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. Author manuscript; available in PMC: 2013 Sep 1.
Published in final edited form as: Nat Struct Mol Biol. 2013 Jan 27;20(3):380–386. doi: 10.1038/nsmb.2487

Figure 2.

Figure 2

AfC3PO Trax-like subunit catalytic sites. (a) Positioning of the Trax-like subunit catalytic sites. The view shows the RNA duplex inside AfC3PO with the two RNA-proximal catalytic sites (Site 1 and Site 2), located on the Trax-like subunits. Catalytic glutamate side chains are colored yellow, metals (M) are shown as green spheres and metal-coordinated waters (W) as blue spheres. Bases on each strand are numbered 1–13 from the 5′ ends. The RNA is shown in cartoon representation for clarity. (b) Schematic representation showing the positioning of the AfC3PO Trax-like subunit catalytic sites relative to the visible RNA duplex in the structure. (c) Detailed view of a Trax-like subunit catalytic site in complex with substrate RNA. Selected side chains are shown in yellow. Catalytic Asp114, mutated to alanine in the complex with RNA, is superimposed from the apo (wild type) structure and shown in white (together with interacting Lys166). The metal (M) coordinated to the scissile phosphate is shown as a green sphere. A coordinated water molecule (W) is shown as a blue sphere. Nucleotides in the RNA (red and blue) are numbered. The putative scissile bond in the RNA is indicated by a red arrow. Parts of the subunits have been removed for visibility.