4GQJ

Complex of a binuclear Ruthenium compound D,D-([mu-(11,11')-bi(dppz)-(1,10-phenanthroline)4-Ru2]4+) bound to d(CGTACG)

PDB DOI: https://doi.org/10.2210/pdb4GQJ/pdb
NAKB: 4GQJ

Classification: DNA
Mutation(s): No

Deposited: 2012-08-23 Released: 2014-03-05
Deposition Author(s): Boer, D.R., Coll, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.206
R-Value Work: 0.177
R-Value Observed: 0.179

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Thread Insertion of a Bis(dipyridophenazine) Diruthenium Complex into the DNA Double Helix by the Extrusion of AT Base Pairs and Cross-Linking of DNA Duplexes.

Boer, D.R., Wu, L., Lincoln, P., Coll, M.

(2014) Angew Chem Int Ed Engl 53: 1949-1952

PubMed: 24449275 Search on PubMed
DOI: https://doi.org/10.1002/anie.201308070
Primary Citation of Related Structures:
4GQJ

PubMed Abstract:
The crystal structure of the Δ,Δ enantiomer of the binuclear "light-switch" ruthenium complex [μ-(11,11'-bidppz)(1,10-phenanthroline)4 Ru2 ](4+) bound to the oligonucleotide d(CGTACG) shows that one dppz moiety of the dumbbell-like compound inserts into the DNA stack through the extrusion of an AT base pair. The second dppz moiety recruits a neighboring DNA molecule, and the complex thus cross-links two adjacent duplexes by bridging their major grooves.

Organizational Affiliation

Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixach 10, 08028 Barcelona (Spain); Institut de Biologia Molecular de Barcelona (CSIC), Baldiri Reixac 10, 08028 Barcelona (Spain).

Macromolecule Content

Total Structure Weight: 5.1 kDa
Atom Count: 357
Modelled Residue Count: 12
Deposited Residue Count: 12
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(CPGPTPAPCPG)-3')	A, B	6	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RR2 Query on RR2 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	(mu-11,11'-bidipyrido[3,2-a:2',3'-c]phenazine-1kappa~2~N~4~,N~5~:2kappa~2~N~4'~,N~5'~)[tetrakis(1,10-phenanthroline-kappa~2~N~1~,N~10~)]diruthenium C₈₄ H₅₀ N₁₆ Ru₂ BGOYAVNVNFHEQU-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.206
R-Value Work: 0.177
R-Value Observed: 0.179
Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.429	α = 90
b = 85.429	β = 90
c = 85.429	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
SHELXS	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-03-05

Deposition Author(s):

Boer, D.R.

Coll, M.

Revision History (Full details and data files)

Version 1.0: 2014-03-05
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations
Version 1.2: 2024-03-13
Changes: Source and taxonomy, Structure summary