Repairs 3'-OH/5'-PO4 nicks in duplex RNA or RNA:DNA hybrid in which the broken 3'-OH strand is RNA (Probable) (PubMed:12611899, PubMed:24158792, PubMed:15494308, PubMed:16671895, PubMed:15851476). The nick ligation reaction entails three nucleotidyl transfer steps (PubMed:24158792, PubMed:15851476). In the first step, the RNA ligase reacts with ATP in the absence of nucleic acid to form a covalent ligase-AMP intermediate and release pyrophosphate (PubMed:24158792, PubMed:15851476). In step 2, the ligase-AMP binds to the nicked duplex nucleic acid and transfers the adenylate to the 5'-PO4 terminus to form an adenylylated nicked intermediate (PubMed:24158792, PubMed:15851476). In step 3, the RNA ligase directs the attack of the nick 3'-OH on the 5'-phosphoanhydride linkage, resulting in a repaired 3' - 5' phosphodiester and release of AMP (PubMed:24158792, PubMed:15851476). ATP + (ribonucleotide)n-3'-hydroxyl + 5'-phospho-(ribonucleotide)m = (ribonucleotide)n+m + AMP + diphosphate. Binds 2 magnesium ions that may perform the catalytic activity via a two-metal mechanism. Optimum pH is 7. The adenylyltransferase domain in the N-terminus performs step 1 and step 3 reactions (PubMed:14962393). The C-terminus domain is required for step 2 of the ligation pathway (PubMed:14962393, PubMed:17018278). Belongs to the RNA ligase 2 family.