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Netropsin interactions in the minor groove of d(GGCCAATTGG) studied by a combination of resolution enhancement and ab initio calculations
Author(s) -
Van Hecke Kristof,
Nam Pham Cam,
Nguyen Minh Tho,
Van Meervelt Luc
Publication year - 2005
Publication title -
the febs journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 204
eISSN - 1742-4658
pISSN - 1742-464X
DOI - 10.1111/j.1742-4658.2005.04773.x
Subject(s) - netropsin , ab initio , crystallography , hydrogen bond , crystal structure , guanine , molecule , chemistry , amide , ab initio quantum chemistry methods , computational chemistry , stereochemistry , minor groove , organic chemistry , nucleotide , biochemistry , gene
The structure of the complex between the minor groove binder netropsin and d(GGCCAATTGG) was determined via single‐crystal X‐ray techniques. The structure was refined to completion using refmac 5.1.24, resulting in a residual R‐factor of 20.0% (including 68 water molecules). Using crystal engineering and cryocooling techniques, the resolution could be enhanced to 1.75 Å, resulting in an unambiguous determination of the drug conformation and orientation. As previously noticed, bifurcated hydrogen bonds are formed between the amide nitrogen atoms of the drug and the N3 and O2 atoms of A and T base pairs, respectively, clearly cataloging the structure to class I. As the bulky NH 2 group on guanine was believed to prevent binding of the drug in the minor groove, the detailed nature of several of the amidinium and guanidinium end contacts were further investigated by ab initio quantum chemical methods.