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Analysis of nucleic acid double helix geometry

Title CRYSTAL STRUCTURE AT 1.7 ANGSTROMS OF THE BOVINE PAPILLOMAVI DNA-BINDING DOMAIN BOUND TO ITS DNA TARGET
PDB code 2BOP   (PDB summary)
NDB code PDV001 (NDB atlas)
Duplex length 16 base pairs
Protein E2 (papillomavirus-1), Transcription factor, DNA binding domain: Beta-barrel, alpha-helix

Only the nucleic acid double helix part of the structure is analysed here. Small ligands, proteins, and overhanging ends are not taken into account. Information on the complete structure is available at the Image Library Entry page and at the Sequence, Chains, Units page.

Strand 1    5' C2 G3 A4 C5 C6 G7 A8 C9 G10 T11 C12 G13 G14 T15 C16 G17 3'
Strand 2    3' G17 C16 T15 G14 G13 C12 T11 G10 C9 A8 G7 C6 C5 A4 G3 C2 5'

Side view 1 Top view
Side view 1 Top view
Side view 2 3-dimensional interactive models
(Help)
  

RASMOL, CHIME, VRML 2.0, PDB

Side view 2  

Figure 1   Three orthogonal views of the double helix (Help). Residues are colored according to the nucleotide type (Help: Color codes). The curvilinear helical axis (green) was calculated with CURVES. The double helix is oriented with respect to the principle axis of inertia of the curvilinear helical axis (see Help for further explanations). This drawing reveals immediately if there is any bending of the helical axis.


Analysis of helical axis bending


Inter base pair parameters

The six inter base pair parameters (rise, shift, slide, twist, roll, tilt) describe the translational and rotational displacement between neighbouring base pairs. See Help for further explanations.

Plot of inter base pair parameters with respect to global and local helical axes:  PDF,   GIF
(Global parameters from CURVES,  local parameters from CURVES and FREEHELIX)

Table 1.  Inter base pair parameters with respect to the global helical axis, calculated with CURVES.


  Strand 1      Strand 2        riseg          shiftg          slideg          twistg         rollg         tiltg    
    / Å / Å / Å      

C2 G17            
    3.2 0.6 0.4 28°
G3 C16            
    3.5 -1.2 0.4 39° -2° -8°
A4 T15            
    3.4 0.9 -0.9 32° -2°
C5 G14            
    3.5 -0.8 -0.7 34° -3°
C6 G13            
    3.2 0.4 0.8 30° 16° -0°
G7 C12            
    3.6 0.0 -0.8 41° -2°
A8 T11            
    3.4 0.6 -0.0 36° -7°
C9 G10            
    3.4 0.0 0.9 41° -9°
G10 C9            
    3.4 -0.6 -0.0 36° -7° -5°
T11 A8            
    3.6 0.0 -0.8 41° -2° -5°
C12 G7            
    3.2 -0.4 0.8 30° 16°
G13 C6            
    3.5 0.8 -0.7 34°
G14 C5            
    3.4 -0.9 -0.9 32°
T15 A4            
    3.5 1.2 0.4 39° -2°
C16 G3            
    3.2 -0.6 0.4 28° -1°
G17 C2            


Backbone parameters

Table 2.  Selected torsional angles and sugar pucker phase angles describing the conformation of the sugar phosphate backbone. (See Help for further explanations.)


 gamma     epsilon-zeta       pucker        chi      Strand 1     Strand 2      chi        pucker       epsilon-zeta     gamma 

    O1'-endo -130° C2 G17 -90° C2'-endo    
 50°   -79° (BI)             40° (BII)   40° 
    C2'-endo -89° G3 C16 -99° C2'-endo    
 47°   74° (BII)             -87° (BI)   54° 
    C2'-endo -110° A4 T15 -121° C1'-exo    
 56°   -101° (BI)             -86° (BI)   52° 
    O1'-endo -130° C5 G14 -131° C1'-exo    
 43°   -74° (BI)             -82° (BI)   60° 
    C4'-exo -132° C6 G13 -95° C3'-exo    
 53°   -74° (BI)             -71° (BI)   59° 
    C2'-endo -94° G7 C12 -141° C3'-endo    
 49°   -82° (BI)             -96° (BI)   44° 
    C2'-endo -108° A8 T11 -121° C1'-exo    
 46°   -85° (BI)             42° (BII)   40° 
    C2'-endo -93° C9 G10 -90° C2'-endo    
 40°   121° (BII)             121° (BII)   46° 
    C2'-endo -90° G10 C9 -93° C2'-endo    
 44°   41° (BII)             -85° (BI)   49° 
    C1'-exo -121° T11 A8 -108° C2'-endo    
 59°   -96° (BI)             -82° (BI)   53° 
    C3'-endo -141° C12 G7 -94° C2'-endo    
 60°   -71° (BI)             -74° (BI)   43° 
    C3'-exo -95° G13 C6 -132° C4'-exo    
 52°   -82° (BI)             -74° (BI)   56° 
    C1'-exo -131° G14 C5 -130° O1'-endo    
 54°   -86° (BI)             -101° (BI)   47° 
    C1'-exo -121° T15 A4 -110° C2'-endo    
 40°   -87° (BI)             74° (BII)   50° 
    C2'-endo -99° C16 G3 -89° C2'-endo    
 55°   40° (BII)             -79° (BI)   55° 
    C2'-endo -90° G17 C2 -130° O1'-endo    


Groove width

Plot of minor groove width:   PDF,   GIF
Plot of major groove width:   PDF,   GIF
(See Help for further explanations.)

Further information

Full output from CURVES  (helical parameters with respect to global and local axes)

Full output from FREEHELIX  (helical parameters with respect to local axis, angles between normal vectors)

Chirality of ribose and phosphate atoms
Check the naming of phosphate and ribose substituents. Recommended for phosphate oxygens and for ribose hydrogens in NMR structures.


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Perl script:    helixparameter.pl  (15 Sep 2016)
Author:    Peter Slickers  (slickers@leibniz-fli.de),  IMB Jena,  Germany