432d | pdb_0000432d
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D(GGCCAATTGG) COMPLEXED WITH DAPI
Overview
The single-crystal X-ray structure of the complex between the minor groove, binder 4',6-diamidino-2-phenylindole (DAPI) and d(GGCCAATTGG) reveals a, novel way of off-centered binding, with an unique hydrogen bond between, the minor groove binder and a CG base pair. Application of crystal, engineering and cryocooling techniques helped to extend the resolution to, 1.9 A, resulting in an unambiguous determination of drug conformation and, orientation. The structure was refined to completion using SHELXL-93, resulting in a residual factor R of 18. 0% for 3562 reflections with F(o), > 4sigma(F(o)) including 81 water molecules. As the bulky NH(2)-group on, guanine is believed to prevent drug binding in the minor groove, the, nature and stability of the CG-DAPI contact was further addressed in full, detail using ab initio quantum chemical methods. The amino groups involved, in the guanine-drug interaction are substantially nonplanar, resulting in, an energy gain of about 5 kcal/mol. The combined structural and, theoretical data suggest that the guanine NH(2)-group does not destabilize, the drug binding to an extent that it prevents complexation.
About this Structure
432D is a Protein complex structure of sequences from [1] with DAP as ligand. Full crystallographic information is available from OCA.
Reference
Crystal structure of d(GGCCAATTGG) complexed with DAPI reveals novel binding mode., Vlieghe D, Sponer J, Van Meervelt L, Biochemistry. 1999 Dec 14;38(50):16443-51. PMID:10600105
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