4UQG

A new bio-isosteric base pair based on reversible bonding


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

"Post-It" Type Connected DNA Created with a Reversible Covalent Cross-Link.

Tomas-Gamasa, M.Serdjukow, S.Su, M.Muller, M.Carell, T.

(2015) Angew.Chem.Int.Ed.Engl. 54: 796

  • DOI: 10.1002/anie.201407854

  • PubMed Abstract: 
  • We report the development of a new heterobase that is held together through reversible bonding. The so-formed cross-link adds strong stabilization to the DNA duplex. Despite this, the cross-link opens and closes through reversible imine bonding. More ...

    We report the development of a new heterobase that is held together through reversible bonding. The so-formed cross-link adds strong stabilization to the DNA duplex. Despite this, the cross-link opens and closes through reversible imine bonding. Moreover, even enzymatic incorporation of the cross-link is possible. The new principle can be used to stabilize DNA duplexes and nanostructures that otherwise require high salt concentrations, which may hinder biological applications.


    Organizational Affiliation

    Department of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377 München (Germany) http://www.carellgroup.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA POLYMERASE
A
579Geobacillus stearothermophilusMutation(s): 0 
Gene Names: polA
EC: 2.7.7.7
Find proteins for E1C9K5 (Geobacillus stearothermophilus)
Go to UniProtKB:  E1C9K5
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*AP*CP*C T0TP*TP*CP*CP*CP*TP)-3'B10unidentified
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*AP*GP*GP*GP*A SAYP*GP*GP*TP*CP)-3'C10unidentified
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SUC
Query on SUC

Download SDF File 
Download CCD File 
A
SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SAY
Query on SAY
C
DNA LINKINGC12 H15 O8 P

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T0T
Query on T0T
B
DNA LINKINGC19 H22 N O6 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 87.442α = 90.00
b = 93.996β = 90.00
c = 105.416γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Database references, Other, Refinement description
  • Version 1.2: 2015-01-28
    Type: Database references
  • Version 1.3: 2017-08-23
    Type: Advisory, Data collection