4E2R | pdb_00004e2r

Interactions of Ba2+ with a non-self-complementary Z-type DNA duplex

• PDB DOI: https://doi.org/10.2210/pdb4E2R/pdb
• NAKB: 4E2R

• Classification: DNA
• Mutation(s): No 


• Deposited: 2012-03-09 Released: 2013-03-13 
• Deposition Author(s): Mandal, P.K., Venkadesh, S., Gautham, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 
  0.227 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: in silico

Literature

Interactions of Ba2+ with a non-self-complementary Z-type DNA duplex

Mandal, P.K., Venkadesh, S., Gautham, N.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 3.76 kDa 
• Atom Count: 292 
• Modeled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 2

Macromolecules

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

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*GP*TP*G)-3')	B	6	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BA	C [auth A]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free:  0.227 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 17.544	α = 90
b = 30.512	β = 90
c = 44.21	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
REFMAC	refinement
AUTOMAR	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-13 
Deposition Author(s): Mandal, P.K., Venkadesh, S., Gautham, N.

Revision History  

• Version 1.0: 2013-03-13
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2024-04-03
  Changes: Refinement description