6IUE

DNA helical wire containing Hg(II)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.901 Å
  • R-Value Free: 0.346 
  • R-Value Work: 0.294 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Novel DNA Helical Wire Containing HgII-Mediated T:T and T:G Pairs.

Ono, A.Kanazawa, H.Ito, H.Goto, M.Nakamura, K.Saneyoshi, H.Kondo, J.

(2019) Angew.Chem.Int.Ed.Engl. --: --

  • DOI: 10.1002/anie.201910029

  • PubMed Abstract: 
  • Numerous applications of metal ion-mediated base pairs (metallo-base pairs) to nucleic acid-based nanodevices and genetic code expansion have extensively been studied. Many of these metallo-base pairs are formed in DNA and RNA duplexes containing Wat ...

    Numerous applications of metal ion-mediated base pairs (metallo-base pairs) to nucleic acid-based nanodevices and genetic code expansion have extensively been studied. Many of these metallo-base pairs are formed in DNA and RNA duplexes containing Watson-Crick base pairs. Recently, a crystal structure of a metal-DNA nanowires with uninterrupted one-dimensional silver array has been reported. Herein, we have determined a crystal structure of a novel DNA helical wire containing Hg(II)-mediated T:T and T:G base pairs and water-mediated C:C base pairs. The Hg-DNA wire contains no Watson-Crick base pair. The crystals of the Hg-DNA wire, the first DNA wire structure driven by Hg(II) ions, were obtained by mixing a short oligonucleotide d(TTTGC) and Hg(II) ions. This study demonstrates potentials of metallo-DNA to form various structural components which can be used for functional nanodevices.


    Organizational Affiliation

    Sophia University, JAPAN.,JAPAN.,Kanagawa University, Department of aterial & Life Chemistry, Faculty of Engineering, 3-27-1 Rokkakubasi, Kanagawa-ku, 221-8686, Yokohama, JAPAN.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*TP*TP*GP*C)-3')A,M,B,N,C,O,D,P,E,Q,F,R,G,T,H,U,I,V,J,W,K,X,L,Y5synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HG
Query on HG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, Q, R, T, U, W, X, Y
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.901 Å
  • R-Value Free: 0.346 
  • R-Value Work: 0.294 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.929α = 90.00
b = 28.215β = 94.97
c = 88.844γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Sir2014phasing
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan17H03033

Revision History 

  • Version 1.0: 2019-10-16
    Type: Initial release
  • Version 1.1: 2019-11-06
    Type: Data collection, Database references