Figure 3.

RsiteDB classification. An example of a cluster of dinucleotide binding sites. RsiteDB details the properties of the binding sites in the cluster (top table) and provides the transformations that can align them in 3D space. The bottom right table details the matched pseudocenters of the common pattern. Each binding site in a cluster is described by its PDB code, chain identifies and nucleotide identities (e.g. 1sj3PRU51G52). It has three columns which provide the following details of its matched pseudocenters: (i) chain identifier and residue number; (ii) residue type and (iii) pseudocenter type. Although the pseudocenters are not required to have the same amino acid identity or origin (backbone or side chain), we indicate the conservation of these (* or b/s, respectively). The RNA dinucleotides are represented as sticks, colored by their atoms.