4LY2 | pdb_00004ly2

X-ray crystal structure of the ruthenium complex [Ru(phen)2(dppz)]2+ bound to d(TCGGTACCGA)

PDB DOI: https://doi.org/10.2210/pdb4LY2/pdb
NAKB: 4LY2

Classification: DNA
Mutation(s): No

Deposited: 2013-07-30 Released: 2014-09-24
Deposition Author(s): Niyazi, H., Teixeira, S., Mitchell, E., Forsyth, T., Cardin, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.219 (Depositor), 0.219 (DCC)
R-Value Work:
0.188 (Depositor), 0.180 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4LY2

Ligand Structure Quality Assessment

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

Literature

X-ray crystal structure of the ruthenium complex [Ru(phen)2(dppz)]2+ bound to d(TCGGTACCGA)

Niyazi, H., Teixeira, S., Mitchell, E., Forsyth, T., Cardin, C.

To be published.

Macromolecule Content

Total Structure Weight: 4.67 kDa
Atom Count: 325
Modeled Residue Count: 10
Deposited Residue Count: 10
Unique nucleic acid chains: 1

Macromolecules

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Molecule	Chains	Length	Organism	Image
Entity ID: 1
DNA	A	10	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RKP Query on RKP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	Lambda-Ru(phen)2(dppz) complex C₄₂ H₂₆ N₈ Ru OYSRBLHMGIHFCB-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
BA Query on BA 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]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.219 (Depositor), 0.219 (DCC)
R-Value Work: 0.188 (Depositor), 0.180 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.45	α = 90
b = 52.45	β = 90
c = 32.58	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-09-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-09-24
Type: Initial release
Version 1.1: 2018-01-24
Changes: Database references, Structure summary
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.