5XEW

Crystal structure of the [Ni2+-(chromomycin A3)2]-CCG repeats complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.238 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CPHClick on this verticalbar to view details

This is version 2.1 of the entry. See complete history


Literature

Induced-Fit Recognition of CCG Trinucleotide Repeats by a Nickel-Chromomycin Complex Resulting in Large-Scale DNA Deformation

Tseng, W.H.Chang, C.K.Wu, P.C.Hu, N.J.Lee, G.H.Tzeng, C.C.Neidle, S.Hou, M.H.

(2017) Angew Chem Int Ed Engl 56: 8761-8765

  • DOI: https://doi.org/10.1002/anie.201703989
  • Primary Citation of Related Structures:  
    5XEW

  • PubMed Abstract: 

    Small-molecule compounds targeting trinucleotide repeats in DNA have considerable potential as therapeutic or diagnostic agents against many neurological diseases. Ni II (Chro) 2 (Chro=chromomycin A3) binds specifically to the minor groove of (CCG) n repeats in duplex DNA, with unique fluorescence features that may serve as a probe for disease detection. Crystallographic studies revealed that the specificity originates from the large-scale spatial rearrangement of the DNA structure, including extrusion of consecutive bases and backbone distortions, with a sharp bending of the duplex accompanied by conformational changes in the Ni II chelate itself. The DNA deformation of CCG repeats upon binding forms a GGCC tetranucleotide tract, which is recognized by Ni II (Chro) 2 . The extruded cytosine and last guanine nucleotides form water-mediated hydrogen bonds, which aid in ligand recognition. The recognition can be accounted for by the classic induced-fit paradigm.


  • Organizational Affiliation

    Institute of Genomics and Bioinformatics, National Chung Hsing University, 250 Kuo-kuang Rd., Taichung, Taiwan.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*TP*CP*CP*GP*CP*CP*GP*CP*CP*GP*AP*A)-3')
A, B
13synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
3-C-methyl-4-O-acetyl-alpha-L-Olivopyranose-(1-3)-(2R,5S,6R)-6-methyltetrahydro-2H-pyran-2,5-diol-(1-3)-(2R,5S,6R)-6-methyltetrahydro-2H-pyran-2,5-diol
C, F
3N/A
Glycosylation Resources
GlyTouCan:  G76712GN
GlyCosmos:  G76712GN
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2,6-dideoxy-4-O-methyl-alpha-D-galactopyranose-(1-3)-(2R,3R,6R)-6-hydroxy-2-methyltetrahydro-2H-pyran-3-yl acetate
D, E
2N/A
Glycosylation Resources
GlyTouCan:  G66610ZG
GlyCosmos:  G66610ZG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 32 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.291α = 90
b = 48.291β = 90
c = 83.356γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-2000data processing
HKL-2000data scaling
SHELXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CPHClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2017-06-28
    Changes: Database references
  • Version 1.2: 2017-07-19
    Changes: Database references
  • Version 1.3: 2018-05-16
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-03-27
    Changes: Data collection, Database references, Derived calculations, Structure summary