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PDBsum entry 152d
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References listed in PDB file
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Key reference
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Title
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Water ring structure at DNA interfaces: hydration and dynamics of DNA-Anthracycline complexes.
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Authors
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L.A.Lipscomb,
M.E.Peek,
F.X.Zhou,
J.A.Bertrand,
D.Vanderveer,
L.D.Williams.
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Ref.
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Biochemistry, 1994,
33,
3649-3659.
[DOI no: ]
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PubMed id
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Abstract
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In crystallographic structures of biological macromolecules, one can observe
many hydration rings that originate at one water molecule, pass via hydrogen
bonds through several others, and return to the original water molecule.
Five-membered water rings have been thought to occur with greater frequency than
other ring sizes. We describe a quantitative assessment of relationships between
water ring size and frequency of occurrence in the vicinity of nucleic acid
interfaces. This report focuses on low-temperature X-ray crystallographic
structures of two anthracyclines, adriamycin (ADRI) and daunomycin (DAUN), bound
to d(CGATCG) and on several DNA structures published previously by others. We
have obtained excellent low-temperature (-160 degrees C, LT) X-ray intensity
data for d(CGATCG)-adriamycin and d(CGATCG)-daunomycin with a multiwire area
detector. The LTX-ray data sets contain 20% (daunomycin, LT-DAUN) and 35%
(adriamycin, LT-ADRI) more reflections than were used to derive the original
room-temperature (15 degrees C) structures [Frederick, C.A., Williams, L.D.,
Ughetto, G., van der Marel, G. A., van Boom, J.H., Rich, A., & Wang, A.H.-J.
(1990) Biochemistry 29, 2538-2549]. The results show that five-membered water
rings are not preferred over other ring sizes. This assessment is consistent
with our observation of broad dispersion W-W-W angles (sigma = 20 degrees). In
addition, we report that the thermal mobility, distinct from the static
disorder, of the amino sugar of daunomycin and adriamycin is significantly
greater than that of the rest of the complex. This mobility implies that if the
central AT base pair is switched to a CG base pair, there should be a low energy
cost in avoiding the guanine amino group. The energy difference (for the
sugar-binding preference) between d(CGTACG) and d(CGCGCG) could be considerably
less than 20 kcal/mol, a value proposed previously from computation.
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Headers
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