8G2N

Crystal structure of Tetrahymena thermophila G-rich DNA with novel ligand PyDH2

• PDB DOI: https://doi.org/10.2210/pdb8G2N/pdb
• NAKB: 8G2N

• Classification: DNA
• Organism(s): Tetrahymena thermophila
• Mutation(s): No 


• Deposited: 2023-02-06 Released: 2024-02-14 
• Deposition Author(s): Martin, K.N., Yatsunyk, L.A.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.194 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 

Literature

Crystal structure of Tetrahymena thermophila G-rich DNA with novel ligand PyDH2

Martin, K.N., Yatsunyk, L.A.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 8.83 kDa 
• Atom Count: 694 
• Modelled Residue Count: 25 
• Deposited Residue Count: 25 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
G-rich DNA	A	25	Tetrahymena thermophila

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YSQ (Subject of Investigation/LOI)	B [auth A]	4,4'-{pyridine-2,6-diylbis[carbonyl-(1E)-hydrazin-2-yl-1-ylidene-(E)-methanylylidene]}bis(1-methylquinolin-1-ium) C29 H25 N7 O2 CVURQMOLKNHXLB-UHFFFAOYSA-P
SPM	G [auth A]	SPERMINE C10 H26 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-N
K	D [auth A], E [auth A], F [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.194 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.332	α = 90
b = 47.314	β = 90
c = 87.106	γ = 90

Software Package:

Software Name	Purpose
PHENIX	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-14 
Deposition Author(s): Martin, K.N., Yatsunyk, L.A.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	1R15CA253134

Revision History  

• Version 1.0: 2024-02-14
  Type: Initial release