Table 2.
Class IV angles and cleavage patterns
| REase | PDB code | Class notation | Blunt/sticky | Subtype | Ωo H1/H2 | Ωαβ S2/H2 | Ωαβ S2/H1 |
|---|---|---|---|---|---|---|---|
| HincII | 1xhvA | H2-H1-S-down | blunt | IIP | 138.1 | 154.5 | 18.1 |
| EcoRV | 1b94A | H2-H1-S-down | blunt | IIP | 131.4 | 143.6 | 12.7 |
| NaeI | 1iawA | H2-H1-S-down | blunt | IIE | 73.5 | 85.8 | 37.6 |
| BgII | 1dmuA | H2-H1-S-down | 3′ end | IIP | 104.3 | 109.3 | 12.3 |
| SfiI | 2ezvA | H2-H1-S-down | 3′ end | IIF | 108.1 | 122.4 | 16.6 |
The columns are ordered as follows: REase column lists the names of the REases; PDB code column lists the pdb files used in the analysis; Class notation describes the sequential order of the elements and the direction of the S5 strand with respect to the S1 strand; Blunt/sticky classification, where ‘sticky’ leave 5′ or 3′ DNA end overhang and blunt leave no overhangs upon cleavage; Subtype lists the functional subtypes as defined in the REase nomenclature (1); Ω columns list the angles, calculated as described in the Material and methods section.