Table 3.

DNA structural parameters

Form	Bend* at center step, °	Bend overall†, °	Roll at center step global (local)	Bend* at adjacent steps, °	Minor groove width at center step, Å	Surface area buried between Q-loop/B-helix and DNA‡, Å2
I	35	60	45.3° (49.9°)	15, 7	11.92	1,551
II	35	57	53.3° (47.7°)	9, 10	10.57	1,402
III	31	46	46.7° (51.1°)	8, 12	10.70	1,335
IV	24	42	33.7° (34.5°)	7, 8	10.70	1,241
Nonspecific	6	23	12.0° (5.7°)	13, 15	10.77	–

^*Bend is defined as the angle between helical axes on either side of the base pairs (21). The center step is TA for the specific site GATATC and GC for the nonspecific site TCGCGA. To establish the significance of the differences among the angles 24° to 35°, bend angles were calculated for four protein–DNA complexes solved in lattices which contain two independent copies of a complete complex in the asymmetric unit. The structures used are three zinc-finger complexes (34–36) and a leucine zipper protein bound to DNA (37). A total of 74 base-pair steps in these four complexes were analyzed for differences in bend angles between the two asymmetric units of each structure. The mean difference is 0.02° with a standard deviation of 1.5°. It thus appears that the overall 11° variation in bend angle at the center TA step in the EcoRV structures is significant. There is no correlation of bending angle with the solution conditions (ionic strength, precipitating agent, or pH) used for crystallization (Table 1). 

^†Bend overall of the helical axis as calculated by curves (21) using a best-fit curvilinear axis. 

^‡Buried surface area is calculated as the sum over both enzyme subunits.