 The structural basis for binding of RNA to the argonaute protein was examined by X @-@ ray crystallography of the binding domain of an RNA @-@ bound argonaute protein . Here , the phosphorylated 5 ' end of the RNA strand enters a conserved basic surface pocket and makes contacts through a divalent cation ( an atom with two positive charges ) such as magnesium and by aromatic stacking ( a process that allows more than one atom to share an electron by passing it back and forth ) between the 5 ' nucleotide in the siRNA and a conserved tyrosine residue . This site is thought to form a nucleation site for the binding of the siRNA to its mRNA target . Analysis of the inhibitory effect of mismatches in either the 5 ’ or 3 ’ end of the guide strand has demonstrated that the 5 ’ end of the guide strand is likely responsible for matching and binding the target mRNA , while the 3 ’ end is responsible for physically arranging target mRNA into a cleavage @-@ favorable RISC region . 
