2FIJ

Crystal Structure Analysis of the A-DNA Decamer GCGT-2'OMeA-aU-ACGC, with Incorporated 2'-O-Methylated-Adenosine (2'OMeA) and Arabino-Uridine (aU)

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 2005-12-29 Released: 2006-05-23 
  • Deposition Author(s): Egli, M., Li, F.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.19 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

2'-Fluoroarabino- and arabinonucleic acid show different conformations, resulting in deviating RNA affinities and processing of their heteroduplexes with RNA by RNase H.

Li, F.Sarkhel, S.Wilds, C.J.Wawrzak, Z.Prakash, T.P.Manoharan, M.Egli, M.

(2006) Biochemistry 45: 4141-4152

  • DOI: https://doi.org/10.1021/bi052322r
  • Primary Citation of Related Structures:  
    2FIH, 2FII, 2FIJ, 2FIL

  • PubMed Abstract: 

    2'-Deoxy-2'-fluoro-arabinonucleic acid (FANA) and arabinonucleic acid (ANA) paired to RNA are substrates of RNase H. The conformation of the natural DNA/RNA hybrid substrates appears to be neither A-form nor B-form. Consistent with this, the conformations of FANA and ANA were found to be intermediate between the A- and B-forms. However, FANA opposite RNA is preferred by RNase H over ANA, and the RNA affinity of FANA considerably exceeds that of ANA. By investigating the conformational boundaries of FANA and ANA residues in crystal structures of A- and B-form DNA duplexes at atomic resolution, we demonstrate that FANA and ANA display subtle conformational differences. The structural data provide insight into the structural requirements at the catalytic site of RNase H. They also allow conclusions with regard to the relative importance of stereoelectronic effects and hydration as modulators of RNA affinity.


  • Organizational Affiliation

    Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*GP*CP*GP*TP*(A2M)P*(UAR)P*AP*CP*GP*C)-3'
A, B
10N/A
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.19 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.277α = 90
b = 32.469β = 90
c = 66.749γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata scaling
EPMRphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-23
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2011-12-28
    Changes: Advisory
  • Version 1.4: 2017-10-18
    Changes: Refinement description
  • Version 1.5: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description