5XWG

Crystal structure of a novel RNA motif that allows for precise positioning of a metal ion

Summary for 5XWG

• Entry DOI: 10.2210/pdb5xwg/pdb
• Descriptor: RNA (5'-R(P*CP*GP*CP*UP*(5BU)P*CP*GP*AP*AP*AP*AP*AP*GP*UP*C)-3'), STRONTIUM ION (2 entities in total)
• Functional Keywords: rna, metal-ion-binding motif, x-ray analysis
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 5117.67

Authors

Kanazawa, H.,Kondo, J. (deposition date: 2017-06-29, release date: 2017-10-11, Last modification date: 2024-03-27)

Primary citation

Kanazawa, H.,Kondo, J.
Crystal structure of a novel RNA motif that allows for precise positioning of a single metal ion.
J. Inorg. Biochem., 176:140-143, 2017

PubMed Abstract: We have determined a crystal structure of an RNA duplex containing a novel metal-binding motif. The motif is composed of two sheared G○A base pairs, two unpaired A residues and four phosphate groups in close proximity. Four A residues make an A-A-A-A stacking column at the minor groove side and two G bases are highly inclined, thereby forming the pocket-shaped motif at the major groove side. In the present structure, a hydrated Sr ion exists in the pocket and binds to the O6 and N7 atoms of the two G bases and four phosphate groups. According to the previously-reported metal-binding properties to RNA molecules, many of divalent cations, such as Mg, Mn, Co, Zn, Ba, Pb and Cd, may bind to the motif. This metal-binding motif can be used as a modular building block that allows for precise positioning of a single metal ion in functional nucleic acid molecules.

PubMed: 28898762
DOI: 10.1016/j.jinorgbio.2017.08.029

Experimental method

X-RAY DIFFRACTION (3.002 Å)