8VIU

The DNA 16-mer sequence 5'-GCTGCGTTAACGCAGC-3' bound by a DB1992 stacked dimer

• PDB DOI: https://doi.org/10.2210/pdb8VIU/pdb
• NAKB: 8VIU

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


• Deposited: 2024-01-05 Released: 2024-10-02 
• Deposition Author(s): Terrell, J.R., Wilson, W.D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 0.249 
• R-Value Work: 0.225 
• R-Value Observed: 0.227 

Starting Model: experimental

Literature

Structural Examination of DNA Minor Groove Binding by Diamidine Stacked Dimers

Terrell, J.R., Paul, A., Ogbonna, E.N., Farahat, A.A., Wilson, W.D.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 5.53 kDa 
• Atom Count: 426 
• Modelled Residue Count: 16 
• Deposited Residue Count: 16 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*TP*GP*CP*GP*TP*TP*AP*AP*CP*GP*CP*AP*GP*C)-3')	A	16	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AB3 (Subject of Investigation/LOI)	B [auth A]	(2M)-2-[(5P)-5-(5-carbamimidoylthiophen-2-yl)furan-2-yl]-1H-benzimidazole-6-carboximidamide C17 H14 N6 O S UUWSLLFRNHISGE-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 0.249 
• R-Value Work: 0.225 
• R-Value Observed: 0.227 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.345	α = 90
b = 38.345	β = 90
c = 162.141	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-02 
Deposition Author(s): Terrell, J.R., Wilson, W.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM111749

Revision History  

• Version 1.0: 2024-10-02
  Type: Initial release