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. 2010 Jan 21;38(9):3119–3132. doi: 10.1093/nar/gkq002

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© The Author(s) 2010. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 3. — Structural details of the Site-I and Site-II base-binding pockets. Close up views of bases bound in the Site-I binding pocket in (A) the Rna15(16-103)-ht-GUUGU and (B) the Rna15(16-111)-GUUGU structure. Uracil (yellow) and guanine (magenta) bases along with the side-chains of S24, I25, Y27 and R87 that form the Site-I base-binding pocket are shown in stick representation, hydrogen bonds are shown as black dashed lines. The remainder of the protein is shown as a semi-transparent surface representation with the backbone highlighted as a cartoon. (C) Comparison of the configuration and complementarity of base pair edges involved in base-backbone pairing at Site-I. Bound guanine (magenta) and uracil (yellow) together with adenine (cyan) and cytosine (green) bases modelled in Site-I are shown in stick representation. Base imino and amino protons are shown and hydrogen bonds to the protein backbone in the SIPY loop are shown as black dashed lines. (D) The Site-II base-binding pocket in the Rna15(16-103)ht-GUUGU structure. The bound dinucleotide guanine (magenta) and uracil (yellow) together with protein residues Y21 and Y93 are shown in stick representation.