131D

THE LOW-TEMPERATURE CRYSTAL STRUCTURE OF THE PURE-SPERMINE FORM OF Z-DNA REVEALS BINDING OF A SPERMINE MOLECULE IN THE MINOR GROOVE

Structural Biology Knowledgebase: 131D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.0 Å
  • R-Value Observed: 0.180

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 131D

Classification: DNA

Total Structure Weight: 4071.10

Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*GP*CP*GP*CP*G)-3') A, B 6 synthetic

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SPM
Query on SPM

A, B SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.0 Å
  • R-Value Observed: 0.180
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 18.26 α = 90.00
b = 30.69 β = 90.00
c = 42.46 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 1993-06-18
  • Released Date: 1993-10-15
  • Deposition author(s): Bancroft, D., Williams, L.D., Rich, A., Egli, M.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4