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Analysis of nucleic acid double helix geometry

Title STRUCTURE OF THE E. COLI ALPHA C-TERMINAL DOMAIN OF RNA POLYMERASE IN COMPLEX WITH CAP AND DNA
PDB code 1LB2   (PDB summary)
NDB code PD0306 (NDB atlas)
Duplex length 20 base pairs
Protein RNA POLYMERASE IN COMPLEX WITH CAP, Polymerase, DNA binding domain: 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' C33 T32 T31 T30 T29 T28 T27 C26 C25 T24 A23 A22 A21 A20 T19 G18 T17 G16 A15 T14 3'

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      

C33            
    3.6 0.1 -0.1 37°
T32 G33            
    3.4 0.1 -0.2 38° -0°
T31 A32            
    3.2 -0.1 0.2 32° -1°
T30 A31            
    3.3 -0.3 -0.1 38° -4° -3°
T29 A30            
    3.3 0.5 -0.1 38°
T28 A29            
    3.3 -0.6 -0.1 31° -2° -2°
T27 A28            
    3.4 0.9 -0.0 35° -1° -3°
C26 A27            
    3.2 0.2 -0.3 33°
C25 G26            
    3.4 -0.3 0.2 27° 14°
T24 G25            
    3.3 -0.6 1.3 43° -14° -1°
A23 A24            
    3.1 0.4 -0.5 36° -4° -0°
A22 T23            
    3.5 -0.1 -0.4 34° -3°
A21 T22            
    3.1 -0.2 -0.2 39° -10° -1°
A20 T21            
    3.4 0.2 -0.7 34°
T19 T20            
    3.5 0.3 0.9 34° -15° -1°
G18 A19            
    3.0 -0.1 -0.5 30° -1°
T17 C18            
    5.9 -0.1 0.3 32° 31°
G16 A17            
    3.6 0.1 0.5 24° -5° -0°
A15 C16            
    2.6 -0.0 -0.8 33° -5° -0°
T14 T15            


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 

    C2'-endo -135° C33 -112° C1'-exo    
 49°   -91° (BI)             -30° (BI)   50° 
    C2'-endo -107° T32 G33 -109° C2'-endo    
 -64°   -47° (BI)             -65° (BI)   -163° 
    C3'-exo -108° T31 A32 -139° C1'-exo    
 54°   -93° (BI)             35° (BII)   37° 
    C1'-exo -111° T30 A31 -93° C2'-endo    
 50°   -47° (BI)             -71° (BI)   47° 
    C2'-endo -121° T29 A30 -114° C2'-endo    
 -53°   -48° (BI)             57° (BII)   35° 
    C3'-exo -105° T28 A29 -87° C2'-endo    
 49°   -91° (BI)             -65° (BI)   49° 
    C2'-endo -114° T27 A28 -109° C2'-endo    
 21°   -95° (BI)             35° (BII)   37° 
    C2'-endo -98° C26 A27 -102° C2'-endo    
 44°   -92° (BI)             100° (BII)   46° 
    C2'-endo -103° C25 G26 -84° C2'-endo    
 50°   -35° (BI)             -71° (BI)   45° 
    C2'-endo -104° T24 G25 -96° C2'-endo    
 54°   62° (BII)             -38° (BI)   39° 
    C2'-endo -107° A23 A24 -115° C2'-endo    
 45°   -100° (BI)             -81° (BI)   44° 
    C2'-endo -103° A22 T23 -112° C2'-endo    
 47°   -68° (BI)             -94° (BI)   49° 
    C2'-endo -117° A21 T22 -108° C2'-endo    
 47°   -67° (BI)             -83° (BI)   44° 
    C2'-endo -108° A20 T21 -108° C2'-endo    
 34°   -98° (BI)             -103° (BI)   37° 
    C2'-endo -99° T19 T20 -100° C2'-endo    
 39°   -28° (BI)             98° (BII)   31° 
    C2'-endo -96° G18 A19 -101° C2'-endo    
 9°   -13° (BI)             -38° (BI)   45° 
    C2'-endo -80° T17 C18 -104° C2'-endo    
 41°   -20° (BI)             5° (BI)   -1° 
    C2'-endo -61° G16 A17 -56° C2'-endo    
 40°   118° (BII)             20° (BII)   -54° 
    C2'-endo -93° A15 C16 -84° C2'-endo    
 46°   -54° (BI)             -67° (BI)   53° 
    C2'-endo -91° T14 T15 -95° 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