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PDBsum entry 3lja
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Structural protein/DNA
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PDB id
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3lja
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Contents |
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99 a.a.
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79 a.a.
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104 a.a.
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99 a.a.
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87 a.a.
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References listed in PDB file
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Key reference
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Title
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Using soft X-Rays for a detailed picture of divalent metal binding in the nucleosome.
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Authors
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B.Wu,
C.A.Davey.
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Ref.
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J Mol Biol, 2010,
398,
633-640.
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PubMed id
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Abstract
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Divalent metals associate with DNA in a site-selective manner, which can
influence nucleosome positioning, mobility, compaction, and recognition by
nuclear factors. We previously characterized divalent metal binding in the
nucleosome core using hard (short-wavelength) X-rays allowing high-resolution
crystallographic determination of the strongest affinity sites, which revealed
that Mn(2+) associates with the DNA major groove in a sequence- and
conformation-dependent manner. In this study, we obtained diffraction data with
soft X-rays at the Mn(2+) absorption edge for a core particle crystal in the
presence of 10 mM MnSO(4), mimicking prevailing Mg(2+) concentration in the
nucleus. This provides an exceptional view of counterion binding in the
nucleosome through identification of 45 divalent metal binding sites. In
addition to that at the well-characterized major interparticle interface, only
one other histone-divalent metal binding site is found, which corresponds to a
symmetry-related counterpart on the 'free' H2B alpha1 helix C-terminus. This
emphasizes the importance of the alpha-helix dipole in ion binding and suggests
that the H2B motif may serve as a nucleation site in nucleosome compaction. The
43 sites associated with the DNA are characterized by (1) high-affinity direct
coordination at the most electrostatically favorable major groove locations, (2)
metal hydrate binding to the major groove, (3) direct coordination to phosphate
groups at sites of high charge density, (4) metal hydrate binding in the minor
groove, or (5) metal hydrate-divalent anion pairing. Metal hydrates are found
within the minor groove only at locations displaying a narrow range of
high-intermediate width and to which histone N-terminal tails are not associated
or proximal. This indicates that divalent metals and histone tails can both
collaborate and compete in minor groove association, which sheds light on
nucleosome solubility and chromatin compaction behavior.
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