2IE1

Polyamines stabilize left-handed Z-DNA. We found new type of polyamine which stabilize left-handed Z-DNA by X-ray crystallography

• PDB DOI: https://doi.org/10.2210/pdb2IE1/pdb
• NAKB: 2IE1

• Classification: DNA
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2006-09-16 Released: 2007-10-09 
• Deposition Author(s): Ohishi, H., Odoko, M., Tsukamoto, K., Hiyama, Y., Maezaki, N., Grzeskowiak, K., Ishida, T., Tanaka, T., Okabe, N., Fukuyama, K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.205 (Depositor) 
• R-Value Work: 
  0.190 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Polyamines stabilize left-handed Z-DNA. We found new type of polyamine which stabilize left-handed Z-DNA by X-ray crystallography

Ohishi, H., Odoko, M., Tsukamoto, K., Hiyama, Y., Maezaki, N., Grzeskowiak, K., Ishida, T., Tanaka, T., Okabe, N., Fukuyama, K.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 4 kDa 
• Atom Count: 321 
• Modelled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*DCP*DGP*DCP*DGP*DCP*DG)-3')	A, B	6	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PAW	C [auth A], D [auth B]	N-(2-AMINOETHYL)-N'-{2-[(2-AMINOETHYL)AMINO]ETHYL}ETHANE-1,2-DIAMINE C8 H23 N5 FAGUFWYHJQFNRV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.205 (Depositor) 
• R-Value Work:  0.190 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 17.64	α = 90
b = 30.38	β = 90
c = 43.63	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MERLOT	phasing
X-PLOR	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-09 
Deposition Author(s): Ohishi, H., Odoko, M., Tsukamoto, K., Hiyama, Y., Maezaki, N., Grzeskowiak, K., Ishida, T., Tanaka, T., Okabe, N., Fukuyama, K.

Revision History  

• Version 1.0: 2007-10-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-29
  Changes: Database references, Source and taxonomy