Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological Assembly Evidence: authors reported there is no experimental evidence

Macromolecule Content

• Total Structure Weight: 6431.48 
• Atom Count: 416 
• Residue Count: 20 
• Unique nucleic acid chains: 1

6DY5

Crystal structure of double-stranded DNA AGGGATCCCT in complex with Zn2+

• DOI: 10.2210/pdb6DY5/pdb

• Classification: DNA
• Organism(s): synthetic construct


• Deposited: 2018-07-01 Released: 2019-01-23 
• Deposition Author(s): Hou, C., Tsodikov, O.V.
• Funding Organization(s): null 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free: 0.254 
• R-Value Work: 0.214 

Literature

Utilizing guanine coordinated Zn2+ to determine DNA crystal structures by single-wavelength anomalous diffraction

Hou, C., Tsodikov, O.V.

(2019) Acta Crystallogr.,Sect.D 75: 32

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Length	Organism
DNA (5'-D(*AP*GP*GP*GP*AP*TP*CP*CP*CP*T)-3')	A,B	10	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
SPD	A	SPERMIDINE N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34) C7 H19 N3 ATHGHQPFGPMSJY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free: 0.254 
• R-Value Work: 0.214 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 25.567	α = 90.00
b = 42.451	β = 90.00
c = 49.212	γ = 90.00

Software Package:

Software Name	Purpose
AutoSol	phasing
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-07-01 
• Released Date: 2019-01-23 
• Deposition Author(s): Hou, C., Tsodikov, O.V.

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Funding Organization	Location	Grant Number
	United States	DoD PC150300P1

Revision History 

• Version 1.0: 2019-01-23
  Type: Initial release