2JJA | pdb_00002jja

Crystal structure of GNA with synthetic copper base pair

• PDB DOI: https://doi.org/10.2210/pdb2JJA/pdb
• NAKB: 2JJA

• Classification: RNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2008-03-28 Released: 2008-07-22 
• Deposition Author(s): Schlegel, M.K., Essen, L.-O., Meggers, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.148 (Depositor), 0.153 (DCC) 
• R-Value Work: 
  0.124 (Depositor), 0.133 (DCC) 
• R-Value Observed: 
  0.126 (Depositor) 

Literature

Duplex Structure of a Minimal Nucleic Acid.

Schlegel, M.K., Essen, L.-O., Meggers, E.

(2008) J Am Chem Soc 130: 8158

• PubMed: 18529005 
• DOI: https://doi.org/10.1021/ja802788g
• Primary Citation Related Structures: 
  2JJA


• PubMed Abstract: 
  

  The crystal structure of an 8-mer (S)-GNA duplex is presented. As a tool for phasing, the anomalous diffraction of two copper(II) ions within two artificial metallo-base pairs was employed. The duplex structure confirms a canonical Watson-Crick base pairing scheme of GNA with antiparallel strands. The duplex secondary structure is distinct from canonical A- and B-form nucleic acids and can be described as a right-handed helical ribbon wrapped around the helix axis, resulting in a large hollow core. Most intriguingly, neighboring base pairs slide strongly against each other, resulting in extensive interstrand base-base hydrophobic interactions along with unusual hydrophobic intrastrand interactions of nucleobases with their backbone. These results reveal how a minimal nucleic acid backbone can support highly stable Watson-Crick-like duplex formation.

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Organizational Affiliation: 
• Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein Strasse, D-35043 Marburg, Germany.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 2.54 kDa 
• Atom Count: 234 
• Modeled Residue Count: 8 
• Deposited Residue Count: 8 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
GNA	A	8	synthetic construct

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCO	E [auth A], F [auth A]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N
CU	B [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
MG	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.148 (Depositor), 0.153 (DCC) 
• R-Value Work:  0.124 (Depositor), 0.133 (DCC) 
• R-Value Observed: 0.126 (Depositor) 

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 18.16	α = 90
b = 48.59	β = 90
c = 59.87	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-22 
Deposition Author(s): Schlegel, M.K., Essen, L.-O., Meggers, E.

Revision History  

• Version 1.0: 2008-07-22
  Type: Initial release
  
• Version 1.1: 2011-05-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2022-06-22
  Changes: Data collection, Database references, Derived calculations, Other, Polymer sequence
• Version 2.1: 2024-06-19
  Changes: Data collection
• Version 2.2: 2025-12-10
  Changes: Advisory, Derived calculations, Structure summary