IMB Jena Image Library of Biological Macromolecules (Last update: November 15, 2004) -------------------------------------------------------------------------- Comprehensive Bending Classification of Nucleic Acid Double Helix Structures Bending classification of helical axis - circular line (arc) -------------------------------------------------------------------------- Table 1b: Structures for which helical axis is best described by a circular line (arc). Sigma2 of a circular line (arc) is significantly smaller (> 0.2) than for the next-best model(s). The structures are listed by the number of base pairs (bp). Number of structures: 56 PDB NDB bp molecule method s(2) r type 1ub8 ud0027 7 nuc diff 1.997 15 466d ar0013 7 nuc diff 0.187 37 8icl pde073 7 prot-nuc diff 0.117 51 9icf pde095 7 prot-nuc diff 0.109 58 9icg pde096 7 prot-nuc diff 0.098 46 9ici pde098 7 prot-nuc diff 0.151 35 159d gdhb25 8 nuc diff 0.211 72 172d adh054 8 nuc diff 0.149 32 173d ddh048 8 nuc diff 0.770 41 1byx ------ 8 nuc NMR 0.426 24 1d18 ------ 8 nuc NMR 0.341 39 1d83 ------ 8 nuc NMR 0.477 30 1ekd ------ 8 nuc NMR 0.876 30 1ekh ------ 8 nuc NMR 1.109 32 1muv ------ 8 nuc NMR 0.265 22 1p3x ------ 8 nuc NMR 0.321 47 1pik ------ 8 nuc NMR 0.198 52 1qaj pd0134 8 prot-nuc diff 0.126 64 1qet ------ 8 nuc NMR 0.517 25 1sa9 ar0048 8 nuc diff 0.552 24 1saq ar0049 8 nuc diff 0.942 25 1yfv ------ 8 nuc NMR 0.357 29 217d ghhb35 8 nuc diff 0.217 57 2d55 ddh037 8 nuc diff 1.207 36 304d gdlb49 8 nuc diff 0.270 66 305d gdlb50 8 nuc diff 0.276 61 306d gdlb51 8 nuc diff 0.181 74 378d gdh060 8 nuc diff 0.217 39 402d ar0001 8 nuc diff 1.463 18 439d ar0012 8 nuc diff 0.374 22 441d ad0004 8 nuc diff 0.153 28 1a34 prv020 9 prot-nuc diff 0.148 19 1dhh ------ 9 nuc NMR 0.222 31 1dn6 adi009 9 nuc diff 0.619 22 1i6h ph0004 9 prot-nuc diff 1.079 31 1kln pde004 9 prot-nuc diff 0.254 40 1ksb ------ 9 nuc NMR 0.201 30 1mnv dd0053 9 prot-nuc diff 0.212 80 1d69 ------ 10 nuc NMR 1.693 32 1lv5 pd0317 10 prot-nuc diff 0.514 54 1njz pd0375 10 prot-nuc diff 0.531 60 1qkg ------ 10 nuc NMR 0.715 22 1snh ------ 10 nuc NMR 0.797 26 213d adjb61 10 nuc diff 0.539 20 321d adj082 10 nuc diff 0.399 21 1cr3 ------ 11 nuc NMR 0.262 44 1dc1 pd0085 11 prot-nuc diff 0.681 79 1n4b ------ 11 nuc NMR 1.847 51 132d ------ 12 nuc NMR 0.138 53 1ig4 ------ 12 prot-nuc NMR 0.150 54 1opq ------ 12 nuc NMR 0.189 69 1pg9 ------ 12 nuc NMR 0.252 54 1tgh pdt024 12 prot-nuc diff 0.476 23 1ytb pdt012 12 prot-nuc diff 0.412 21 1bf5 pdr052 17 prot-nuc diff 0.549 56 1am9 pdt062 38 prot-nuc diff 0.626 141 -------------------------------------------------------------------------- Abbreviations -------------------------------------------------------------------------- PDB Protein Data Bank NDB Nucleic Acid Database bp base pair number diff diffraction model theoretical model NMR nuclear magnetic resonance spectroscopy prot protein nuc nucleic acid prot-nuc protein-nucleic acid complex carb carbohydrate plane plane s(2) goodness of fit r radius of curvature (circular line) a kink angle (single-kink line) a1, a2 kink angles (double-kink line) o twist angle (double-kink line) l1, l2, l3 lenght of segments 1, 2, and 3 measured in bp (double-kink model)