8CE2 | pdb_00008ce2

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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free: 
  0.223 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.203 (DCC) 

Starting Model: experimental

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 
• DOI: https://doi.org/10.1039/d3dt00320e
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo via Cintia, I-80126 Napoli, Italy. [e-mail].
Department of Chemistry "U. Schiff", University of Florence, via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.59 kDa 
• Atom Count: 658 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')	A, B	12	DNA molecule

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RH	D [auth A], E [auth A]	Rhodium Rh OBDSITLACDGNMC-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free:  0.223 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.203 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.53	α = 90
b = 40.31	β = 90
c = 65.71	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-05-31 
Deposition Author(s): Tito, G., Troisi, R., Ferraro, G., Sica, F., Merlino, A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-05-31
  Type: Initial release
  
• Version 1.1: 2023-06-07
  Changes: Database references
• Version 1.2: 2024-06-19
  Changes: Data collection