6IUE

DNA helical wire containing Hg(II)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.346 
  • R-Value Work: 0.294 
  • R-Value Observed: 0.298 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A 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 58: 16835-16838

  • DOI: https://doi.org/10.1002/anie.201910029
  • Primary Citation of Related Structures:  
    6IUE

  • PubMed Abstract: 

    Numerous applications of metal-mediated base pairs (metallo-base-pairs) to nucleic acid based nanodevices and genetic code expansion have been extensively 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 nanowire with an uninterrupted one-dimensional silver array was reported. We now report the 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 does not contain any Watson-Crick base pairs. Crystals of the Hg-DNA wire, which is the first DNA wire structure driven by Hg II ions, were obtained by mixing the short oligonucleotide d(TTTGC) and Hg II ions. This study demonstrates the potential of metallo-DNA to form various structural components that can be used for functional nanodevices.


  • Organizational Affiliation

    Department of Materials & Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, 221-8686, Kanagawa, Japan.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*TP*TP*GP*C)-3')5synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HG (Subject of Investigation/LOI)
Query on HG

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth H]
BA [auth M]
BB [auth U]
CA [auth B]
AA [auth A],
AB [auth H],
BA [auth M],
BB [auth U],
CA [auth B],
CB [auth U],
DA [auth B],
DB [auth U],
EA [auth B],
EB [auth I],
FA [auth N],
FB [auth I],
GA [auth C],
GB [auth I],
HA [auth C],
HB [auth I],
IA [auth O],
IB [auth J],
JA [auth O],
JB [auth J],
KA [auth D],
KB [auth J],
LA [auth D],
LB [auth W],
MA [auth D],
MB [auth K],
NA [auth D],
NB [auth K],
OA [auth E],
OB [auth K],
PA [auth E],
PB [auth X],
QA [auth E],
QB [auth L],
RA [auth Q],
RB [auth L],
SA [auth F],
SB [auth L],
TA [auth F],
TB [auth Y],
UA [auth F],
VA [auth R],
WA [auth G],
XA [auth G],
Y [auth A],
YA [auth T],
Z [auth A],
ZA [auth T]
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.346 
  • R-Value Work: 0.294 
  • R-Value Observed: 0.298 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.929α = 90
b = 28.215β = 94.97
c = 88.844γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
Sir2014phasing
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-16
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Database references
  • Version 1.3: 2024-03-27
    Changes: Data collection, Database references, Derived calculations