3MGP

Binding of Cobalt ions to the Nucleosome Core Particle


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Perturbations in nucleosome structure from heavy metal association.

Mohideen, K.Muhammad, R.Davey, C.A.

(2010) Nucleic Acids Res 38: 6301-6311

  • DOI: 10.1093/nar/gkq420
  • Primary Citation of Related Structures:  
    3MGP, 3MGQ, 3MGR, 3MGS

  • PubMed 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 ...

    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+).


    Organizational Affiliation

    Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2AE135Xenopus laevisMutation(s): 0 
Gene Names: Histone 3 or H3
Find proteins for P84233 (Xenopus laevis)
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Go to UniProtKB:  P84233
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4BF102Xenopus laevisMutation(s): 0 
Gene Names: Histone 4 or H4
Find proteins for P62799 (Xenopus laevis)
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Go to UniProtKB:  P62799
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2ACG119Xenopus laevisMutation(s): 0 
Gene Names: Histone 2A or H2ALOC494591h2ac14.Lh2ac14hist1h2ajXELAEV_18003602mg
Find proteins for Q6AZJ8 (Xenopus laevis)
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Go to UniProtKB:  Q6AZJ8
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1DH125Xenopus laevisMutation(s): 0 
Gene Names: Histone 2B or H2B
Find proteins for P02281 (Xenopus laevis)
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Go to UniProtKB:  P02281
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (147-MER)I147N/A
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (147-MER)J147N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CO
Query on CO

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C, D, E, H, I, J
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, D, E, G
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.502α = 90
b = 109.94β = 90
c = 183.352γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-05-21
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description
  • Version 1.4: 2019-11-20
    Changes: Advisory, Database references, Derived calculations