[JenaLib Home] [Helix analysis Home] [JenaLib Entry] [Sequence, Chains, Units] [Helix analysis Entry] [Bending Classification]

Bending of the helical axis

Title		`A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A CYTOS THYMINE MISMATCH AFTER A SINGLE ROUND OF PRIMER EXTENSION, INCORPORATION OF DCTP.`
PDB code		`1NKE (PDB summary)`
NDB code		`PD0385 (NDB atlas)`
Duplex length		`11 base pairs`
Protein		`DNA POLYMERASE I (ANALOGOUS TO THE E. COLI KLENOW FRAGMENT), Polymerase, DNA binding domain: Alpha-helix\|beta-barrel`

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	0.147
Straight line (x-axis)	1.304
Arc	0.278	Radius of curvature: r = 58 Å
Kinked line	0.339	Kink angle: alpha = 19° Lengths of straight segments: l₁ = 5 bp, l₂ = 6 bp