PDBsum entry 1j8g

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_NA ×2
_CA ×3
_SR ×8
Waters ×127

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Key reference
Title X-Ray analysis of an RNA tetraplex (uggggu)(4) with divalent sr(2+) ions at subatomic resolution (0.61 a).
Authors J.Deng, Y.Xiong, M.Sundaralingam.
Ref. Proc Natl Acad Sci U S A, 2001, 98, 13665-13670. [DOI no: 10.1073/pnas.241374798]
PubMed id 11707581
Four-stranded guanine tetraplexes in RNA have been identified to be involved in crucial biological functions, such as dimerization of retroviral RNA, translational repression, and mRNA turnover. However, the structural basis for these biological processes is still largely unknown. Here we report the RNA tetraplex structure (UGGGGU)(4) at ultra-high resolution (0.61 A). The space group is P42(1)2, and cell constants are a = b = 36.16 A and c = 74.09 A. The structure was solved by the multiple-wavelength anomalous dispersion method using a set of three-wavelength data of the isomorphous bromo derivative (br)UGGGGU and refined to 0.61-A resolution. Each of the four strands in the asymmetric unit forms a parallel tetraplex with symmetry-related molecules. The tetraplex molecules stack on one another in opposite polarity (head-to-head or tail-to-tail) to form a pseudocontinuous column. All of the 5'-end uridines rotate around the backbone of G2, swing out, and form unique octaplexes with the neighboring G tetraplexes, whereas the 3'-end uridines are stacked-in and form uridine tetrads. All of the bases are anti, and the riboses are in the mixed C2'- and C3'-puckering mode. Strontium ions are observed in every other guanine tetrad plane, sitting on the fourfold axis and associated to the eight O6 atoms of neighboring guanine bases in a bipyramidal-antiprism geometry. The hydrogens are clearly observed in the structure.
Figure 4.
Fig. 4. The coordination geometries of the metal ions and the spermine molecule. (a) The Sr2+ ion (purple) is coordinated to eight guanine O6 atoms. (b) Three Ca^2+ ions are coordinated to U6 (Ca1), U7 (Ca2), and U12 (Ca3) residues, respectively. (c) Coordination of the spermine molecule (blue) in stereoview. Hydrogen bonds are shown in white dashed lines. Individual RNA strands are depicted in different colors.
Figure 7.
Fig. 7. Hydrogen bonding in the G and U tetrads. The 2F[o] F[c] maps are calculated at 2 level and shown in blue. Top views are shown in the upper row and side views in the lower row. (a and b) G tetrads. The guanines are hydrogen bonded to each other by clockwise Hoogsteen-like pairing (N1H O4) with near ideal planarity. (c and d) The U6/U12 tetrad. It is formed with a single hydrogen bond between N3 and O4 atoms in a counterclockwise pattern. (e and f) The U24 tetrad is flipped over in a clockwise N3-H---O4 hydrogen-bonding pattern.