7SM7

[U:Hg2+/Ag+:U--pH 9] Metal-mediated DNA base pair in tensegrity triangle in Ag+ and Hg2+ solution

  • Classification: DNA
  • Organism(s): synthetic construct
  • Mutation(s): No 

  • Deposited: 2021-10-25 Released: 2022-11-23 
  • Deposition Author(s): Lu, B., Vecchioni, S., Seeman, N.C., Sha, R., Ohayon, Y.P.
  • Funding Organization(s): Office of Naval Research (ONR), Department of Energy (DOE, United States), National Science Foundation (NSF, United States), Human Frontier Science Program (HFSP), National Aeronautic Space Administration (NASA, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Crystallographic pH Titration of Silver and Mercury Mediated DNA Base Pairs

Lu, B.Ohayon, Y.P.Sha, R.Woloszyn, K.Rothschild, L.Wind, S.Hendrickson, W.Mao, C.Seeman, N.C.Vecchioni, S.

To be published.

Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*UP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')A21synthetic construct
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*CP*CP*AP*UP*AP*CP*A)-3')B7synthetic construct
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')C7synthetic construct
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')D7synthetic construct
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HG (Subject of Investigation/LOI)
Query on HG

Download Ideal Coordinates CCD File 
F [auth B]MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
AG (Subject of Investigation/LOI)
Query on AG

Download Ideal Coordinates CCD File 
E [auth B]SILVER ION
Ag
FOIXSVOLVBLSDH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.445α = 90
b = 106.445β = 90
c = 92.002γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
STARANISOdata scaling
AutoSolphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Office of Naval Research (ONR)United StatesN000141912596
Department of Energy (DOE, United States)United StatesDE-SC0007991
National Science Foundation (NSF, United States)United States2106790
Human Frontier Science Program (HFSP)United StatesRPG0010/2017
National Science Foundation (NSF, United States)United StatesDMR-1420073
National Aeronautic Space Administration (NASA, United States)United States2020 NASA Center Innovation Fund

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release