HHAI methyltransferase (blue ribbon) bound to oligonucleotide (strands with bonds colored yellow and green) containing a pseudorotationally constrained sugar analogue at the target position (orange bonds with cyan atoms). The south-constrained pseudosugar is rotated about its flanking phosphodiester bonds, 90° from its initial position in B-form DNA, but short of a completely flipped position with 180° rotation. Thus, it is trapped in the middle of the flipping pathway via the major groove side. This structure provides clues to DNA-protein interactions in a potential transition state.
See: Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase by John R. Horton, Gary Ratner, Nilesh K. Banavali, Niu Huang, Yongseok Choi, Martin A. Maier, Victor E. Marquez, Alexander D. MacKerell Jr and Xiaodong Cheng in Nucleic Acids Res. 2004, 32 (13), 3877–3886.