Spatial conservation of active site and nucleotide-binding residues in the MID and PIWI domains. (A) Topology diagram depicting the structural features and critical binding regions in the domains. MID and PIWI designations are provided at the top of the diagram. The β-sheet extension unique to the PIWI clade of the RNase H fold is labeled and shaded in grey. Locations of key active site residues are marked with green lines. Active site and general regions of nucleotide-binding are shaded and labeled. (B and C) Cartoon renderings of active site and nucleotide binding regions of a solved PIWI domain structure in complex with double-stranded nucleotide guide/passenger strands (PDB: 3HO1 ). Residues in the structure involved in guide strand binding with cognate conserved residues in pPIWI-RE and MedPIWI families are colored in yellow. The guide strand is colored in tan, passenger strand in light blue.