4YMC

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

PDB DOI: https://doi.org/10.2210/pdb4YMC/pdb
NAKB: 4YMC

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

Deposited: 2015-03-06 Released: 2016-03-23
Deposition Author(s): Gurung, S.P., Hall, J.P., Cardin, C.J.
Funding Organization(s): Biotechnology and Biological Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.257
R-Value Work: 0.198
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Reversal of a single base pair step controls guanine photo-oxidation by an intercalating Ru(II) dipyridophenazine complex.

Keane, P.M., Gurung, S.P., Niyazi, H., Poynton, F.E., Hall, J.P., Sazanovich, I.V., Towrie, M., Teixeira, S., Mitchell, E., Forsyth, T., Gunnlaugsson, T., Quinn, S.J., Cardin, C.J., Kelly, J.M.

To be published.

Macromolecule Content

Total Structure Weight: 3.97 kDa
Atom Count: 275
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
DNA (5'-D(CPCPGPGPAPTPCPCPGPG)-3')	A	10	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RKL Query on RKL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	Ru(tap)2(dppz) complex C₃₈ H₂₂ N₁₂ Ru PIKVAZQLFXBUSD-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] mmCIF 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]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.257
R-Value Work: 0.198
R-Value Observed: 0.200
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.38	α = 90
b = 47.38	β = 90
c = 33.83	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Coot	model building
SHELX	phasing
xia2	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-03-23

Deposition Author(s):

Gurung, S.P.

Hall, J.P.

Cardin, C.J.

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/K019279/1

Revision History (Full details and data files)

Version 1.0: 2016-03-23
Type: Initial release
Version 2.0: 2017-08-30
Changes: Atomic model, Author supporting evidence, Derived calculations
Version 2.1: 2024-05-08
Changes: Data collection, Database references, Derived calculations

Prepare Data

Validate Data

Deposit Data

Help and Resources