The current understanding of RNA-protein cross-linking is that close contact between nucleotides and amino acids is the main pre-requisite for a cross-linking event . However, only three from the seven nucleotides of FOXRBE engaged in efficent cross-linking, despite close contact between all nucleotides and amino acids in the binding site. In an effort to resolve this apparent contradiction, we investigated two obvious parameters that could influence cross-linking: the chemical reactivities of the nucleotides and the amino acids, as well as their relative positioning of the reactive pair in space. By mutating selected nucleotides and amino acids in the binding pocket, we created a cross-linking structureactivity relationship for the FOXRRM-FOXRBE interaction.