4E60 | pdb_00004e60

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

• PDB DOI: https://doi.org/10.2210/pdb4E60/pdb
• NAKB: 4E60

• Classification: DNA
• Mutation(s): No 


• Deposited: 2012-03-15 Released: 2013-03-20 
• Deposition Author(s): Mandal, P.K., Venkadesh, S., Gautham, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.231 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.216 (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)

Biological Assembly 2  

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

Macromolecule Content 

• Total Structure Weight: 4.93 kDa 
• Atom Count: 339 
• Modeled Residue Count: 16 
• Deposited Residue Count: 16 
• Unique nucleic acid chains: 3

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

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*G)-3')	C, D	2	N/A

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.231 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.177	α = 90
b = 35.177	β = 90
c = 44.341	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-20 
Deposition Author(s): Mandal, P.K., Venkadesh, S., Gautham, N.

Revision History  

• Version 1.0: 2013-03-20
  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