5XUV

Crystal structure of DNA duplex containing 4-thiothymine-2Ag(I)-4-thiothymine base pairs

PDB DOI: https://doi.org/10.2210/pdb5XUV/pdb
NAKB: 5XUV

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

Deposited: 2017-06-26 Released: 2017-09-20
Deposition Author(s): Kondo, J., Sugawara, T., Saneyoshi, H., Ono, A.
Funding Organization(s): MEXT

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.222
R-Value Work: 0.185
R-Value Observed: 0.189

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a DNA duplex containing four Ag(i) ions in consecutive dinuclear Ag(i)-mediated base pairs: 4-thiothymine-2Ag(i)-4-thiothymine

Kondo, J., Sugawara, T., Saneyoshi, H., Ono, A.

(2017) Chem Commun (Camb) 53: 11747-11750

PubMed: 28991300 Search on PubMed
DOI: https://doi.org/10.1039/c7cc06153f
Primary Citation of Related Structures:
5XUV

PubMed Abstract:
Herein, we determined a high-resolution crystal structure of a B-form DNA duplex containing consecutive dinuclear metal ion-mediated base pairs, namely, 4-thiothymine-2Ag(i)-4-thiothymine (S-2Ag(i)-S), and four Ag(i) ions form a rectangular network and the distances between the Ag(i) ions are 2.8-3.2 Å, which may indicate the existence of metallophilic attractions.

Organizational Affiliation

Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554, Japan. j.kondo@sophia.ac.jp.

Macromolecule Content

Total Structure Weight: 7.82 kDa
Atom Count: 513
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(CPGPCPGPAP(8RO)P(8RO)PTPCPGPCPG)-3')	A, B	12	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AG (Subject of Investigation/LOI) Query on AG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B]	C [auth A], D [auth A], G [auth B], H [auth B]	SILVER ION Ag FOIXSVOLVBLSDH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A]	E [auth A], F [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.222
R-Value Work: 0.185
R-Value Observed: 0.189
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.213	α = 90
b = 40.487	β = 90
c = 66.432	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2017-09-20

Deposition Author(s):

Funding Organization	Location	Grant Number
MEXT	Japan	17H03033

Revision History (Full details and data files)

Version 1.0: 2017-09-20
Type: Initial release
Version 1.1: 2017-11-08
Changes: Database references
Version 1.2: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description

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