8CE2

X-ray structure of the adduct formed upon reaction of a B-DNA double helical dodecamer with dirhodium tetraacetate

PDB DOI: https://doi.org/10.2210/pdb8CE2/pdb
NAKB: 8CE2

Classification: DNA
Organism(s): DNA molecule
Mutation(s): No

Deposited: 2023-02-01 Released: 2023-05-31
Deposition Author(s): Tito, G., Troisi, R., Ferraro, G., Sica, F., Merlino, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.24 Å
R-Value Free: 0.223
R-Value Work: 0.197

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Dirhodium tetraacetate binding to a B-DNA double helical dodecamer probed by X-ray crystallography and mass spectrometry.

Tito, G., Troisi, R., Ferraro, G., Geri, A., Massai, L., Messori, L., Sica, F., Merlino, A.

(2023) Dalton Trans 52: 6992-6996

PubMed: 37199244 Search on PubMed
DOI: https://doi.org/10.1039/d3dt00320e
Primary Citation of Related Structures:
8CE2

PubMed Abstract:
The reaction of the cytotoxic compound dirhodium tetraacetate with a B-DNA double helical dodecamer was studied by X-ray crystallography and mass spectrometry. The structure of the dirhodium/DNA adduct reveals a dimetallic center binding to an adenine via axial coordination. Complementary information has been gained through ESI MS measurements. Comparison between the present data and those previously obtained for cisplatin indicates that the two metallodrugs react with this DNA dodecamer in a significantly different fashion.

Organizational Affiliation

Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo via Cintia, I-80126 Napoli, Italy. antonello.merlino@unina.it.

Macromolecule Content

Total Structure Weight: 7.59 kDa
Atom Count: 658
Modelled Residue Count: 24
Deposited Residue Count: 24
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(CPGPCPGPAPAPTPTPCPGPCPG)-3')	A, B	12	DNA molecule
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RH Query on RH Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	D [auth A], E [auth A]	Rhodium Rh OBDSITLACDGNMC-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]