2H0N | pdb_00002h0n

Structure of the fully modified left-handed cyclohexene nucleic acid sequence GTGTACAC

• PDB DOI: https://doi.org/10.2210/pdb2H0N/pdb
• NAKB: 2H0N

• Classification: DNA
• Mutation(s): No 


• Deposited: 2006-05-15 Released: 2007-04-24 
• Deposition Author(s): Robeyns, K., Van Meervelt, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Work: 
  0.158 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Structure of the fully modified left-handed cyclohexene nucleic acid sequence GTGTACAC.

Robeyns, K., Herdewijn, P., Van Meervelt, L.

(2008) J Am Chem Soc 130: 1979-1984

• PubMed: 18198873 
• DOI: https://doi.org/10.1021/ja077313f
• Primary Citation Related Structures: 
  2H0N


• PubMed Abstract: 
  

  CeNA oligonucleotides consist of a phosphorylated backbone where the deoxyribose sugars are replaced by cyclohexene moieties. The X-ray structure determination and analysis of a fully modified octamer sequence GTGTACAC, which is the first crystal structure of a carbocyclic-based nucleic acid, is presented. This particular sequence was built with left-handed building blocks and crystallizes as a left-handed double helix. The helix can be characterized as belonging to the (mirrored) A-type family. Crystallographic data were processed up to 1.53 A, and the octamer sequence crystallizes in the space group R32. The sugar puckering is found to adopt the 3H2 half-chair conformation which mimics the C3'-endo conformation of the ribose sugar. The double helices stack on top of each other to form continuous helices, and static disorder is observed due to this end-to-end stacking.

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Organizational Affiliation: 
• Katholieke Universiteit Leuven, Department of Chemistry, Biomolecular Architecture and BioMacS, Celestijnenlaan 200F, B-3001 Leuven, Belgium.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 5.21 kDa 
• Atom Count: 406 
• Modeled Residue Count: 16 
• Deposited Residue Count: 16 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-(*(XGL)P*(XTL)P*(XGL)P*(XTL)P*(XAL)P*(XCL)P*(XAL)P*(XCL)-Phosphate)-3'	A, B	8	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2HP	C [auth A], D [auth B]	DIHYDROGENPHOSPHATE ION H2 O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Work:  0.158 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.455	α = 90
b = 41.455	β = 90
c = 65.58	γ = 120

Software Package:

Software Name	Purpose
SHELXL-97	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-24 
Deposition Author(s): Robeyns, K., Van Meervelt, L.

Revision History  

• Version 1.0: 2007-04-24
  Type: Initial release
  
• Version 1.1: 2008-03-17
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Data collection, Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-04-03
  Changes: Refinement description