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Bending of the helical axis

Title D34G MUTANT OF PVUII ENDONUCLEASE COMPLEXED WITH COGNATE DNA SHOWS THAT ASP34 IS DIRECTLY INVOLVED IN DNA RECOGNITION AND INDIRECTLY INVOLVED IN CATALYSIS
PDB code 3PVI   (PDB summary)
NDB code PD0006 (NDB atlas)
Duplex length 12 base pairs
Protein Restriction endonuclease PvuII, Nuclease

Table 1.   Bending parameters determined with the program ARC_FIT.  
The curvilinear helical axis is calculated with CURVES, and bending of this axis is analysed with ARC_FIT. This program allows to fit a straight line, a plane, an arc, a kinked line, and a double kinked line to the helical axis. Good fits are indicated by low values of sigma2. An arc is fitted if there are at least 7 bp. A kinked line requires at least 8 bp, and the double kinked line requires at least 13 bp. The geometrical parameters are given for all models fitted, but they characterize the shape of the helical axis only if the fit is good. See Help for further explanations.

 Model      sigma2 / Å2   Geometrical parameters 
 Plane  0.143  
 Straight line (x-axis) 1.207  
 Arc  0.976 Radius of curvature:  r = 127 Å
 Kinked line  0.870 Kink angle:  alpha = 12°
 Lengths of straight segments:  l1 = 7 bp,  l2 = 5 bp