3NP6

The crystal structure of Berberine bound to DNA d(CGTACG)

• PDB DOI: https://doi.org/10.2210/pdb3NP6/pdb
• NAKB: 3NP6

• Classification: DNA
• Mutation(s): No 


• Deposited: 2010-06-28 Released: 2011-05-04 
• Deposition Author(s): Ferraroni, M., Bazzicalupi, C., Gratteri, P., Bilia, A.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.301 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: experimental

Literature

X-Ray diffraction analyses of the natural isoquinoline alkaloids Berberine and Sanguinarine complexed with double helix DNA d(CGTACG)

Ferraroni, M., Bazzicalupi, C., Bilia, A.R., Gratteri, P.

(2011) Chem Commun (Camb) 47: 4917-4919

• PubMed: 21431128 
• DOI: https://doi.org/10.1039/c1cc10971e
• Primary Citation of Related Structures:  
  3NP6, 3NX5


• PubMed Abstract: 
  

  The first crystal structures of Berberine and Sanguinarine intercalated with a d(CGTACG)(2) DNA sequence were obtained by X-ray diffraction analysis at 2.3 Å resolution. Both drugs join the end of two "two-molecules" DNA units, stacked in a non-classic intercalation site formed by six bases. Sanguinarine interacts with d(CGTACG)(2) DNA in its iminium form.

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Organizational Affiliation: 

Department of Chemistry Ugo Schiff, University of Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Firenze, Italy.

Biological Assembly 1  

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

Biological Assembly 2  

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 7.61 kDa 
• Atom Count: 477 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*GP*TP*AP*CP*G)-3'	A, B, C, D	6	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BER	F [auth C]	BERBERINE C20 H18 N O4 YBHILYKTIRIUTE-UHFFFAOYSA-N
CA	E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.301 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.37	α = 90
b = 30.37	β = 90
c = 118.26	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-04 
Deposition Author(s): Ferraroni, M., Bazzicalupi, C., Gratteri, P., Bilia, A.R.

Revision History  

• Version 1.0: 2011-05-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description