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Analysis of nucleic acid double helix geometry

Title CRYSTAL STRUCTURE OF TN5 TRANSPOSASE COMPLEXED WITH ME DNA
PDB code 1MM8   (PDB summary)
NDB code PD0340 (NDB atlas)
Duplex length 18 base pairs
Protein TN5 TRANSPOSASE, Recombinase, DNA binding domain: Alpha-helix|beta-barrel

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' G101 A102 G103 A104 T105 G106 T107 G108 T109 A110 T111 A112 A113 G114 A115 G116 A117 C118 3'
Strand 2    3' C220 T219 C218 T217 A216 C215 A214 C213 A212 T211 A210 T209 T208 C207 T206 C205 T204 G203 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      

G101 C220            
    2.8 -0.5 0.8 38° -5° -11°
A102 T219            
    3.5 0.5 -0.0 34° -2°
G103 C218            
    2.9 0.1 -0.1 35° -9° -10°
A104 T217            
    3.5 -0.2 -0.4 35° -1° -1°
T105 A216            
    3.6 0.1 0.1 39°
G106 C215            
    3.2 -0.8 -0.7 31° -1° -3°
T107 A214            
    3.2 -0.1 0.6 36°
G108 C213            
    2.7 0.2 0.1 32° -1° -3°
T109 A212            
    3.8 0.3 -0.5 30° 18°
A110 T211            
    2.8 0.1 0.3 33° -1° -7°
T111 A210            
    3.2 0.1 -0.5 27°
A112 T209            
    3.0 0.5 -0.2 27° -3° -1°
A113 T208            
    3.5 -0.8 0.4 40° -3° -3°
G114 C207            
    3.4 0.3 0.1 40° -4°
A115 T206            
    3.7 0.4 -0.2 37°
G116 C205            
    2.6 -0.4 -0.2 23° -2° -8°
A117 T204            
    3.1 0.1 0.2 30°
C118 G203            


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 -114° G101 C220 -66° C3'-exo    
 47°   -85° (BI)             -77° (BI)   41° 
    C3'-exo -94° A102 T219 -101° C2'-endo    
 34°   -108° (BI)             -81° (BI)   -79° 
    C3'-exo -92° G103 C218 -105° C3'-exo    
 162°   -109° (BI)             -56° (BI)   -72° 
    C3'-exo -136° A104 T217 -122° C3'-exo    
 31°   -84° (BI)             -49° (BI)   47° 
    C2'-endo -97° T105 A216 -112° C2'-endo    
 47°   -62° (BI)             -84° (BI)   -79° 
    C3'-exo -113° G106 C215 -117° C3'-exo    
 34°   -100° (BI)             -51° (BI)   38° 
    C3'-exo -104° T107 A214 -80° C2'-endo    
 -59°   -51° (BI)             -60° (BI)   36° 
    C3'-exo -95° G108 C213 -81° C2'-endo    
 -63°   -65° (BI)             -71° (BI)   31° 
    C3'-exo -94° T109 A212 -97° C2'-endo    
 -66°   -61° (BI)             -90° (BI)   -27° 
    C3'-exo -113° A110 T211 -86° C3'-exo    
 35°   -91° (BI)             -36° (BI)   -74° 
    C2'-endo -98° T111 A210 -118° C3'-exo    
 -55°   -58° (BI)             -56° (BI)   -47° 
    C3'-exo -101° A112 T209 -98° C3'-exo    
 35°   -93° (BI)             -72° (BI)   -60° 
    C2'-endo -89° A113 T208 -106° C3'-exo    
 52°   11° (BI)             -49° (BI)   52° 
    C2'-endo -111° G114 C207 -114° C2'-endo    
 -52°   -48° (BI)             -87° (BI)   47° 
    C3'-exo -104° A115 T206 -115° C2'-endo    
 -66°   -79° (BI)             -49° (BI)   168° 
    C3'-exo -111° G116 C205 -136° C2'-endo    
 16°   -86° (BI)             -125° (BI)   -44° 
    C2'-endo -96° A117 T204 -106° C3'-exo    
 45°   -52° (BI)             -44° (BI)   150° 
    C2'-endo -86° C118 G203 -130° C2'-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