6DY5

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*GP*GP*GP*AP*TP*CP*CP*CP*T)-3')A,B10synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SPD
Query on SPD

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Download CCD File 
A
SPERMIDINE
N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34)
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
 Ligand Interaction
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 = 25.567α = 90.00
b = 42.451β = 90.00
c = 49.212γ = 90.00
Software Package:
Software NamePurpose
AutoSolphasing
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United StatesDoD PC150300P1

Revision History 

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