7EDV | pdb_00007edv

DNA duplex containing C-G-Au-C base triple

PDB DOI: https://doi.org/10.2210/pdb7EDV/pdb
NAKB: 7EDV

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

Deposited: 2021-03-17 Released: 2022-03-23
Deposition Author(s): Kondo, J., Iwase, E.
Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free:
0.191 (Depositor), 0.192 (DCC)
R-Value Work:
0.164 (Depositor), 0.166 (DCC)
R-Value Observed:
0.167 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7EDV

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

Literature

Gold-Mediated Base Pairs in Nucleic Acids: Selective Coordination to Natural and Thiocarbonyl-Modified Cytosines Dependent upon the Oxidation State of Gold

Kosugi, K., Sugawara, A., Iwase, E., Park, H., Fujiwara, S., Kanazawa, H., Ono, A., Kondo, J.

(2025) Chembiochem 26

DOI: https://doi.org/10.1002/cbic.202500565

Macromolecule Content

Total Structure Weight: 3.82 kDa
Atom Count: 278
Modeled Residue Count: 12
Deposited Residue Count: 12
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 1
DNA (5'-D(GPGPAPCPCPCPCPGPGPTPCPC)-3')	A	12	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AU (Subject of Investigation/LOI) Query on AU Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GOLD ION Au ZBKIUFWVEIBQRT-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.191 (Depositor), 0.192 (DCC)
R-Value Work: 0.164 (Depositor), 0.166 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.595	α = 90
b = 38.595	β = 90
c = 46.688	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
XDS	data reduction
AutoSol	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-03-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	24245037

Revision History (Full details and data files)

Version 1.0: 2022-03-23
Type: Initial release
Version 1.1: 2024-05-29
Changes: Data collection
Version 1.2: 2025-11-26
Changes: Database references, Structure summary

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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.