4E95

Lambda-[Ru(TAP)2(dppz-(Me)2)]2+ bound to CCGGATCCGG

PDB DOI: https://doi.org/10.2210/pdb4E95/pdb
NAKB: 4E95

Classification: DNA
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2012-03-20 Released: 2013-03-20
Deposition Author(s): Hall, J.P., Cardin, C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.246
R-Value Work: 0.183
R-Value Observed: 0.186

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The effects of disubstitution on the binding of ruthenium complexes to DNA

Hall, J.P.

(2014) Thesis

Macromolecule Content

Total Structure Weight: 3.96 kDa
Atom Count: 294
Modelled Residue Count: 10
Deposited Residue Count: 10
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(CPCPGPGPAPTPCPCPGPG)-3'	A	10	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RML Query on RML Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	(11,12-dimethyldipyrido[3,2-a:2',3'-c]phenazine-kappa~2~N~4~,N~5~)[bis(pyrazino[2,3-f]quinoxaline-kappa~2~N~1~,N~10~)]ruthenium(2+) C₄₀ H₂₆ N₁₂ Ru GGHWDMRPXFPGCU-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
BA Query on BA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.246
R-Value Work: 0.183
R-Value Observed: 0.186
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.44	α = 90
b = 47.44	β = 90
c = 34.53	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
SHELXCD	phasing
SHELXE	model building
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-03-20

Deposition Author(s):

Hall, J.P.

Cardin, C.J.

Revision History (Full details and data files)

Version 1.0: 2013-03-20
Type: Initial release
Version 1.1: 2017-03-08
Changes: Database references
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2024-02-28
Changes: Data collection, Database references, Derived calculations

Prepare Data

Validate Data

Deposit Data

Help and Resources