6RNL

L-[Ru(TAP)2(dppz)]2+ bound to the G-quadruplex forming sequence d(TAGGGTT)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Three thymine/adenine binding modes of the ruthenium complex Lambda-[Ru(TAP)2(dppz)]2+to the G-quadruplex forming sequence d(TAGGGTT) shown by X-ray crystallography.

McQuaid, K.Hall, J.P.Baumgaertner, L.Cardin, D.J.Cardin, C.J.

(2019) Chem.Commun.(Camb.) 55: 9116-9119

  • DOI: 10.1039/c9cc04316k

  • PubMed Abstract: 
  • Λ-[Ru(TAP)2(dppz)]2+ was crystallised with the G-quadruplex-forming heptamer d(TAGGGTT). Surprisingly, even though there are four unique binding sites, the complex is not in contact with any G-quartet surface. Two complexes stabilise cavities formed ...

    Λ-[Ru(TAP)2(dppz)]2+ was crystallised with the G-quadruplex-forming heptamer d(TAGGGTT). Surprisingly, even though there are four unique binding sites, the complex is not in contact with any G-quartet surface. Two complexes stabilise cavities formed from terminal T·A and T·T mismatched pairs. A third shows kinking by a TAP ligand between T·T linkages, while the fourth shows sandwiching of a dppz ligand between a T·A/T·A quadruplex and a T·T mismatch, stabilised by an additional T·A base pair stacking interaction on a TAP surface. Overall, the structure shows an unexpected affinity for thymine, and suggests models for G-quadruplex loop binding.


    Organizational Affiliation

    Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK. c.j.cardin@reading.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*AP*GP*GP*GP*TP*T)-3')A,B,C,D7synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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A, C
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
RKL
Query on RKL

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Download CCD File 
A, C, D
Ru(tap)2(dppz) complex
C38 H22 N12 Ru
PIKVAZQLFXBUSD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.187 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 38.514α = 90.00
b = 38.514β = 90.00
c = 128.804γ = 120.00
Software Package:
Software NamePurpose
xia2data scaling
DIALSdata reduction
SHELXDEphasing
DIALSdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/K019279/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M004635/1

Revision History 

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2019-09-11
    Type: Data collection, Database references