7SB8 | pdb_00007sb8

d(GA(CGA)5) parallel-stranded homo-duplex

PDB DOI: https://doi.org/10.2210/pdb7SB8/pdb
NAKB: 7SB8

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

Deposited: 2021-09-24 Released: 2021-10-06
Deposition Author(s): Luteran, E.M., Paukstelis, P.J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.32 Å
R-Value Free:
0.214 (Depositor), 0.214 (DCC)
R-Value Work:
0.171 (Depositor), 0.172 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

The parallel-stranded d(CGA) duplex is a highly predictable structural motif with two conformationally distinct strands.

Luteran, E.M., Paukstelis, P.J.

(2022) Acta Crystallogr D Struct Biol 78: 299-309

PubMed: 35234144 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2059798322000304
Primary Citation Related Structures:
7SB8, 7T6Y

PubMed Abstract:
DNA can adopt noncanonical structures that have important biological functions while also providing structural diversity for applications in nanotechnology. Here, the crystal structures of two oligonucleotides composed of d(CGA) triplet repeats in the parallel-stranded duplex form are described. The structure determination of four unique d(CGA)-based parallel-stranded duplexes across two crystal structures has allowed the structural parameters of d(CGA) triplets in the parallel-stranded duplex form to be characterized and established. These results show that d(CGA) units are highly uniform, but that each strand in the duplex is structurally unique and has a distinct role in accommodating structural asymmetries induced by the C-CH ⁺ base pair.

Organizational Affiliation

Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.

Macromolecule Content

Total Structure Weight: 33.66 kDa
Atom Count: 2,680
Modeled Residue Count: 102
Deposited Residue Count: 102
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 1
GA(CGA)5	A B C [auth D] D [auth E] E [auth F] A, B, C [auth D], D [auth E], E [auth F], F [auth C]	17	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NCO Query on NCO Download:Ideal Coordinates CCD File SDF format, chain X [auth F] SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain N [auth B] SDF format, chain M [auth B] MOL2 format, chain X [auth F] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] mmCIF format, chain X [auth F] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B]	M [auth B] N [auth B] Q [auth D] R [auth D] S [auth D] M [auth B], N [auth B], Q [auth D], R [auth D], S [auth D], X [auth F]	COBALT HEXAMMINE(III) Co H₁₈ N₆ DYLMFCCYOUSRTK-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain X [auth F] Interactions & Density Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain X [auth F]
SR Query on SR Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain W [auth F] SDF format, chain V [auth F] SDF format, chain U [auth E] SDF format, chain T [auth E] SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain W [auth F] MOL2 format, chain V [auth F] MOL2 format, chain U [auth E] MOL2 format, chain T [auth E] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain W [auth F] mmCIF format, chain V [auth F] mmCIF format, chain U [auth E] mmCIF format, chain T [auth E] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] J [auth B] K [auth B] G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], O [auth D], P [auth D], T [auth E], U [auth E], V [auth F], W [auth F], Y [auth C], Z [auth C]	STRONTIUM ION Sr PWYYWQHXAPXYMF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth D] Focus chain P [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth F] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain O [auth D] Focus chain P [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth F] Focus chain Y [auth C] Focus chain Z [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]