Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Endonucleolytic cleavage to 5'-phosphomonoester. Manganese or magnesium. Binds 1 divalent metal ion per monomer in the absence of substrate. May bind a second metal ion after substrate binding. Probably essential, it was not disrupted in a global transposon mutagenesis study. Belongs to the RNase HII family. RnhC subfamily.