9KCC | pdb_00009kcc

DNA duplex containing copper-mediated 5-fluorouracil-cytosine base pairs

• PDB DOI: https://doi.org/10.2210/pdb9KCC/pdb
• NAKB: 9KCC

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


• Deposited: 2024-11-01 Released: 2025-09-10 
• Deposition Author(s): Kondo, J., Hirabayashi, K., Torigoe, H., Adachi, S.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 
  0.208 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: in silico

Literature

Novel specific binding of copper ions to naturally modified base pairs involving 5-fluorouracil in duplex DNA.

Torigoe, H., Hirabayashi, K., Adachi, S., Kondo, J.

(2025) Dalton Trans 54: 7208-7213

• PubMed: 40265694 
• DOI: https://doi.org/10.1039/d5dt00619h
• Primary Citation of Related Structures:  
  9KCC


• PubMed Abstract: 
  

  Only mercury(II) and silver(I) ions are known to specifically bind to natural and naturally modified base pairs in duplex DNA to form metal-mediated base pairs. We found novel, specific binding of copper ions to naturally modified base pairs involving 5-fluorouracil (FdU) in duplex DNA, forming C-Cu-FdU and FdU-Cu-C base pairs.

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Organizational Affiliation: 
• Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan. [e-mail].
Department of Materials and Life Sciences, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554, Japan.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 3.71 kDa 
• Atom Count: 242 
• Modeled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*AP*CP*CP*CP*(UFP)P*GP*GP*TP*CP*C)-3')	A	12	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	B [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free:  0.208 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.467	α = 90
b = 39.467	β = 90
c = 74.577	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-10 
Deposition Author(s): Kondo, J., Hirabayashi, K., Torigoe, H., Adachi, S.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	--

Revision History  

• Version 1.0: 2025-09-10
  Type: Initial release