2FIH

Crystal Structure Analysis of the B-DNA Dodecamer CGCGAA-aU-TCGCG, with Incorporated Arabino-Uridine (aU)

  • Classification: DNA

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1021/bi052322r
  • Primary Citation of Related Structures:  

  • 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 conforma ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*GP*CP*GP*AP*AP*(UAR)P*TP*CP*GP*CP*G)-3'A,B12N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UAR
Query on UAR
A, B
RNA LINKINGC9 H13 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 25.474α = 90.00
b = 39.757β = 90.00
c = 65.345γ = 90.00
Software Package:
Software NamePurpose
EPMRphasing
SCALEPACKdata scaling
DENZOdata reduction
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

  • Version 1.0: 2006-05-23
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-12-28
    Type: Advisory