293D

INTERACTION BETWEEN THE LEFT-HANDED Z-DNA AND POLYAMINE-2: THE CRYSTAL STRUCTURE OF THE D(CG)3 AND SPERMIDINE COMPLEX

Structural Biology Knowledgebase: 293D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.0 Å
  • R-Value Observed: 0.191

Literature

Macromolecules
Sequence Display for 293D

Classification: DNA

Total Structure Weight: 3861.59

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

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

A SPERMIDINE
N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34) (Synonym)
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.0 Å
  • R-Value Observed: 0.191
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 17.93 α = 90.00
b = 31.23 β = 90.00
c = 44.64 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 1996-10-09
  • Released Date: 1996-12-02
  • Deposition author(s): Ohishi, H., Nakanishi, I., Inubushi, K., Van Der Marel, G.A., Van Boom, J.H., Rich, A., Wang, A.H.-J., Hakoshima, T., Tomita, K.

Revision History

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