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Analysis of nucleic acid double helix geometry

Title RESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA AND MANGANESE IONS (POST-REACTIVE COMPLEX)
PDB code 3BAM   (PDB summary)
NDB code PD0031 (NDB atlas)
Duplex length 10 base pairs
Protein Restriction endonuclease BamHI, Nuclease

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' A2 T3 G4 G5 A6 T7 C8 C9 A10 T11 3'
Strand 2    3' T7 A6 C5 C4 T3 A2 G1 G4 T3 A2 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      

A2 T7            
    3.9 -1.6 0.1 -3°
T3 A6            
    2.9 -0.5 0.9 38°
G4 C5            
    4.4 0.9 -0.8 31° -1°
G5 C4            
    3.0 -1.2 0.4 36°
A6 T3            
    3.5 0.4 -0.2 25°
T7 A2            
    3.4 0.0 0.2 36°
C8 G1            
    4.3 -0.6 -1.0 32°
C9 G4            
    2.8 -0.1 0.7 39°
A10 T3            
    3.9 0.5 -0.2 23°
T11 A2            


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 

    C3'-exo -118° A2 T7 -105° C3'-exo    
 39°   -88° (BI)             -56° (BI)   34° 
    C2'-endo -83° T3 A6 -90° C3'-exo    
 43°   -1° (BI)             -63° (BI)   47° 
    C2'-endo -98° G4 C5 -109° C2'-endo    
 180°   -115° (BI)             -82° (BI)   -174° 
    C2'-endo -165° G5 C4 -133° C2'-endo    
 24°   -54° (BI)             -83° (BI)   -70° 
    C2'-endo -88° A6 T3 -123° C3'-exo    
 12°   -79° (BI)             -44° (BI)   7° 
    C2'-endo -97° T7 A2 -94° C3'-exo    
 63°   -59° (BI)             -74° (BI)   -67° 
    C2'-endo -110° C8 G1 -137° C3'-exo    
 27°   -59° (BI)             0° (BI)   44° 
    C2'-endo -116° C9 G4 -103° C2'-endo    
 35°   -75° (BI)             -16° (BI)   41° 
    C3'-exo -91° A10 T3 -85° C2'-endo    
 30°   -78° (BI)             -76° (BI)   55° 
    C2'-endo -80° T11 A2 -82° C3'-exo    


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