Fig. 2. Reaction schemes for cross-linking AZTMP-terminated template–primers at the P (priming) (A) or N (nucleotide-binding) (B) sites of HIV-1 RT. Cross-linking takes place when Cys258 of the αH helix of the p66 thumb of HIV-1 RT is aligned with the cross-linkable nucleotide analog. Complex P [RT(P)–AZTMP complex] is formed after addition of AZTMP (A), whereas complex N [RT(N)– AZTMP complex] is formed with in situ incorporation of dAMP and AZTMP (B). Z is AZTMP.