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IMAGES

STRUCTURES

GIF
InsightII

• spacefill, chain A (mono, stereo)
• surface (mono, stereo)
• ribbon, spacefill: poly-nucleotide base-base H-bond interactions (mono, stereo)
• RNA backbone: ribbon; cluster of nucleotides forming an uninterrupted network linked by base-base base-backbone and backbone-backbine H-bonds (mono, stereo)

Setor

• ribbon, Mg, water, cobalt hexammine (mono, stereo)
• ribbon, Mg, water, cobalt hexammine, different view (mono, stereo)
• spacefill (mono, stereo)
• ribbon, labeling, chain A (mono, stereo)
• ribbon, sticks, chain A, labeling, (mono, stereo)
• sticks, chain A (mono, stereo)
• ribbon, bases involved in poly-nucleotide base H-bond interactions, chain A (mono, stereo)
• ribbon, sticks, chain A (mono, stereo)

• RNA backbone: ribbon; cluster of nucleotides forming an uninterrupted network linked by base-base, base-backbone and backbone-backbone H-bonds: sticks; chain A (Cover page of the Febuary 25, 2002 Issue of Biopolymers (Nucleic Acid Sciences)) (mono)

  DISTANCE PLOTS

  • representative atom O3*, chain A (GIF, PDF)
  • representative atom O3* (GIF, PDF)

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  COMMENTS

  Numbering            Numbering             Record     Chain
  (original)           (without gaps)
  
   103 -  260             1 -  158           ATOM         A    
   103 -  260           159 -  316           ATOM         B    
     1 -   34           317 -  350           HETATM            
  
  
  Length:                                      350
  Length (ATOM records):                       316
  Length (ATOM+HETATM-records without water):  344
  
  ATOM      residues                         fraction                  fraction
                                          (ATOM records)            (ATOM+HETATM records
                                                                       without water)
  
                   G             88           27.85                      25.58
                   A             90           28.48                      26.16
                   U             72           22.78                      20.93
                   C             66           20.89                      19.19
                ------ 
                   4   
  
  
  
  HETATM    residues
  
                 NCO              4                                       1.16
                  MG             24                                       6.98
                 HOH              6
                ------ 
                   3   
  
  
  
  Residues with more than 1 conformation:
  
                ------
                   0
  

  The poly-nucleotide base-base H-bond interactions were scanned using our program HBexplore (Lindauer, Bendic, Sühnel, CABIOS 1996, 12, 281-289; full-text version (PDF).

  It adds hydrogens according to standard geometrical rules and identifies hydrogen bonds by geometrical criteria.
  In this case we have used:

  dAH < 2.5 A, aDHA > 90 deg, a HAA1 > 90 deg, a DAA1 > 90 deg.

  • H - hydrogen atom,
  • D - hydrogen bond donor
  • A - hydrogen bond acceptor
  • d - distance
  • a - angle

  See als the HBexplore homepage

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