 16.297, c = 9.332 A ̊ and β = 90.54 °. Two molecules of GpC related by the 2-fold axis of the crystal form a small segment of right-handed, anti-parallel double-helical RNA in the crystal. Guanine is paired to cytosine through three hydrogen bonds of lengths 2.91, 2.95 and 2.86 Å. The bases along each strand are heavily stacked at a distance of about 3.4 Å. The fragments form skewed flattened rods within the lattice by the inter-molecular stacking of guanines with each other and the stacking of cytosine with the guanosine Ol′atom. The sodium cations are bound only to the ionized phosphate groups in this structure and exhibit face-sharing octahedral co-ordination. The sodium cations serve to bridge the rods of GpC fragments and organize them into sheets within the crystal. There are 18 water molecules per double-helical fragment which are all part of the first co-ordination shell of nitrogen, oxygen or sodium atoms.

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