7XKM

Crystal structure of DNA-Ag(I) rod comprising a one-dimensional array of 11 silver ions

PDB DOI: https://doi.org/10.2210/pdb7XKM/pdb
NAKB: 7XKM

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

Deposited: 2022-04-20 Released: 2022-07-06
Deposition Author(s): Kondo, J., Ono, A., Atsugi, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free: 0.217
R-Value Work: 0.187
R-Value Observed: 0.190

wwPDB Validation 3D Report Full Report

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

Literature

A Novel Ag I -DNA Rod Comprising a One-Dimensional Array of 11 Silver Ions within a Double Helical Structure.

Atsugi, T., Ono, A., Tasaka, M., Eguchi, N., Fujiwara, S., Kondo, J.

(2022) Angew Chem Int Ed Engl 61: e202204798-e202204798

PubMed: 35641885 Search on PubMed
DOI: https://doi.org/10.1002/anie.202204798
Primary Citation of Related Structures:
7XKM

PubMed Abstract:
DNA/RNA duplexes containing metal-ion-mediated base pairs (metallo-base pairs) have potential applications in developing nucleic acid-based nanodevices and genetic code expansion. Many metallo-base pairs are formed within duplexes stabilized by Watson-Crick base pairs. Recently, the crystal structure of an Ag ^I -DNA nanowire with an uninterrupted one-dimensional silver array was determined. Here, we present a new DNA helical wire, the "Ag ^I -DNA rod", containing an uninterrupted array of 11 Ag ^I ions. The Ag ^I -DNA rod consisted of only C-Ag ^I -C, G-Ag ^I -G, G-Ag ^I -5-bromouracil ( ^Br U), and ^Br U-Ag ^I - ^Br U metallo base pairs, with no Watson-Crick pairs. The Ag ^I -DNA rods were connected by non-canonical G-G pairs in crystals. Notably, data from our absorbance, circular dichroism, nuclear magnetic resonance, and mass spectrometry analyses suggested that the Ag ^I -DNA rods formed in solution, as well as within crystals.

Organizational Affiliation

Department of Materials & Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama, 221-8686, Kanagawa, Japan.

Macromolecule Content

Total Structure Weight: 17.46 kDa
Atom Count: 985
Modelled Residue Count: 48
Deposited Residue Count: 48
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(CPGPCPGPCP(BRU)PCP(BRU)PCPGPCPG)-3')	A, B, C, D	12	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 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 AA [auth D] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D]	AA [auth D] E [auth A] F [auth A] G [auth A] H [auth A] AA [auth D], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth B], O [auth B], P [auth B], Q [auth C], R [auth C], S [auth C], T [auth C], U [auth C], V [auth C], W [auth D], X [auth D], Y [auth D], Z [auth D]	SILVER ION Ag FOIXSVOLVBLSDH-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]