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 I (double-kink: M = a1 + a2) ----------------------------------------------------------------- Number of structures: 114 + 22 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 1j46 ------ 14 prot-nuc NMR double-kink 0.278 13 34 47 47 1j59 pd0299 13 prot-nuc diff double-kink 0.372 15 32 47 47 1l3l pd0298 20 prot-nuc diff double-kink 0.236 19 28 47 47 1mm8 pd0340 18 prot-nuc diff double-kink 0.261 31 16 47 47 1mus pd0350 18 prot-nuc diff double-kink 0.209 29 18 47 47 1nk3 ------ 14 prot-nuc NMR double-kink 0.446 28 19 47 47 1zme pdt044 16 prot-nuc diff double-kink 0.408 26 21 47 47 2pub pdr041 16 prot-nuc diff single-kink 0.455 47 47 1an4 pdt027 20 prot-nuc diff double-kink 1.782 25 23 48 48 1dp7 pd0111 16 prot-nuc diff double-kink 0.366 24 24 48 48 1j5n ------ 15 prot-nuc NMR single-kink 0.419 48 48 1muh pd0347 18 prot-nuc diff double-kink 0.212 29 19 48 48 1o3t pd0401 13 prot-nuc diff double-kink 0.306 36 12 48 48 1qrv pd0110 9 prot-nuc diff single-kink 0.412 48 48 1b3t pd0024 18 prot-nuc diff double-kink 0.196 25 24 49 49 1iha ah0018 8 nuc diff single-kink 0.993 49 49 1j5o pd0316 18 prot-nuc diff double-kink 0.807 31 18 49 49 1k3w pd0253 18 prot-nuc diff double-kink 0.218 19 30 49 49 1mur pd0349 18 prot-nuc diff double-kink 0.218 19 30 49 49 1rcs ------ 20 prot-nuc NMR double-kink 0.148 20 29 49 49 1ysa pdt002 16 prot-nuc diff double-kink 0.385 16 33 49 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 1g9y pd0189 24 prot-nuc diff double-kink 0.702 28 22 50 50 1idw ah0017 8 nuc diff single-kink 1.023 50 50 1lb2 pd0306 20 prot-nuc diff double-kink 0.191 19 31 50 50 1ub8 ud0027 7 nuc diff circular 1.997 15 50 1eo4 pd0130 9 prot-nuc diff single-kink 0.342 51 51 1hlv pd0192 21 prot-nuc diff double-kink 0.237 16 35 51 51 1rpd ------ 42 prot-nuc model double-kink 1.081 24 27 51 51 399d adl047 12 nuc diff single-kink 1.203 51 51 1bgb pd0010 10 prot-nuc diff single-kink 0.340 52 52 2bop pdv001 16 prot-nuc diff double-kink 0.505 26 26 52 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 1c7u ------ 20 prot-nuc NMR double-kink 0.524 27 27 54 54 1co0 ------ 20 prot-nuc NMR double-kink 0.772 16 38 54 54 2stt ------ 17 prot-nuc NMR double-kink 0.722 17 37 54 54 4kbd ------ 16 nuc NMR double-kink 0.298 21 34 55 55 1au5 ------ 8 nuc NMR single-kink 0.833 56 56 1bl0 pdr056 22 prot-nuc diff double-kink 0.428 29 27 56 56 1fok pde0127 19 prot-nuc diff double-kink 0.483 28 28 56 56 1ir5 ------ 17 nuc NMR double-kink 0.598 35 21 56 56 1eoo pd0132 12 prot-nuc diff single-kink 0.235 57 57 1exj pd0146 21 prot-nuc diff double-kink 0.605 16 41 57 57 1hbx pd0233 25 prot-nuc diff single-kink 1.881 57 57 4rve pde003 10 prot-nuc diff single-kink 0.503 57 57 1akh pdr049 19 prot-nuc diff double-kink 0.289 20 38 58 58 1c0w pd0069 21 prot-nuc diff double-kink 1.309 30 28 58 58 1eo3 pd0129 9 prot-nuc diff single-kink 0.184 58 58 1kfo ar0039 18 nuc diff double-kink 0.135 29 29 58 58 1nk2 ------ 16 prot-nuc NMR double-kink 0.646 32 27 59 59 1efa pd0118 17 prot-nuc diff double-kink 0.465 40 20 60 60 1le8 pd0308 19 prot-nuc diff double-kink 0.366 30 31 61 61 433d ar0008 14 nuc diff double-kink 0.488 31 30 61 61 1ckt pd0051 16 prot-nuc diff double-kink 0.240 24 38 62 62 1yrn pdt028 18 prot-nuc diff double-kink 0.339 29 33 62 62 1ytf pdt036 16 prot-nuc diff double-kink 0.204 22 40 62 62 1a73 pd0002 20 prot-nuc diff double-kink 0.238 33 30 63 63 1je8 pd0219 20 prot-nuc diff double-kink 0.138 32 31 63 63 1nh2 pd0369 16 prot-nuc diff double-kink 0.161 25 38 63 63 1oh8 ------ 10 prot-nuc diff single-kink 1.397 63 63 1ouq pd0404 21 prot-nuc diff double-kink 0.663 35 28 63 63 1a74 pde140 20 prot-nuc diff double-kink 0.237 33 31 64 64 1mnm pdr036 25 prot-nuc diff double-kink 1.552 40 24 64 64 1cz0 pd0097 20 prot-nuc diff double-kink 0.259 34 31 65 65 1jj4 pd0227 16 prot-nuc diff double-kink 0.518 32 33 65 65 1cyq pd0096 20 prot-nuc diff double-kink 0.291 35 31 66 66 1ic8 pd0208 21 prot-nuc diff double-kink 0.737 18 48 66 66 1tc3 pde0128 19 prot-nuc diff double-kink 0.407 34 32 66 66 1ewq pd0142 21 prot-nuc diff double-kink 0.660 27 40 67 67 2lef ------ 15 prot-nuc NMR double-kink 0.407 37 30 67 67 1e3m pd0201 17 prot-nuc diff single-kink 1.164 70 70 1jwl pd0250 14 prot-nuc diff double-kink 0.786 40 31 71 71 1lwt pd0320 36 prot-nuc diff double-kink 1.483 52 19 71 71 1ng9 pd0367 17 prot-nuc diff single-kink 1.020 71 71 1gt0 ------ 23 prot-nuc diff double-kink 0.821 55 17 72 72 2gli pdt008 20 prot-nuc diff double-kink 1.264 31 41 72 72 1iaw pd0207 16 prot-nuc diff double-kink 0.590 52 21 73 73 1lws pd0319 34 prot-nuc diff double-kink 1.163 56 17 73 73 1qn4 pd0154 14 prot-nuc diff double-kink 0.307 41 32 73 73 1ipp pde0144 20 prot-nuc diff double-kink 0.311 62 12 74 74 2cgp pdt049 26 prot-nuc diff double-kink 0.153 37 37 74 74 1gdt pde0115 34 prot-nuc diff double-kink 0.588 44 31 75 75 1n14 ------ 13 nuc NMR double-kink 0.990 37 38 75 75 1a84 ------ 12 nuc NMR single-kink 0.852 78 78 1ais pdr031 17 prot-nuc diff double-kink 0.617 49 29 78 78 1k6o pd0258 23 prot-nuc diff double-kink 1.853 21 57 78 78 2kbd ------ 16 nuc NMR double-kink 0.231 30 48 78 78 1jfi pd0221 17 prot-nuc diff double-kink 0.508 41 39 80 80 2rve pde002 16 prot-nuc diff double-kink 0.454 43 40 83 83 1qne pd0163 14 prot-nuc diff double-kink 0.376 49 37 86 86 1c9b pd0112 17 prot-nuc diff double-kink 0.914 43 44 87 87 1owf pd0406 20 prot-nuc diff double-kink 0.579 24 65 89 89 1run pdr024 30 prot-nuc diff double-kink 0.527 48 42 90 90 1cgp pdr006 30 prot-nuc diff double-kink 0.389 48 44 92 92 1l1m ------ 23 prot-nuc NMR double-kink 0.217 51 41 92 92 1ouz pd0405 20 prot-nuc diff double-kink 0.574 25 67 92 92 1ruo pdr025 30 prot-nuc diff double-kink 1.164 46 47 93 93 1ngm pd0368 19 prot-nuc diff double-kink 0.573 57 38 95 95 1owg pd0407 20 prot-nuc diff double-kink 0.468 28 67 95 95 1d3u pd0070 23 prot-nuc diff double-kink 0.683 58 44 102 102 1cdw pdt034 16 prot-nuc diff double-kink 0.533 56 48 104 104 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: 22 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 1fjl pde025 41 prot-nuc diff double-kink 2.521 31 31 62 62 1ju1 ------ 23 nuc NMR double-kink 3.481 32 32 64 64 1n96 ------ 8 nuc NMR circular 34.159 9 76 1dfu pr0018 15 prot-nuc diff double-kink 3.516 62 31 93 93 1bpz pde0124 16 prot-nuc diff double-kink 2.241 64 32 96 96 1nzb pd0392 36 prot-nuc diff double-kink 4.446 24 78 102 102 4crx pd0047 34 prot-nuc diff double-kink 3.227 24 82 106 106 5crx pd0048 32 prot-nuc diff double-kink 2.926 29 83 112 112 1ihf pdt040 34 prot-nuc diff double-kink 3.423 92 82 174 174 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)