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PDBsum entry 1em0
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References listed in PDB file
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Key reference
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Title
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A DNA-Porphyrin minor-Groove complex at atomic resolution: the structural consequences of porphyrin ruffling.
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Authors
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M.Bennett,
A.Krah,
F.Wien,
E.Garman,
R.Mckenna,
M.Sanderson,
S.Neidle.
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Ref.
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Proc Natl Acad Sci U S A, 2000,
97,
9476-9481.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of a B-type DNA hexanucleotide duplex complexed with the
porphyrin has been solved by
multiwavelength anomalous diffraction phasing and refined to an R factor of
11.5% at a resolution of 0.9 A. The structure has been solved and refined as two
crystallographically independent duplexes, stacked end to end. Contrary to
expectation, the porphyrin molecule is not intercalated into the duplex but is
stacked onto the ends of the two-duplex stack. The porphyrin molecule is highly
buckled as a consequence of the nickel coordination, which produces large
changes in local DNA structure. A second mode of porphyrin binding is apparent
as a consequence of crystal packing, which places the ligand in the minor groove
of an adjacent duplex. This structure thus provides, to our knowledge, the first
atomic visualization of minor-groove binding for a porphyrin molecule. The
geometry of groove binding provides a ready explanation for porphyrin-induced
DNA strand cleavage at deoxyribose residues.
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Figure 1.
Fig. 1. (a) The structure of the Ni2+-TMPy ligand. (b)
Final 2F[o]  F[c]
electron density map, calculated in the plane of the Ni2+-TMPy
ligand. (c) plot of the 2:2 complex in the crystallographic
asymmetric unit.
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Figure 4.
Fig. 4. View of the end of one hexamer duplex with bases
shown as idealized polygons and the end-capping Ni2+-TMPy ligand.
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Headers
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