6J0I

Structure of [Co2+-(Chromomycin A3)2]-d(TTGGCGAA)2 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.290 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.257 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.259 (Depositor) 

Starting Model: experimental
View more details

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 CRHClick on this verticalbar to view details

This is version 2.1 of the entry. See complete history


Literature

Polymorphic G:G mismatches act as hotspots for inducing right-handed Z DNA by DNA intercalation.

Satange, R.Chuang, C.Y.Neidle, S.Hou, M.H.

(2019) Nucleic Acids Res 47: 8899-8912

  • DOI: https://doi.org/10.1093/nar/gkz653
  • Primary Citation of Related Structures:  
    6J0H, 6J0I

  • PubMed Abstract: 

    DNA mismatches are highly polymorphic and dynamic in nature, albeit poorly characterized structurally. We utilized the antitumour antibiotic CoII(Chro)2 (Chro = chromomycin A3) to stabilize the palindromic duplex d(TTGGCGAA) DNA with two G:G mismatches, allowing X-ray crystallography-based monitoring of mismatch polymorphism. For the first time, the unusual geometry of several G:G mismatches including syn-syn, water mediated anti-syn and syn-syn-like conformations can be simultaneously observed in the crystal structure. The G:G mismatch sites of the d(TTGGCGAA) duplex can also act as a hotspot for the formation of alternative DNA structures with a GC/GA-5' intercalation site for binding by the GC-selective intercalator actinomycin D (ActiD). Direct intercalation of two ActiD molecules to G:G mismatch sites causes DNA rearrangements, resulting in backbone distortion to form right-handed Z-DNA structures with a single-step sharp kink. Our study provides insights on intercalators-mismatch DNA interactions and a rationale for mismatch interrogation and detection via DNA intercalation.


  • Organizational Affiliation

    Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan.


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*TP*GP*GP*CP*GP*AP*A)-3')
A, B, C, D, E
8synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
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
G, J, K, N, O
2N/A
Glycosylation Resources
GlyTouCan:  G66610ZG
GlyCosmos:  G66610ZG
Entity ID: 3
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
H, I, L, M, P
3N/A
Glycosylation Resources
GlyTouCan:  G76712GN
GlyCosmos:  G76712GN
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CRH
Query on CRH

Download Ideal Coordinates CCD File 
BA [auth E]
DA [auth F]
S [auth A]
V [auth B]
W [auth C]
1,2-HYDRO-1-OXY-3,4-HYDRO-3-(1-METHOXY-2-OXY-3,4-DIHYDROXYPENTYL)-8,9-DIHYROXY-7-METHYLANTHRACENE
C21 H24 O7
XBKVKSRQTHGEJA-FAGSEQTRSA-N
CO
Query on CO

Download Ideal Coordinates CCD File 
AA [auth D]
CA [auth E]
EA [auth F]
T [auth A]
U [auth A]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.290 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.257 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.259 (Depositor) 
Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.826α = 90
b = 48.096β = 90
c = 96.725γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

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 CRHClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-08-21
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-30
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary