In order to determine systematically the propensity for cross-linking at each site in FOXRBE when a more photo-reactive nucleotide (i.e. U or G) is present, we performed CLIR-MS on six additional positional FOXRBE mutants. Thus, we exchanged *U for C3 and A4 in FOXRBE (UG*UAUGU, UGC*UUGU, resp.), and *G for C3, A4, U5 and U7 (UG*GAUGU, UGC*GUGU, UGCA*GGU, UGCAUG*G, resp.). In each case, we confirmed that the mutants bound and cross-linked to FOXRRM using SPR and SDS-PAGE gels (Fig. and Fig. , resp.). Remarkably, in none of these six examples, did the mutated nucleotides cross-link efficiently to the protein (Fig. ). The lack of reactivity at U3 (in mutant UG*UAUGU) was particularly surprising give the close proximity of C3 to F126 in the NMR structure.