8RI3 | pdb_00008ri3

Crystal structure of transplatin/B-DNA adduct obtained upon 7 days of soaking

• PDB DOI: https://doi.org/10.2210/pdb8RI3/pdb
• NAKB: 8RI3

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


• Deposited: 2023-12-18 Released: 2024-02-28 
• 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: 1.40 Å
• R-Value Free: 
  0.257 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.222 (DCC) 

Starting Model: experimental

Literature

On the mechanism of action of arsenoplatins: arsenoplatin-1 binding to a B-DNA dodecamer.

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

(2024) Dalton Trans 53: 3476-3483

• PubMed: 38270175 
• DOI: https://doi.org/10.1039/d3dt04302a
• Primary Citation Related Structures: 
  8C62, 8C63, 8C64, 8RI3, 8RI5


• PubMed Abstract: 
  

  The reaction of Pt-based anticancer agents with arsenic trioxide affords robust complexes known as arsenoplatins. The prototype of this family of anticancer compounds is arsenoplatin-1 (AP-1) that contains an As(OH) ₂ fragment linked to a Pt(II) moiety derived from cisplatin. Crystallographic and spectrometric studies of AP-1 binding to a B-DNA double helix dodecamer are presented here, in comparison with cisplatin and transplatin. Results reveal that AP-1, cisplatin and transplatin react differently with the DNA model system. Notably, in the AP-1/DNA systems, the Pt-As bond can break down with time and As-containing fragments can be released. These results have implications for the understanding of the mechanism of action of arsenoplatins.

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Organizational Affiliation: 
• Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, via Cintia, 80126, Naples, Italy. [e-mail].
Institute of Biostructures and Bioimaging, CNR, via Pietro Castellino 111, 80131 Naples, Italy.
Department of Chemistry "U. Schiff", University of Florence, via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
Department of Chemistry and Industrial Chemistry (DCCI), University of Pisa, Via Giuseppe Moruzzi 13, 56124 Pisa, Italy.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 8.02 kDa 
• Atom Count: 603 
• 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	synthetic construct

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PT (Subject of Investigation/LOI)	D [auth A], F [auth A], I [auth B]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N
CL	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NH3	E [auth A], G [auth A], J [auth B]	AMMONIA H3 N QGZKDVFQNNGYKY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.257 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.222 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.56	α = 90
b = 40.39	β = 90
c = 65.67	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: 2024-02-28 
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: 2024-02-28
  Type: Initial release