Fig. 5. Two patterns of DNA recognition of the endonucleases. (A) The β-strand recognition for subgroup I endonucleases consists of two elements: a β-strand (NaeI 1 in this figure and R1 in Figure 2A) and a β-like turn (NaeI 2 in this figure and R2 in Figure 2A). The color codes are red for NaeI (100–113 and 135–158), gold for PvuII (75–88 and 129–152), green for BglI (149–162 and 256–279) and blue for EcoRV (101–113 and 175–195). The 8 bp double helix DNA is adopted from the PvuII–DNA structure (Cheng et al., 1994). (B) The helix recognition for subgroup II endonucleases of BamHI (gold; BamHI 1 for 113–126 and BamHI 2 for 145–165), Cfr10I (blue; 192–206), EcoRI (magenta; 137–152) and MunI (red; 113–128). The double helix DNA is adopted from the BamHI–DNA structure (Newman et al., 1995).