3MGQ: Binding of Nickel ions to the Nucleosome Core Particle

Citation:
Abstract
Heavy metals have the potential to engage in strong bonding interactions and can thus function in essential as well as toxic or therapeutic capacities. We conducted crystallographic analyses of heavy cation binding to the nucleosome core particle and found that Co(2+) and Ni(2+) preferentially associate with the DNA major groove, in a sequence- and conformation-dependent manner. Conversely, Rb(+) and Cs(+) are found to bind only opportunistically to minor groove elements of the DNA, in particular at narrow AT dinucleotide sites. Furthermore, relative to Mn(2+) the aggressive coordination of Co(2+) and Ni(2+) to guanine bases is observed to induce a shift in histone-DNA register around the nucleosome center by stabilizing DNA stretching over one region accompanied by expulsion of two bases at an opposing location. These 'softer' transition metals also associate with multiple histone protein sites, including inter-nucleosomal cross-linking, and display a proclivity for coordination to histidine. Sustained binding and the ability to induce structural perturbations at specific locations in the nucleosome may contribute to genetic and epigenetic mechanisms of carcinogenesis mediated by Co(2+) and Ni(2+).
PDB ID: 3MGQDownload
MMDB ID: 82830
PDB Deposition Date: 2010/4/7
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 2.65  Å
Source Organism:
Xenopus laevis
Similar Structures:
Biological Unit for 3MGQ: decameric; determined by author and by software (PISA)
Molecular Components in 3MGQ
Label Count Molecule
Proteins (8 molecules)
2
Histone H3.2(Gene symbol: hist2h3c.L)
Molecule annotation
2
Histone H4(Gene symbol: hist1h4a.L)
Molecule annotation
2
Histone H2A
Molecule annotation
2
Histone H2B 1.1(Gene symbol: hist1h2bj.S)
Molecule annotation
Nucleotides(2 molecules)
1
DNA (147-mer)
Molecule annotation
1
DNA (147-mer)
Molecule annotation
Chemicals (51 molecules)
1
47
2
4
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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