4U3O

Octameric RNA duplex soaked in manganese(II)chloride

Summary for 4U3O

• Entry DOI: 10.2210/pdb4u3o/pdb
• Related: 4U3L
• Descriptor: RNA (5'-R(*UP*CP*GP*UP*AP*CP*GP*A)-3'), MANGANESE (II) ION (3 entities in total)
• Functional Keywords: rna, duplex, di- and trivalent metal ions
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 5272.87

Authors

Schaffer, M.F.,Spingler, B.,Schnabl, J.,Peng, G.,Olieric, V.,Sigel, R.K.O. (deposition date: 2014-07-22, release date: 2015-07-29, Last modification date: 2023-12-20)

Primary citation

Schaffer, M.F.,Peng, G.,Spingler, B.,Schnabl, J.,Wang, M.,Olieric, V.,Sigel, R.K.
The X-ray Structures of Six Octameric RNA Duplexes in the Presence of Different Di- and Trivalent Cations.
Int J Mol Sci, 17:-, 2016

PubMed Abstract: Due to the polyanionic nature of RNA, the principles of charge neutralization and electrostatic condensation require that cations help to overcome the repulsive forces in order for RNA to adopt a three-dimensional structure. A precise structural knowledge of RNA-metal ion interactions is crucial to understand the mechanism of metal ions in the catalytic or regulatory activity of RNA. We solved the crystal structure of an octameric RNA duplex in the presence of the di- and trivalent metal ions Ca(2+), Mn(2+), Co(2+), Cu(2+), Sr(2+), and Tb(3+). The detailed investigation reveals a unique innersphere interaction to uracil and extends the knowledge of the influence of metal ions for conformational changes in RNA structure. Furthermore, we could demonstrate that an accurate localization of the metal ions in the X-ray structures require the consideration of several crystallographic and geometrical parameters as well as the anomalous difference map.

PubMed: 27355942
DOI: 10.3390/ijms17070988

Experimental method

X-RAY DIFFRACTION (1.8 Å)