420D

CRYSTAL STRUCTURE OF A 16-MER RNA DUPLEX WITH NON-ADJACENT A(ANTI).G(SYN) MISMATCHES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.197 

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This is version 1.2 of the entry. See complete history

Literature

Crystal structure of an RNA 16-mer duplex R(GCAGAGUUAAAUCUGC)2 with nonadjacent G(syn).A+(anti) mispairs.

Pan, B.Mitra, S.N.Sundaralingam, M.

(1999) Biochemistry 38: 2826-2831

  • DOI: 10.1021/bi982122y

  • PubMed Abstract: 
  • G.A mispairs are one of the most common noncanonical structural motifs of RNA. The 1.9 A resolution crystal structure of the RNA 16-mer r(GCAGAGUUAAAUCUGC)2 has been determined with two isolated or nonadjacent G.A mispairs. The molecule crystallizes ...

    G.A mispairs are one of the most common noncanonical structural motifs of RNA. The 1.9 A resolution crystal structure of the RNA 16-mer r(GCAGAGUUAAAUCUGC)2 has been determined with two isolated or nonadjacent G.A mispairs. The molecule crystallizes with one duplex in the asymmetric unit in space group R3 and unit cell dimensions a = b = c = 49.24 A and alpha = beta = gamma = 51.2 degrees. It is the longest known oligonucleotide duplex at this resolution and isomorphous to the 16-mer duplex with the C.A+ mispairs [Pan, et al., (1998) J. Mol. Biol. 283, 977-984]. The C.A+ mispair behaves like a wobble pair while the G.A+ does not. The G.A mispairs are protonated at N1 of the adenines as in the C.A+ mispairs, and two hydrogen bonds in the G(syn).A+(anti) conformation are formed. The syn guanine is stabilized by an intranucleotide hydrogen bond between the 2-amino and the 5'-phosphate groups. The G(syn).A+(anti) conformation can provide a different surface for recognition in the grooves compared to other G.A hydrogen bonding schemes. The major groove is widened between the two mispairs allowing access to ligands. One of the 3-fold axes is occupied by a sodium ion and a water molecule, while a second is occupied by another water molecule.


    Organizational Affiliation

    Biological Macromolecular Structure Center, Department of Chemistry, The Ohio State University, Columbus 43210-1002, USA.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*CP*AP*GP*AP*GP*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3')A,B16N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.197 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 42.530α = 90.00
b = 42.530β = 90.00
c = 128.060γ = 120.00
Software Package:
Software NamePurpose
MSCdata scaling
X-PLORrefinement
R-AXISdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-01-13
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance