The identification of RNA 3D motifs and their organization into larger subassemblies is of fundamental interest in the analysis ,prediction and design of 3D structures of large RNAs. New methods are described for finding recurrent three-dimensional (3D) motifs in RNA atomic-resolution structures. Sarcin/Ricin motif (or loop E) is a structural RNA motif which is found in 23S rRNA and 28S rRNA of ribosomal subunits. FR3D (Find RNA 3D) is a suite of Matlab programs that implement the geometric and symbolic search algorithms. Here, we present the comparison of sarcin/ricin motif tertiary structure of Haloarcula marismortui, intron group I Azoarcus (of proteobacteria), and 28S rRNA rat with one another using FR3D. In this study, five nucleotides were considered and in all 3 species tHS bound between 1-2 nucleotides, tWH bound between 3-4 nucleotides, and cHS bound between 3-5 nucleotides were found. tWH and cHS bounds exist in all 3 species between homologous basepairs. tHS bound is mostly formed between A/G nucleotides but in intron group I Azoarcus in A/C and G/G basepaires and in 28S rRNA of rat in C/C basepaires were found in high percent.

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