6114 Nucleic Acids Research, 2008, Vol. 36, No. 19 Figure 3. Speciﬁc DNA recognition. (A) Superposition of the DNA duplexes in the PspGI-DNA (yellow/orange) and Ecl18kI-DNA (light/dark green) complexes. DNA colors are consistent with Figure 2. Please note the diﬀerent conformation of the central base pairs in the two structures. Hydrogen bonding interactions between PspGI and the (B) outer and (C) inner C/G pairs of the recognition sequence. The electron density is taken from the original ARP/wARP map and contoured at 1 s. Figure 4. DNA distortion in the (A) PspGI and (B) Ecl18kI structures. The bond thickness corresponds to the angular diﬀerence with respect to the regular B-DNA. Discrepancies >1008 are marked (n3 angle diﬀerence is not shown since it overlaps with d). Color coding is consistent with Figure 2. Idealized B-DNA values used: a 308, b 1368, g 318, d 1438, e 1418, z 1618, w 988, n0 338, n1 458, n2 408 and n4 68 (20). of Ecl18kI (11). On the basis of a slightly better ﬁt to the density, we had previously modeled the ﬂipped A- and T- nucleotides in this complex as syn and anti, respectively. This is consistent with the new and more reliable assign- ment for the PspGI-DNA co-crystals. Disregarding the dihedral angles of the ﬂipped central nucleotides, DNA backbones within one complex are more similar than between diﬀerent complexes (Figure 4). PspGI interactions with the specifically recognized bases PspGI and Ecl18kI recognize the outer and inner G/C base pairs of their target sequences in very similar ways, via interactions that follow the 2-fold symmetry as pre- dicted (7,8). Following a DNA strand in 50–30 direction, the scissile phosphoester bond is located upstream of two cytosine residues. The PspGI subunit that would catalyze the hydrolysis of this phosphoester bond approaches the