IMB Jena Image Library of Biological Macromolecules (Last update: November 15, 2004) ----------------------------------------------------------------- Comprehensive Bending Classification of Nucleic Acid Double Helix Structures Strong bending (M > 45 °) Classification II (double-kink: M = max(a1, a2)) ----------------------------------------------------------------- Number of structures: 53 + 20 PDB NDB bp molecule method helical s(2) r a/a2 a2 a1+a2 M type axis shape 1azq pdr048 8 prot-nuc diff single-kink 0.364 46 46 1jh9 pd0226 16 prot-nuc diff single-kink*0.369 46 46 1rvb pde015 10 prot-nuc diff single-kink 0.217 46 46 2puc pdr042 16 prot-nuc diff single-kink 0.442 46 46 2pud pdr046 16 prot-nuc diff single-kink 0.470 46 46 1cw0 pd0100 12 prot-nuc diff single-kink 0.508 47 47 1icg ah0015 8 nuc diff single-kink 1.101 47 47 1id9 ah0016 8 nuc diff single-kink 1.296 47 47 1ruo pdr025 30 prot-nuc diff double-kink 1.164 46 47 93 47 2pub pdr041 16 prot-nuc diff single-kink 0.455 47 47 1cgp pdr006 30 prot-nuc diff double-kink 0.389 48 44 92 48 1ic8 pd0208 21 prot-nuc diff double-kink 0.737 18 48 66 48 1j5n ------ 15 prot-nuc NMR single-kink 0.419 48 48 1qrv pd0110 9 prot-nuc diff single-kink 0.412 48 48 1run pdr024 30 prot-nuc diff double-kink 0.527 48 42 90 48 2kbd ------ 16 nuc NMR double-kink 0.231 30 48 78 48 1ais pdr031 17 prot-nuc diff double-kink 0.617 49 29 78 49 1iha ah0018 8 nuc diff single-kink 0.993 49 49 1qne pd0163 14 prot-nuc diff double-kink 0.376 49 37 86 49 1b95 pd0038 10 prot-nuc diff single-kink 0.307 50 50 1bsu pde0145 10 prot-nuc diff single-kink 0.050 50 50 1eon pd0131 10 prot-nuc diff single-kink 0.238 50 50 1idw ah0017 8 nuc diff single-kink 1.023 50 50 1ub8 ud0027 7 nuc diff circular 1.997 15 50 1eo4 pd0130 9 prot-nuc diff single-kink 0.342 51 51 1l1m ------ 23 prot-nuc NMR double-kink 0.217 51 41 92 51 399d adl047 12 nuc diff single-kink 1.203 51 51 1bgb pd0010 10 prot-nuc diff single-kink 0.340 52 52 1iaw pd0207 16 prot-nuc diff double-kink 0.590 52 21 73 52 1lwt pd0320 36 prot-nuc diff double-kink 1.483 52 19 71 52 1b94 pd0037 10 prot-nuc diff single-kink 0.190 53 53 1b96 pd0039 10 prot-nuc diff single-kink 0.211 53 53 422d ar0007 8 nuc diff single-kink 1.338 53 53 1b97 pd0040 10 prot-nuc diff single-kink 0.272 54 54 1gt0 ------ 23 prot-nuc diff double-kink 0.821 55 17 72 55 1au5 ------ 8 nuc NMR single-kink 0.833 56 56 1cdw pdt034 16 prot-nuc diff double-kink 0.533 56 48 104 56 1lws pd0319 34 prot-nuc diff double-kink 1.163 56 17 73 56 1eoo pd0132 12 prot-nuc diff single-kink 0.235 57 57 1hbx pd0233 25 prot-nuc diff single-kink 1.881 57 57 1k6o pd0258 23 prot-nuc diff double-kink 1.853 21 57 78 57 1ngm pd0368 19 prot-nuc diff double-kink 0.573 57 38 95 57 4rve pde003 10 prot-nuc diff single-kink 0.503 57 57 1d3u pd0070 23 prot-nuc diff double-kink 0.683 58 44 102 58 1eo3 pd0129 9 prot-nuc diff single-kink 0.184 58 58 1ipp pde0144 20 prot-nuc diff double-kink 0.311 62 12 74 62 1oh8 ------ 10 prot-nuc diff single-kink 1.397 63 63 1owf pd0406 20 prot-nuc diff double-kink 0.579 24 65 89 65 1ouz pd0405 20 prot-nuc diff double-kink 0.574 25 67 92 67 1owg pd0407 20 prot-nuc diff double-kink 0.468 28 67 95 67 1e3m pd0201 17 prot-nuc diff single-kink 1.164 70 70 1ng9 pd0367 17 prot-nuc diff single-kink 1.020 71 71 1a84 ------ 12 nuc NMR single-kink 0.852 78 78 The following structures cannot be described by one of the models adopted for the description of the helical axis, like the superhelical structures 1aoi, 1eqz, 1f66 and 1id3, or have goodness-of-fit values larger than 2. The latter duplexes can nevertheless roughly be classified as double-kink structures. This Table includes the most strongly bent structures currently known: 1aoi, 1ihf, 5crx, 4crx. Number of structures: 20 PDB NDB bp molecule method helical s(2) r a/a2 a2 a1+a2 M type axis shape 2d47 adl025 12 nuc diff single-kink 3.186 53 53 1j9h ar0034 9 nuc diff circular 3.280 12 60 1dfu pr0018 15 prot-nuc diff double-kink 3.516 62 31 93 62 1bpz pde0124 16 prot-nuc diff double-kink 2.241 64 32 96 64 1n96 ------ 8 nuc NMR circular 34.159 9 76 1nzb pd0392 36 prot-nuc diff double-kink 4.446 24 78 102 78 4crx pd0047 34 prot-nuc diff double-kink 3.227 24 82 107 82 5crx pd0048 32 prot-nuc diff double-kink 2.926 29 83 111 83 1ihf pdt040 34 prot-nuc diff double-kink 3.423 92 82 174 92 1nyd ------ 9 nuc NMR circular 2.264 3 188 1aoi pd0001 146 prot-nuc diff 1eqz pd0137 146 prot-nuc diff 1f66 pd0171 146 prot-nuc diff 1id3 pd0209 146 prot-nuc diff 1kx3 pd0285 146 prot-nuc diff 1kx4 pd0286 146 prot-nuc diff 1m18 pd0328 146 prot-nuc diff 1m19 pd0329 146 prot-nuc diff 1m1a pd0330 146 prot-nuc diff 1kx5 pd0287 147 prot-nuc diff -------------------------------------------------------------------------- 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)