7ATG

Crystal structure of Z-DNA in complex with putrescinium and potassium cations at ultrahigh-resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.60 Å
  • R-Value Free: 0.095 
  • R-Value Work: 0.088 
  • R-Value Observed: 0.089 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of Z-DNA in complex with the polyamine putrescine and potassium cations at ultra-high resolution.

Drozdzal, P.Gilski, M.Jaskolski, M.

(2021) Acta Crystallogr B Struct Sci Cryst Eng Mater 77: 331-338

  • DOI: 10.1107/S2052520621002663
  • Primary Citation of Related Structures:  
    7ATG

  • PubMed Abstract: 
  • The X-ray crystal structure of the d(CGCGCG) 2 /putrescine(2+)/K + complex has been determined at 0.60 Å resolution. Stereochemical restraints were used only for the putrescinium dication, and 23 bonds and 18 angles of the Z-DNA nucleotides with dual conformation ...

    The X-ray crystal structure of the d(CGCGCG) 2 /putrescine(2+)/K + complex has been determined at 0.60 Å resolution. Stereochemical restraints were used only for the putrescinium dication, and 23 bonds and 18 angles of the Z-DNA nucleotides with dual conformation. The N atoms of the putrescine(2+) dication form three direct hydrogen bonds with the N7_G atoms of three different Z-DNA molecules, plus three water-mediated hydrogen bonds with cytosine, guanine and phosphate acceptors. A unique potassium cation was also unambiguously identified in the structure, albeit at a ∼0.5 occupation site shared with a water molecule, providing the first example of such a complex with Z-DNA. The K + cation has coordination number of eight and an irregular coordination sphere, formed by four water molecules and four O atoms from two phosphate groups of the Z-DNA, including ligands present at fractional occupancy. The structural disorder of the Z-DNA duplex is manifested by the presence of alternate conformations along the DNA backbone. Comparison of the position and interactions of putrescine(2+) in the present structure with other ultra-high-resolution structures of Z-DNA in complexes with Mn 2+ and Zn 2+ ions shows that the dicationic putrescinium moiety can effectively substitute these metal ions for stabilization of Z-type DNA duplexes. Furthermore, this comparison also suggests that the spermine(4+) tetracation has a higher affinity for Z-DNA than K + .


    Organizational Affiliation

    Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')A, B6synthetic construct
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    58I (Subject of Investigation/LOI)
    Query on 58I

    Download Ideal Coordinates CCD File 
    D [auth B]4-azaniumylbutylazanium
    C4 H14 N2
    KIDHWZJUCRJVML-UHFFFAOYSA-P
     Ligand Interaction
    K (Subject of Investigation/LOI)
    Query on K

    Download Ideal Coordinates CCD File 
    C [auth A]POTASSIUM ION
    K
    NPYPAHLBTDXSSS-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 17.97α = 90
    b = 31.02β = 90
    c = 43.86γ = 90
    Software Package:
    Software NamePurpose
    SHELXLrefinement
    XDSdata reduction
    XSCALEdata scaling
    PHASERphasing
    PDB_EXTRACTdata extraction

    Structure Validation

    View Full Validation Report




    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Polish National Science CentrePoland2013/10/M/NZ1/00251

    Revision History  (Full details and data files)

    • Version 1.0: 2021-08-11
      Type: Initial release
    • Version 1.1: 2021-10-06
      Changes: Data collection, Database references, Structure summary