461D

A "HYDRAT-ION SPINE" IN A B-DNA MINOR GROOVE

Structural Biology Knowledgebase: 461D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Observed: 0.186

Literature

Macromolecules
Sequence Display for 461D

Classification: DNA

Total Structure Weight: 7496.90

Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*GP*CP*GP*AP*AP*(TAF)P*TP*CP*GP*CP*G)-3') A, B 12 synthetic

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

A RUBIDIUM ION
Rb
NCCSSGKUIKYAJD-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)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
TAF
Query on TAF
A, B DNA LINKING C10 H14 F N2 O8 P DT

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Observed: 0.186
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 25.07 α = 90.00
b = 39.72 β = 90.00
c = 65.77 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 1999-03-12
  • Released Date: 1999-04-08
  • Deposition author(s): Tereshko, V., Minasov, G., Egli, M.

Revision History

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