3GVN

The 1.2 Angstroem crystal structure of an E.coli tRNASer acceptor stem microhelix reveals two magnesium binding sites


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.190 

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Literature

The 1.2A crystal structure of an E. coli tRNASer)acceptor stem microhelix reveals two magnesium binding sites.

Eichert, A.Furste, J.P.Schreiber, A.Perbandt, M.Betzel, C.Erdmann, V.A.Forster, C.

(2009) Biochem Biophys Res Commun 386: 368-373

  • DOI: 10.1016/j.bbrc.2009.06.048
  • Primary Citation of Related Structures:  
    3GVN

  • PubMed Abstract: 
  • tRNA identity elements assure the correct aminoacylation of tRNAs by the cognate aminoacyl-tRNA synthetases. tRNA(Ser) belongs to the so-called class II system, in which the identity elements are rather simple and are mostly located in the acceptor stem region, in contrast to 'class I', where tRNA determinants are more complex and are located within different regions of the tRNA ...

    tRNA identity elements assure the correct aminoacylation of tRNAs by the cognate aminoacyl-tRNA synthetases. tRNA(Ser) belongs to the so-called class II system, in which the identity elements are rather simple and are mostly located in the acceptor stem region, in contrast to 'class I', where tRNA determinants are more complex and are located within different regions of the tRNA. The structure of an Escherichia coli tRNA(Ser) acceptor stem microhelix was solved by high resolution X-ray structure analysis. The RNA crystallizes in the space group C2, with one molecule per asymmetric unit and with the cell constants a=35.79, b=39.13, c=31.37A, and beta=111.1 degrees . A defined hydration pattern of 97 water molecules surrounds the tRNA(Ser) acceptor stem microhelix. Additionally, two magnesium binding sites were detected in the tRNA(Ser) aminoacyl stem.


    Organizational Affiliation

    Institute of Chemistry and Biochemistry, Free University Berlin, Thielallee 63, 14195 Berlin, Germany.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-R(*GP*GP*UP*GP*AP*GP*G)-3'A7N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-R(*CP*CP*UP*CP*AP*CP*C)-3'B7N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      MG
      Query on MG

      Download Ideal Coordinates CCD File 
      C [auth A], D [auth A]MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.20 Å
      • R-Value Free: 0.201 
      • R-Value Work: 0.190 
      • Space Group: C 1 2 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 35.793α = 90
      b = 39.126β = 111.08
      c = 31.367γ = 90
      Software Package:
      Software NamePurpose
      HKL-2000data collection
      PHASERphasing
      REFMACrefinement
      HKL-2000data reduction
      HKL-2000data scaling

      Structure Validation

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      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2009-07-28
        Type: Initial release
      • Version 1.1: 2011-07-13
        Changes: Version format compliance