461D | pdb_0000461d

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

• PDB DOI: https://doi.org/10.2210/pdb461D/pdb
• NAKB: 461D

• Classification: DNA
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Work: 
  0.170 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

A "Hydrat-Ion Spine" in a B-DNA minor groove

Tereshko, V., Minasov, G., Egli, M.

(1999) J Am Chem Soc 121: 3590-3595

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.5 kDa 
• Atom Count: 671 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*GP*AP*AP*(TAF)P*TP*CP*GP*CP*G)-3')	A, B	12	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RB	C [auth A]	RUBIDIUM ION Rb NCCSSGKUIKYAJD-UHFFFAOYSA-N
MG	D [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Work:  0.170 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.07	α = 90
b = 39.72	β = 90
c = 65.77	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 1999-04-08
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations