7BSE

Crystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster (T5A mutant)

PDB DOI: https://doi.org/10.2210/pdb7BSE/pdb
NAKB: 7BSE

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

Deposited: 2020-03-30 Released: 2020-12-16
Deposition Author(s): Kondo, J., Cerretani, C., Vosch, T.
Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.137
R-Value Work: 0.124
R-Value Observed: 0.126

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Mutation of position 5 as a crystal engineering tool for a NIR-emitting DNA-stabilized Ag16 nanocluster.

Cerretani, C., Kondo, J., Vosch, T.

(2020) CrystEngComm 22: 8136-8141

DOI: https://doi.org/10.1039/D0CE01225D

Macromolecule Content

Total Structure Weight: 16.3 kDa
Atom Count: 943
Modelled Residue Count: 40
Deposited Residue Count: 40
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(CPAPCPCPAPAPGPCPGPA)-3')	A, B, C, D	10	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 BA [auth C] SDF format, chain G [auth A] SDF format, chain IA [auth C] SDF format, chain NA [auth D] SDF format, chain O [auth B] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain R [auth B] SDF format, chain SA [auth D] SDF format, chain UA [auth D] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain E [auth A] SDF format, chain EA [auth C] SDF format, chain F [auth A] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth C] 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 OA [auth D] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain RA [auth D] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain TA [auth D] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain VA [auth D] MOL2 format, chain BA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain SA [auth D] MOL2 format, chain UA [auth D] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] 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 OA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain RA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth D]	BA [auth C] CA [auth C] DA [auth C] E [auth A] EA [auth C] BA [auth C], CA [auth C], DA [auth C], E [auth A], EA [auth C], F [auth A], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], L [auth A], M [auth A], N [auth B], NA [auth D], O [auth B], OA [auth D], P [auth B], PA [auth D], Q [auth B], QA [auth D], R [auth B], RA [auth D], S [auth B], SA [auth D], T [auth B], TA [auth D], U [auth B], UA [auth D], V [auth B], VA [auth D]	SILVER ION Ag FOIXSVOLVBLSDH-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain NA [auth D] Focus chain O [auth B] Focus chain OA [auth D] Focus chain P [auth B] Focus chain PA [auth D] Focus chain Q [auth B] Focus chain QA [auth D] Focus chain R [auth B] Focus chain RA [auth D] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain NA [auth D] Focus chain O [auth B] Focus chain OA [auth D] Focus chain P [auth B] Focus chain PA [auth D] Focus chain Q [auth B] Focus chain QA [auth D] Focus chain R [auth B] Focus chain RA [auth D] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain MA [auth C] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain AA [auth B] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain W [auth B] SDF format, chain Z [auth B] MOL2 format, chain MA [auth C] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain Z [auth B]	AA [auth B] KA [auth C] LA [auth C] MA [auth C] W [auth B] AA [auth B], KA [auth C], LA [auth C], MA [auth C], W [auth B], X [auth B], Y [auth B], Z [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]