8RER | pdb_00008rer

Major groove intercalation with Polypyridyl Ruthenium complex

PDB DOI: https://doi.org/10.2210/pdb8RER/pdb
NAKB: 8RER

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

Deposited: 2023-12-12 Released: 2025-01-01
Deposition Author(s): Abdullrahman, A., Cardin, C.J., Hall, J.P.
Funding Organization(s): H2020 Marie Curie Actions of the European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.203 (Depositor), 0.198 (DCC)
R-Value Work:
0.172 (Depositor), 0.164 (DCC)
R-Value Observed:
0.173 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Ruthenium Polypyridyl complex intercalating in Major and Minor Groove DNA

Abdullrahman, A., McQuaid, K., Cardin, C.J., Hall, J.P.

To be published.

Macromolecule Content

Total Structure Weight: 11.97 kDa
Atom Count: 1,048
Modeled Residue Count: 28
Deposited Residue Count: 28
Unique nucleic acid chains: 2

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 1
DNA (5'-D(GPAPAPTPAPGP*G)-3')	A, C	7	synthetic construct
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 2
DNA (5'-D(CPCPTPAPTPTP*C)-3')	B, D	7	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KSB (Subject of Investigation/LOI) Query on KSB Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain O [auth C] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain T [auth D] MOL2 format, chain O [auth C] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain T [auth D] mmCIF format, chain O [auth C] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B], O [auth C], T [auth D]	lambda-[Ru(tap2-dppz-CN)]2+ C₃₉ H₂₁ N₁₃ Ru HNFPSJMHTKCUIN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain T [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain S [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain V [auth D] MOL2 format, chain S [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain V [auth D] mmCIF format, chain S [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] M [auth B] N [auth B] S [auth C] H [auth A], I [auth A], M [auth B], N [auth B], S [auth C], V [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain S [auth C] Focus chain V [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain S [auth C] Focus chain V [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain U [auth D] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain U [auth D] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] K [auth B] L [auth B] P [auth C] F [auth A], G [auth A], K [auth B], L [auth B], P [auth C], Q [auth C], R [auth C], U [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D]