IMB Jena Image Library of Biological Macromolecules (Last update: November 15, 2004) ----------------------------------------------------------------- Comprehensive Bending Classification of Nucleic Acid Double Helix Structures ----------------------------------------------------------------- Table 2b: Structures for which the helical axis is best described by a straight line. Sigma2 of the straight line is only slightly smaller (<0.2) than for the next-best model(s). The structures are listed by the goodness of fit sigma2(straight line) s(2)). Number of structures: 136 PDB NDB bp molecule method helical s(2) r a/a1 a2 o l1 l2 l3 type axes shape 1axp ------ 10 nuc NMR straight 0.004 circular 0.006 >1000 single-kink 0.007 1 6 3 1dns adh014 8 nuc diff straight 0.008 circular 0.016 >1000 single-kink 0.018 3 2 6 1g80 ------ 8 nuc NMR straight 0.014 circular 0.028 >1000 single-kink 0.048 3 1 7 189d adh058 8 nuc diff straight 0.026 circular 0.052 >1000 single-kink 0.086 2 3 5 1d82 adh041 8 nuc diff straight 0.031 circular 0.063 >1000 single-kink 0.099 4 2 6 1rrr ------ 10 nuc NMR straight 0.031 circular 0.038 439 single-kink 0.040 6 2 8 1d26 adhp36 8 nuc diff straight 0.034 circular 0.068 >1000 single-kink 0.117 2 2 5 274d gdjb29 10 nuc diff straight 0.034 circular 0.051 >1000 single-kink 0.056 2 7 2 295d adh033 8 nuc diff straight 0.034 circular 0.055 347 single-kink 0.098 2 3 4 375d gdj059 10 nuc diff straight 0.037 circular 0.050 848 single-kink 0.062 1 4 5 169d ------ 10 nuc NMR straight 0.044 single-kink 0.045 88 9 1 circular 0.064 883 476d bd0018 10 nuc diff straight 0.046 circular 0.059 618 single-kink 0.061 3 3 6 1ehv bd0032 10 nuc diff straight 0.048 circular 0.050 413 single-kink 0.066 3 3 7 345d adhb100 8 nuc diff straight 0.049 circular 0.097 >1000 single-kink 0.168 3 6 2 307d bdj081 10 nuc diff straight 0.050 single-kink 0.057 3 3 6 circular 0.061 508 338d adhb92 8 nuc diff straight 0.051 circular 0.102 >1000 single-kink 0.180 3 6 2 341d adhb95 8 nuc diff straight 0.051 circular 0.103 >1000 single-kink 0.171 4 6 2 118d adh047 8 nuc diff straight 0.052 circular 0.105 >1000 single-kink 0.113 4 4 3 1but ------ 8 nuc NMR straight 0.055 circular 0.056 184 single-kink 0.062 8 2 6 187d adh056 8 nuc diff straight 0.057 circular 0.061 200 single-kink 0.124 4 5 3 340d adhb94 8 nuc diff straight 0.058 circular 0.116 >1000 single-kink 0.201 3 6 2 8icn pde075 7 prot-nuc diff straight 0.059 circular 0.084 166 1zqk pde037 7 prot-nuc diff straight 0.060 circular 0.180 >1000 1o3z ar0046 7 nuc diff straight 0.067 circular 0.154 143 8drh ------ 8 nuc NMR straight 0.067 circular 0.108 226 single-kink 0.171 5 6 2 8ich pde069 7 prot-nuc diff straight 0.068 circular 0.118 173 8ics pde080 7 prot-nuc diff straight 0.069 circular 0.134 198 252d bdj069 10 nuc diff straight 0.070 circular 0.094 640 single-kink 0.101 3 6 3 1k2z dd0046 8 nuc diff straight 0.071 circular 0.119 353 single-kink 0.204 4 2 6 2d94 adh026 8 nuc diff straight 0.074 circular 0.148 >1000 single-kink 0.197 4 4 3 250d bdh071 8 nuc diff straight 0.079 circular 0.144 497 single-kink 0.236 4 5 2 1h38 ------ 8 prot-nuc diff straight 0.080 circular 0.148 351 single-kink 0.267 3 4 4 339d adhb93 8 nuc diff straight 0.080 circular 0.160 >1000 single-kink 0.262 5 2 6 382d adj0109 10 nuc diff straight 0.080 circular 0.094 250 single-kink 0.109 6 2 7 1k4s pd0255 10 prot-nuc diff straight 0.081 circular 0.103 464 single-kink 0.153 2 3 7 342d adhb96 8 nuc diff straight 0.082 circular 0.163 >1000 single-kink 0.251 5 2 6 346d adhb101 8 nuc diff straight 0.084 circular 0.169 >1000 single-kink 0.263 5 6 2 8icz pde087 7 prot-nuc diff straight 0.086 circular 0.157 167 8icv pde083 7 prot-nuc diff straight 0.096 circular 0.167 140 1mwg ------ 8 nuc NMR straight 0.097 circular 0.193 >1000 1lai ------ 13 nuc NMR straight 0.101 double-kink 0.107 6 10 173 3 8 2 single-kink 0.122 5 2 11 circular 0.130 >1000 4bna bdlb04 12 nuc diff straight 0.103 single-kink 0.118 5 2 9 circular 0.127 830 1jtl dd0042 8 nuc diff straight 0.104 circular 0.128 182 single-kink 0.221 6 3 5 9ica pde091 7 prot-nuc diff straight 0.105 circular 0.145 130 337d adhb91 8 nuc diff straight 0.107 circular 0.214 >1000 3orc pd0022 8 prot-nuc diff straight 0.108 circular 0.126 171 single-kink 0.192 5 4 4 1d19 ------ 8 nuc NMR straight 0.109 circular 0.200 335 single-kink 0.303 5 2 5 9icj pde099 7 prot-nuc diff straight 0.109 circular 0.116 111 9icy pde0114 7 prot-nuc diff straight 0.109 circular 0.118 111 8icj pde071 7 prot-nuc diff straight 0.110 circular 0.172 127 8icp pde077 7 prot-nuc diff straight 0.113 circular 0.214 141 1nxr ------ 8 nuc NMR straight 0.121 circular 0.174 127 single-kink 0.291 9 2 6 1rrd ------ 10 nuc NMR straight 0.126 single-kink 0.153 7 2 7 circular 0.156 272 1gm5 pd0267 9 prot-nuc diff straight 0.127 circular 0.192 353 single-kink 0.245 5 3 6 8ice pde066 7 prot-nuc diff straight 0.128 circular 0.235 128 8icm pde074 7 prot-nuc diff straight 0.128 circular 0.150 107 8icr pde079 7 prot-nuc diff straight 0.128 circular 0.176 108 1da3 bdjb48 10 nuc diff straight 0.129 circular 0.145 289 single-kink 0.179 4 6 4 1huz pd0197 8 prot-nuc diff straight 0.129 circular 0.167 158 1zqp pde042 7 prot-nuc diff straight 0.129 circular 0.250 139 9dna adh008 8 nuc diff straight 0.129 circular 0.131 121 single-kink 0.244 6 4 4 8icu pde082 7 prot-nuc diff straight 0.137 circular 0.178 106 1qps pd0055 12 prot-nuc diff straight 0.143 circular 0.191 >1000 single-kink 0.223 3 2 10 8ico pde076 7 prot-nuc diff straight 0.145 circular 0.167 100 1lc4 dr0007 8 nuc diff straight 0.158 circular 0.262 152 1cw9 bd0021 10 nuc diff straight 0.159 circular 0.180 279 single-kink 0.221 4 4 5 8icc pde065 7 prot-nuc diff straight 0.161 circular 0.240 104 425d bd0003 12 nuc diff straight 0.162 single-kink 0.177 9 10 2 circular 0.188 624 1d02 pd0151 10 prot-nuc diff straight 0.163 circular 0.239 936 single-kink 0.289 2 4 5 1eri pde001 12 prot-nuc diff straight 0.163 circular 0.217 >1000 single-kink 0.260 1 12 0 1zql pde038 7 prot-nuc diff straight 0.163 circular 0.214 99 1bhm pde020 10 prot-nuc diff straight 0.164 circular 0.214 381 single-kink 0.248 4 4 5 8icq pde078 7 prot-nuc diff straight 0.164 circular 0.188 94 3dnb bdj008 10 nuc diff straight 0.168 circular 0.252 >1000 single-kink 0.289 90 9 1 1gau ------ 8 prot-nuc NMR straight 0.169 circular 0.214 141 single-kink 0.264 8 3 5 8icy pde086 7 prot-nuc diff straight 0.172 circular 0.240 96 8icw pde084 7 prot-nuc diff straight 0.174 circular 0.235 96 1zqi pde035 7 prot-nuc diff straight 0.181 circular 0.325 111 424d bd0002 12 nuc diff straight 0.181 circular 0.195 394 single-kink 0.200 5 8 4 1ene bd0036 10 nuc diff straight 0.186 single-kink 0.268 11 8 2 circular 0.279 >1000 1enn bd0037 8 nuc diff straight 0.186 circular 0.301 193 157d arl048 12 nuc diff straight 0.187 circular 0.194 230 single-kink 0.194 7 3 8 1lej ------ 13 nuc NMR straight 0.191 single-kink 0.203 8 10 2 double-kink 0.213 90 104 -173 10 1 2 circular 0.222 569 423d bd0001 12 nuc diff straight 0.191 circular 0.215 414 single-kink 0.294 2 3 8 1zqf pde032 7 prot-nuc diff straight 0.197 circular 0.373 110 8icb pde064 7 prot-nuc diff straight 0.198 circular 0.335 99 1dsd ------ 8 prot-nuc NMR straight 0.200 circular 0.219 140 472d ar0022 8 nuc diff straight 0.205 circular 0.258 79 single-kink 0.345 10 3 5 1en9 bd0035 10 nuc diff straight 0.206 single-kink 0.298 4 4 5 circular 0.309 >1000 435d ar0010 7 nuc diff straight 0.206 circular 0.262 64 1aay pdt039 10 prot-nuc diff straight 0.209 circular 0.210 188 single-kink 0.230 6 5 4 1bd1 bdj017 10 nuc diff straight 0.210 single-kink 0.299 12 8 2 circular 0.316 >1000 1ckq pd0049 12 prot-nuc diff straight 0.216 circular 0.263 593 single-kink 0.300 3 6 6 1eka ------ 8 nuc NMR straight 0.218 circular 0.373 176 183d bdjb57 10 nuc diff straight 0.222 single-kink 0.311 13 1 9 circular 0.333 >1000 1d62 bd0055 10 nuc diff straight 0.223 single-kink 0.331 27 1 9 circular 0.335 >1000 8ica pde089 7 prot-nuc diff straight 0.224 circular 0.237 78 1zqb pde028 7 prot-nuc diff straight 0.236 circular 0.322 83 1hu0 pd0195 7 prot-nuc diff straight 0.238 circular 0.435 92 1ku7 pd0284 10 prot-nuc diff straight 0.238 circular 0.328 343 single-kink 0.349 10 8 2 1zqj pde036 7 prot-nuc diff straight 0.239 circular 0.298 76 209d ddh051 8 nuc diff straight 0.242 circular 0.272 148 1zqn pde040 7 prot-nuc diff straight 0.245 circular 0.399 86 1cl8 pd0054 12 prot-nuc diff straight 0.247 circular 0.328 >1000 single-kink 0.387 1 6 5 1qri pd0063 12 prot-nuc diff straight 0.247 circular 0.329 >1000 single-kink 0.334 3 7 4 1nfk pdt015 10 prot-nuc diff straight 0.255 circular 0.299 223 single-kink 0.303 7 3 7 371d adh0105 8 nuc diff straight 0.255 circular 0.279 79 single-kink 0.344 12 5 3 1zqt pde046 7 prot-nuc diff straight 0.256 circular 0.328 81 1nnj pd0389 7 prot-nuc diff straight 0.259 circular 0.370 79 1zqg pde033 7 prot-nuc diff straight 0.259 circular 0.392 83 473d dd0016 8 nuc diff straight 0.259 circular 0.419 155 1zqo pde041 7 prot-nuc diff straight 0.261 circular 0.293 75 2bam pd0029 10 prot-nuc diff straight 0.275 circular 0.353 269 single-kink 0.457 4 4 6 1di2 pr0020 10 prot-nuc diff straight 0.277 circular 0.362 209 single-kink 0.376 11 8 2 1d0e pd0135 8 prot-nuc diff straight 0.285 single-kink 0.287 13 3 5 circular 0.306 93 318d adjb79 10 nuc diff straight 0.289 circular 0.433 >1000 single-kink 0.461 10 8 2 1zqs pde045 7 prot-nuc diff straight 0.293 circular 0.385 74 1drn ------ 9 nuc NMR straight 0.302 circular 0.313 129 single-kink 0.490 7 3 6 1p78 pd0431 7 prot-nuc diff straight 0.304 circular 0.414 70 325d adjb86 10 nuc diff straight 0.318 circular 0.478 >1000 1p71 pd0430 7 prot-nuc diff straight 0.325 circular 0.463 71 1zqr pde044 7 prot-nuc diff straight 0.335 circular 0.429 68 123d bdjb50 10 nuc diff straight 0.343 circular 0.394 198 single-kink 0.403 10 7 3 1zqc pde029 7 prot-nuc diff straight 0.344 circular 0.347 64 1mwl dr0008 8 nuc diff straight 0.359 circular 0.382 62 5dnb bdj019 10 nuc diff straight 0.359 single-kink 0.511 16 2 8 circular 0.538 >1000 122d bdjb49 10 nuc diff straight 0.368 single-kink 0.400 13 8 2 circular 0.418 188 108d ------ 8 nuc NMR straight 0.381 circular 0.451 140 single-kink 0.492 15 6 2 1en3 bd0033 10 nuc diff straight 0.391 single-kink 0.558 16 8 2 circular 0.587 >1000 158d bdj052 10 nuc diff straight 0.394 single-kink 0.519 14 8 2 circular 0.527 269 1cqo ------ 10 nuc NMR straight 0.395 circular 0.487 197 single-kink 0.496 14 8 2 1d61 bdjb44 10 nuc diff straight 0.418 single-kink 0.609 16 8 2 322d adjb83 10 nuc diff straight 0.615 circular 0.695 107 single-kink 0.769 12 3 7 1gd2 pd0180 12 prot-nuc diff straight 0.650 circular 0.690 200 single-kink 0.727 11 3 9 1dsc ------ 8 prot-nuc NMR straight 0.749 circular 0.822 65 315d ahh077 8 nuc diff straight 0.836 circular 1.008 52 -------------------------------------------------------------------------- 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)