IMB Jena Image Library of Biological Macromolecules (Last update: November 15, 2004) ----------------------------------------------------------------- Comprehensive Bending Classification of Nucleic Acid Double Helix Structures ----------------------------------------------------------------- Table 1a: Structures for which helical axis is best described by a straight line. Sigma2 of the straight line is significantly 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: 177 PDB NDB bp molecule method s(2) type 1qaa ------ 20 prot-nuc model 0.000 1uqd ------ 6 nuc NMR 0.027 251d bdf068 6 nuc diff 0.048 1bce ------ 6 nuc NMR 0.049 1uqa ------ 6 nuc NMR 0.050 377d arf0108 6 nuc diff 0.055 1pbm ------ 6 nuc NMR 0.056 1n0o ------ 6 nuc NMR 0.062 1kfv pd0277 6 prot-nuc diff 0.067 282d ddf069 6 nuc diff 0.073 310d arfs26 6 nuc diff 0.081 224d ddf052 6 nuc diff 0.089 1buf ------ 6 nuc NMR 0.091 1uqb ------ 6 nuc NMR 0.091 1bcb ------ 6 nuc NMR 0.098 1lww pd0322 7 prot-nuc diff 0.103 1d21 ddfa14 6 nuc diff 0.105 1d17 ddfa16 6 nuc diff 0.107 1m5r pd0334 6 prot-nuc diff 0.108 1gj1 ------ 6 nuc NMR 0.112 275d adfb63 6 nuc diff 0.116 1zqa pde027 7 prot-nuc diff 0.120 245d ddf063 6 nuc diff 0.120 1d1u pd0152 6 prot-nuc diff 0.125 1k9g dd0047 6 nuc diff 0.126 1ixy pd0333 6 prot-nuc diff 0.127 1l2b pd0294 6 prot-nuc diff 0.128 1f6c bd0040 6 nuc diff 0.136 1f69 bd0039 6 nuc diff 0.142 1d22 ddfa15 6 nuc diff 0.143 1lwv pd0321 7 prot-nuc diff 0.145 254d adfb62 6 nuc diff 0.145 1uqg ------ 6 nuc NMR 0.146 1i7j ar0031 6 nuc diff 0.147 1ih3 ad0022 6 nuc diff 0.147 1p25 bd0064 6 nuc diff 0.150 7icr pde060 6 prot-nuc diff 0.152 9ick pde0100 6 prot-nuc diff 0.153 7ick pde053 6 prot-nuc diff 0.154 1pbl ------ 6 nuc NMR 0.155 1uqf ------ 6 nuc NMR 0.162 1g00 ad0010 6 nuc diff 0.163 182d ddf049 6 nuc diff 0.164 1p26 bd0065 6 nuc diff 0.164 7ics pde061 6 prot-nuc diff 0.167 1l3z ar0040 6 nuc diff 0.169 256d adfb72 6 nuc diff 0.170 1m0e pd0327 6 prot-nuc diff 0.174 366d ddf073 6 nuc diff 0.176 1mtg ------ 6 nuc NMR 0.179 146d ------ 6 nuc NMR 0.180 7icn pde056 6 prot-nuc diff 0.181 9icl pde0101 6 prot-nuc diff 0.183 9icm pde0102 6 prot-nuc diff 0.183 1l1z pd0293 6 prot-nuc diff 0.185 7icg pde049 6 prot-nuc diff 0.187 1ih1 bd0050 6 nuc diff 0.189 1s9b bd0069 6 nuc diff 0.194 9ico pde0104 6 prot-nuc diff 0.195 1dl8 dd0023 6 nuc diff 0.196 9icp pde0105 6 prot-nuc diff 0.198 1n3a pd0355 7 prot-nuc diff 0.200 1i6j pd0202 6 prot-nuc diff 0.206 1k82 pd0264 6 prot-nuc diff 0.209 7icp pde058 6 prot-nuc diff 0.211 9icu pde0110 6 prot-nuc diff 0.212 1n3c pd0356 7 prot-nuc diff 0.214 1uqe ------ 6 nuc NMR 0.216 9icn pde0103 6 prot-nuc diff 0.216 28dn adh023 8 nuc diff 0.218 7icm pde055 6 prot-nuc diff 0.221 9icq pde0106 6 prot-nuc diff 0.222 9icx pde0113 6 prot-nuc diff 0.222 452d dd0012 6 nuc diff 0.224 1lwy pd0323 7 prot-nuc diff 0.226 1g5k ------ 6 nuc NMR 0.231 1ih4 ad0023 6 nuc diff 0.234 465d dd0015 6 nuc diff 0.234 367d ddf074 6 nuc diff 0.235 7ict pde062 6 prot-nuc diff 0.235 7icl pde054 6 prot-nuc diff 0.242 1qch ------ 6 nuc NMR 0.243 5ana adh024 8 nuc diff 0.245 1l1t pd0292 6 prot-nuc diff 0.247 1d37 ddf028 6 nuc diff 0.248 7ice pde047 6 prot-nuc diff 0.251 1ih2 ad0021 6 nuc diff 0.259 1d3r bd0017 6 nuc diff 0.263 7ico pde057 6 prot-nuc diff 0.263 1cx3 ------ 6 nuc NMR 0.264 9icw pde0112 6 prot-nuc diff 0.265 7icq pde059 6 prot-nuc diff 0.269 1kci dd0048 6 nuc diff 0.271 1em0 dd0027 6 nuc diff 0.276 1k2k ------ 6 nuc NMR 0.276 234d ddf054 6 nuc diff 0.277 9ict pde0109 6 prot-nuc diff 0.284 9icr pde0107 6 prot-nuc diff 0.285 1n39 pd0357 7 prot-nuc diff 0.288 1lyr ------ 7 prot-nuc model 0.297 1k2j ------ 6 nuc NMR 0.303 206d bdf062 6 nuc diff 0.303 385d ddf078 6 nuc diff 0.305 1uqc ------ 6 nuc NMR 0.311 7ici pde051 6 prot-nuc diff 0.315 1q2r pr0101 6 prot-nuc diff 0.319 1d97 bdfp24 6 nuc diff 0.320 235d ddf055 6 nuc diff 0.324 1zqd pde030 7 prot-nuc diff 0.325 1agl ddf072 6 nuc diff 0.327 198d ddf050 6 nuc diff 0.329 9ics pde0108 6 prot-nuc diff 0.342 1q2s pr0102 6 prot-nuc diff 0.343 288d ddf065 6 nuc diff 0.344 7icj pde052 6 prot-nuc diff 0.353 1d36 ddf026 6 nuc diff 0.354 258d ddf064 6 nuc diff 0.355 1c9z dd0018 6 nuc diff 0.359 236d ddf056 6 nuc diff 0.361 7icv pde088 6 prot-nuc diff 0.361 1d67 ddf038 6 nuc diff 0.366 1ih6 ad0024 6 nuc diff 0.366 1x95 ------ 6 nuc NMR 0.369 1imr ddf061 6 nuc diff 0.370 1p24 bd0063 6 nuc diff 0.371 276d ddf066 6 nuc diff 0.372 386d ddf079 6 nuc diff 0.374 1msw pd0345 6 prot-nuc diff 0.379 2d34 ddfb24 6 nuc diff 0.381 2bpf pde011 7 prot-nuc diff 0.384 7icf pde048 6 prot-nuc diff 0.385 152d ddf045 6 nuc diff 0.391 1ims ddf062 6 nuc diff 0.393 1d11 ddf001 6 nuc diff 0.395 1d12 ddf019 6 nuc diff 0.405 1d15 ddf022 6 nuc diff 0.407 1d10 ddf020 6 nuc diff 0.422 151d ddf044 6 nuc diff 0.430 7ich pde050 6 prot-nuc diff 0.433 1p20 dd0056 6 nuc diff 0.434 1d38 ddf029 6 nuc diff 0.442 257d adf073 6 nuc diff 0.445 482d dd0017 6 nuc diff 0.446 215d ddf053 6 nuc diff 0.453 1d33 ddf023 6 nuc diff 0.455 1d35 ddfb25 6 nuc diff 0.455 1d58 ddf036 6 nuc diff 0.467 185d ------ 6 nuc NMR 0.470 7icu pde063 6 prot-nuc diff 0.472 332d ahh089 6 nuc diff 0.475 1d14 ddfp21 6 nuc diff 0.486 1ao1 ------ 6 nuc NMR 0.494 1p51 pd0426 6 prot-nuc diff 0.503 203d ------ 8 nuc NMR 0.506 1oup pd0403 8 prot-nuc diff 0.514 380d ddfb76 6 nuc diff 0.531 2des ddf041 6 nuc diff 0.557 308d ddfb70 6 nuc diff 0.590 1cp8 ------ 8 nuc NMR 0.631 1d54 ddf035 6 nuc diff 0.634 1da0 ddf018 6 nuc diff 0.639 278d ddf068 6 nuc diff 0.663 110d ddf039 6 nuc diff 0.676 418d dr0001 6 nuc diff 0.729 277d ddf067 6 nuc diff 0.776 343d adfb97 6 nuc diff 0.778 1vaq dd0063 8 nuc diff 0.821 2da8 ------ 6 nuc NMR 0.855 1l2d pd0296 6 prot-nuc diff 0.859 1da9 ddf040 6 nuc diff 0.865 1qda dd0022 6 nuc diff 0.886 1nab dd0054 6 nuc diff 0.887 1n0k ------ 6 nuc NMR 0.897 1eki ------ 8 nuc NMR 0.962 1i5v ------ 6 nuc NMR 1.326 1j7t dr0006 6 nuc diff 1.360 1l2c pd0295 6 prot-nuc diff 1.543 -------------------------------------------------------------------------- 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)