*HEADER DNA 22-MAY-02 1LUH *TITLE SOLUTION NMR STRUCTURE OF SELF-COMPLIMENTARY DUPLEX 5'- *TITLE 2 D(TCCG*CGGA)2 CONTAINING A TRIMETHYLENE CROSSLINK AT THE *TITLE 3 N2 POSITION OF G* *COMPND MOL_ID: 1; *COMPND 2 MOLECULE: 5'-D(*TP*CP*CP*(TME)GP*CP*GP*GP*A)-3'; *COMPND 3 CHAIN: A, B; *COMPND 4 ENGINEERED: YES *SOURCE MOL_ID: 1; *SOURCE 2 SYNTHETIC: YES; *SOURCE 3 OTHER_DETAILS: DETAILS OF THE SYNTHESIS ARE DESCRIBED IN *SOURCE 4 THE JOURNAL ARTICLE. *KEYWDS DNA DUPLEX, GUANINE N2-GUANINE N2 INTERSTRAND CROSSLINK *EXPDTA NMR, MINIMIZED AVERAGE STRUCTURE *AUTHOR P.D.DOOLEY, M.ZHANG, G.A.KORBEL, L.V.NECHEV, C.M.HARRIS, *AUTHOR 2 M.P.STONE, T.M.HARRIS *REVDAT 1 11-FEB-03 1LUH 0 RCSB ID: RCSB016282. Distance Restraints Derived from NOE Data Using MARDIGRAS for the Crosslinked 5'-d(TCCG*CGGA)2 Oligodeoxynucleotide Class 1 Distance Restraints Residue 1 Atom Residue 2 Atom Distance (Å) Lower Limit Upper Limit 1 H6 1 H1' 3.992 3.544 4.441 1 M 1 H6 2.955 2.655 3.255 1 H2'' 1 H6 2.804 2.504 3.104 1 H3' 1 H2' 2.844 2.544 3.144 2 H1' 1 H1' 3.662 3.310 4.014 2 H1' 2 H4' 3.119 2.819 3.419 2 H3' 2 H4' 2.898 2.598 3.198 3 H1' 3 H4' 3.066 2.766 3.366 3 H3' 3 H4' 2.759 2.459 3.059 3 H3' 3 H6 3.548 3.125 3.971 3 H3' 3 H2' 2.535 2.235 2.835 4 H2' 4 H1' 3.118 2.735 3.502 4 H2'' 4 H1' 2.291 1.991 2.591 4 H2'' 4 H8 3.434 2.574 4.295 4 H3' 4 H4' 2.658 2.358 2.958 4 H3' 4 H2'' 2.527 2.227 2.827 5 H6 5 H1' 2.998 2.698 3.298 5 H3' 5 H6 3.120 2.820 3.420 6 H1' 6 H4' 3.410 3.110 3.710 6 H8 6 H1' 3.374 3.074 3.674 6 H3' 6 H4' 2.757 2.457 3.057 6 H3' 6 H8 3.150 2.850 3.450 7 H1' 7 H4' 2.995 2.695 3.295 7 H2' 7 H1' 2.986 2.686 3.286 7 H2'' 7 H1' 2.326 2.026 2.626 7 H3' 7 H4' 2.699 2.399 2.999 8 H1' 8 H4' 3.364 3.064 3.664 8 H3' 8 H4' 2.997 2.697 3.297 8 H3' 8 H8 3.597 3.297 3.897 12 HX21 12 HX11 2.300 2.000 2.600 8 H3' 8 H2'' 3.229 2.929 3.529 12 HX21 12 HX12 2.357 2.057 2.657 3 H2'' 3 H4' 3.854 3.554 4.154 4 H2' 4 H8 2.059 1.759 2.359 1 H1' 1 H4' 3.596 3.296 3.896 2 H2'' 2 H1' 2.540 2.240 2.840 8 H2' 8 H1' 3.478 3.178 3.778 3 H2' 3 H4' 4.347 3.721 4.974 2 H2'' 2 H4' 3.041 2.741 3.341 2 H3' 2 H2'' 2.777 2.477 3.077 7 H3' 7 H2'' 2.400 2.100 2.700 3 H5 2 H2'' 3.840 2.644 5.036 3 H2'' 3 H1' 2.490 2.190 2.790 3 H3' 3 H1' 4.084 3.784 4.384 2 H3' 2 H6 4.419 3.726 5.112 7 H3' 7 H2' 2.313 2.013 2.613 3 H2' 3 H1' 3.327 2.977 3.678 8 H2'' 8 H8 3.015 2.697 3.333 2 H2' 2 H1' 3.539 2.543 4.536 3 H6 2 H1' 4.008 3.525 4.492 7 H2' 7 H8 2.152 1.852 2.452 2 H3' 2 H1' 4.371 3.866 4.877 3 H5 2 H1' 4.053 3.615 4.492 3 H6 2 H2'' 2.997 2.697 3.297 8 H8 8 H1' 3.973 3.673 4.273 2 H5 2 H1' 3.146 2.846 3.446 7 H1' 7 H5' 3.463 3.126 3.801 2 H2'' 2 H6 2.873 2.131 3.615 7 H2'' 7 H8 3.211 2.402 4.020 2 H2' 2 H4' 4.666 3.628 5.705 3 H5 2 H6 4.129 3.142 5.117 2 H5 1 H2' 3.179 2.879 3.479 6 H3' 6 H1' 4.216 3.438 4.994 5 H5 4 H2'' 3.363 2.898 3.828 1 H2'' 1 H2' 1.902 1.602 2.202 8 H2'' 8 H1' 2.757 2.457 3.057 4 H5' 3 H1' 4.324 2.901 5.748 1 H3' 1 H2'' 3.481 2.644 4.318 7 H2'' 7 H4' 3.617 3.129 4.106 4 H8 3 H2'' 3.409 3.109 3.709 1 H2' 1 H6 3.729 3.143 4.315 3 H2' 3 H6 2.237 1.937 2.537 8 H3' 8 H5' 2.676 2.376 2.976 8 H3' 8 H2' 2.918 2.618 3.218 7 H2' 7 H4' 3.918 3.355 4.482 2 H6 1 H2'' 3.327 2.830 3.824 2 H6 2 H1' 3.817 3.274 4.361 3 H6 3 H1' 3.924 3.024 4.825 1 H2'' 1 H4' 4.099 3.410 4.788 1 H3' 1 H4' 3.309 2.887 3.732 2 H2' 2 H6 2.222 1.922 2.522 3 H2'' 3 H5 3.647 2.514 4.780 2 H5 1 H2'' 4.600 3.269 5.931 4 H8 4 H1' 3.695 3.389 4.002 4 H8 3 H1' 4.456 4.156 4.756 8 H3' 8 H1' 5.003 3.820 6.186 3 H2'' 3 H2' 1.943 1.643 2.243 1 H2' 1 H4' 4.602 4.018 5.186 4 H3' 4 H1' 4.073 3.515 4.631 3 H5 3 H1' 3.552 3.252 3.852 Class 2 Distance Restraints Residue 1 Atom Residue 2 Atom Distance (Å) Lower Limit Upper Limit 4 H2'' 4 H4' 3.720 3.195 4.245 7 H1' 7 H5'' 4.640 3.952 5.329 7 H3' 7 H8 3.788 2.449 5.127 5 H6 4 H1' 3.569 3.268 3.871 2 H2'' 2 H2' 1.986 1.671 2.302 4 H8 3 H2' 4.068 3.420 4.717 8 H2' 8 H8 2.680 2.380 2.980 3 H2' 2 H2'' 3.555 2.730 4.380 7 H8 7 H1' 5.068 0.656 9.480 5 H6 4 H2'' 3.177 2.844 3.510 4 H3' 4 H8 3.801 3.148 4.454 4 H2' 4 H4' 4.426 3.297 5.556 7 H3' 7 H1' 4.249 3.364 5.135 12 HX12 12 HX11 2.008 1.671 2.346 8 H2'' 8 H2' 1.967 1.667 2.267 5 H5 4 H2' 3.609 3.098 4.121 3 H6 2 H6 4.461 3.527 5.396 3 H2' 3 H5 4.199 3.504 4.894 5 H5 4 H8 4.194 3.672 4.716 4 H8 3 H3' 4.658 4.358 4.958 8 H8 8 H4' 4.841 3.963 5.720 5 H6 4 H2' 3.209 2.267 4.151 3 H4' 2 H1' 5.053 4.567 5.539 Class 3 Distance Restraints Residue 1 Atom Residue 2 Atom Distance (Å) Lower Limit Upper Limit 7 H4' 6 H1' 5.210 4.013 6.407 8 H8 7 H1' 4.403 3.603 5.203 8 H3' 8 H5'' 3.110 2.362 3.859 3 H5 2 H3' 5.140 3.745 6.536 4 H8 3 H6 4.730 4.061 5.400 4 H1' 4 H5'' 4.057 3.663 4.451 3 H6 3 H4' 5.144 3.882 6.407 6 H8 5 H2'' 3.071 2.426 3.717 7 H8 6 H1' 3.995 3.520 4.471 5 H6 5 H4' 4.841 3.781 5.902 6 H8 6 H5'' 3.547 3.131 3.963 8 H8 8 H5' 4.299 3.672 4.926 4 H8 4 H5'' 4.418 3.657 5.180 2 H6 2 H4' 4.472 3.921 5.023 2 H6 1 H3' 4.289 3.424 5.154 Class 4 Distance Restraints Residue 1 Atom Residue 2 Atom Distance (Å) Lower Limit Upper Limit 8 H8 8 H5'' 4.635 4.048 5.222 2 H6 1 H1' 4.585 3.850 5.320 1 H3' 1 H6 3.137 2.837 3.437 5 H5 4 H3' 4.831 3.601 6.061 Class 5 Distance Restraints Residue 1 Atom Residue 2 Atom Distance (Å) Lower Limit Upper Limit 4 H8 4 H4' 4.844 4.187 5.501 6 H8 5 H6 5.361 4.518 6.204 8 H8 7 H8 4.807 4.217 5.398 4 H8 4 H5' 4.580 3.581 5.579 1 H6 1 H4' 4.611 3.826 5.397 7 H8 7 H4' 5.043 3.477 6.610 8 H8 7 H3' 3.883 3.470 4.297 6 H8 6 H4' 5.305 4.050 6.561 1 H3' 1 H1' 4.051 3.334 4.768 6 H8 5 H3' 4.185 3.710 4.660 6 H8 6 H5' 4.219 3.903 4.536 2 H5 1 H1' 5.458 4.438 6.478 2 H5 1 H3' 5.112 4.246 5.978 4 H1' 4 H5' 4.763 4.390 5.136 8 H1' 8 H5'' 5.521 4.984 6.058 2 H4' 1 H1' 5.336 4.247 6.426 4 H4' 3 H1' 5.984 4.870 7.099 5 H3' 5 H5 5.809 4.929 6.689 8 H1' 8 H5' 4.715 4.415 5.015 7 H8 6 H4' 5.658 5.358 5.958 2 H3' 2 H5 6.013 3.877 8.149 4 H8 3 H4' 6.531 4.588 8.474 Dooley, P. A., et al. 1 Entry H atom name Submitted Coord H atom name 1 1H5* T 1 H5' T 1 5.876 -6.602 -2.323 2 2H5* T 1 2H5* T 1 7.234 -6.949 -1.234 3 H4* T 1 H4' T 1 7.197 -4.577 -2.022 4 H3* T 1 H3' T 1 7.368 -5.628 0.761 5 1H2* T 1 1H2* T 1 5.817 -3.885 1.994 6 2H2* T 1 2H2* T 1 6.621 -2.680 1.019 7 H1* T 1 H1' T 1 4.910 -2.364 -0.327 8 H3 T 1 H3 T 1 0.532 -3.868 0.065 9 1H5M T 1 H51 T 1 3.222 -5.619 4.244 10 2H5M T 1 H52 T 1 3.264 -7.042 3.176 11 3H5M T 1 H53 T 1 1.704 -6.403 3.745 12 H6 T 1 H6 T 1 4.749 -4.914 2.121 13 H5T T 1 H5T T 1 4.548 -6.424 -0.465 14 1H5* C 2 1H5* C 2 9.174 -1.543 -0.061 15 2H5* C 2 2H5* C 2 10.337 -0.842 1.083 16 H4* C 2 H4' C 2 8.390 0.692 0.675 17 H3* C 2 H3' C 2 9.299 -0.184 3.280 18 H1* C 2 H1' C 2 5.494 0.652 1.774 19 1H4 C 2 H41 C 2 1.288 -3.227 4.124 20 2H4 C 2 H42 C 2 2.435 -4.069 5.143 21 H5 C 2 H5 C 2 4.845 -3.639 5.039 22 H6 C 2 H6 C 2 6.556 -2.172 4.105 23 1H2* C 2 1H2* C 2 7.189 -0.105 4.286 24 2H2* C 2 2H2* C 2 7.077 1.493 3.450 25 1H5* C 3 1H5* C 3 6.314 3.306 2.262 26 2H5* C 3 2H5* C 3 7.489 4.600 2.559 27 H4* C 3 H4' C 3 5.448 5.631 3.010 28 H3* C 3 H3' C 3 7.113 5.063 5.193 29 H1* C 3 H1' C 3 3.136 5.153 5.045 30 1H4 C 3 H41 C 3 1.927 -1.218 6.405 31 2H4 C 3 H42 C 3 0.439 -0.351 6.711 32 H5 C 3 H5 C 3 3.981 -0.108 5.699 33 H6 C 3 H6 C 3 5.055 2.028 5.409 34 1H2* C 3 1H2* C 3 5.493 3.905 6.575 35 2H2* C 3 2H2* C 3 4.840 5.683 6.714 36 1H5* +G 4 1H5* G 4 7.390 7.033 8.507 37 2H5* +G 4 2H5* G 4 6.152 5.972 7.873 38 H4* +G 4 H4' G 4 5.471 8.303 9.586 39 H3* +G 4 H3' G 4 6.981 6.218 10.407 40 H1* +G 4 H1' G 4 3.133 6.363 10.942 41 H8 +G 4 H8 G 4 4.692 3.474 9.035 42 H1 +G 4 H1 G 4 -1.585 2.936 9.775 43 1H2 +G 4 H2X G 4 -1.346 6.214 11.101 44 1H2* +G 4 1H2* G 4 5.472 4.532 10.625 45 2H2* +G 4 2H2* G 4 4.972 5.493 11.997 46 1H5* C 5 1H5* C 5 6.046 6.147 15.618 47 2H5* C 5 2H5* C 5 4.770 4.986 15.213 48 H4* C 5 H4' C 5 4.501 7.997 15.631 49 H3* C 5 H3' C 5 4.138 5.679 17.243 50 H1* C 5 H1' C 5 1.048 7.176 15.265 51 1H4 C 5 H41 C 5 1.086 1.482 12.072 52 2H4 C 5 H42 C 5 -0.605 1.680 12.472 53 H5 C 5 H5 C 5 2.824 3.037 12.807 54 H6 C 5 H6 C 5 3.168 5.042 14.278 55 1H2* C 5 1H2* C 5 1.968 5.141 17.006 56 2H2* C 5 2H2* C 5 1.508 6.812 17.440 57 1H5* G 6 1H5* G 6 1.362 9.270 19.205 58 2H5* G 6 2H5* G 6 1.807 9.010 20.907 59 H4* G 6 H4' G 6 -0.706 9.157 20.399 60 H3* G 6 H3' G 6 0.751 7.648 22.219 61 H1* G 6 H1' G 6 -1.999 5.968 19.959 62 H8 G 6 H8 G 6 1.492 5.344 20.207 63 H1 G 6 H1 G 6 -1.446 1.251 16.393 64 1H2 G 6 H21 G 6 -3.568 1.872 16.164 65 2H2 G 6 H22 G 6 -4.221 3.281 16.967 66 1H2* G 6 1H2 G 6 0.152 5.533 21.728 67 2H2* G 6 2H2 G 6 -1.539 5.973 22.075 68 1H5* G 7 1H5* G 7 -0.778 6.051 23.638 69 2H5* G 7 2H5* G 7 -2.516 6.238 23.961 70 H4* G 7 H4' G 7 -2.067 5.046 26.048 71 H3* G 7 H3' G 7 0.406 6.178 25.900 72 H1* G 7 H1' G 7 -0.301 2.649 25.467 73 H8 G 7 H8 G 7 1.069 4.097 22.218 74 H1 G 7 H1 G 7 0.702 -2.266 22.273 75 1H2 G 7 H21 G 7 -0.338 -2.951 24.100 76 2H2 G 7 H22 G 7 -0.938 -1.841 25.311 77 1H2* G 7 1H2* G 7 1.234 4.882 24.212 78 2H2* G 7 2H2* G 7 1.593 3.991 25.687 79 1H5* A 8 1H5* A 8 -0.254 2.718 27.723 80 2H5* A 8 2H5* A 8 -1.107 1.748 28.914 81 H4* A 8 H4' A 8 0.688 1.641 30.426 82 H3* A 8 H3' A 8 1.170 4.352 29.301 83 H1* A 8 H1' A 8 3.695 0.712 29.267 84 H8 A 8 H8 A 8 3.409 3.594 26.597 85 1H6 A 8 H61 A 8 5.580 -0.488 22.558 86 2H6 A 8 H62 A 8 5.129 1.183 22.815 87 H2 A 8 H2 A 8 4.842 -2.641 26.437 88 H3T A 8 H3T A 8 0.849 3.739 31.494 89 1H2* A 8 1H2* A 8 3.685 3.838 28.492 90 2H2* A 8 2H2* A 8 3.962 3.141 30.192 91 1H5* T 9 1H5* T 9 4.428 -8.152 25.815 92 2H5* T 9 2H5* T 9 4.276 -9.532 24.707 93 H4* T 9 H4' T 9 2.066 -8.722 25.519 94 H3* T 9 H3' T 9 2.983 -9.127 22.714 95 1H2* T 9 1H2* T 9 1.859 -7.034 21.567 96 2H2* T 9 2H2* T 9 0.458 -7.423 22.533 97 H1* T 9 H1' T 9 0.740 -5.762 23.946 98 H3 T 9 H3 T 9 3.608 -2.119 23.676 99 1H5M T 9 H51 T 9 4.364 -5.098 19.391 100 2H5M T 9 H52 T 9 5.697 -5.631 20.441 101 3H5M T 9 H53 T 9 5.599 -3.932 19.923 102 H6 T 9 H6 T 9 3.187 -6.368 21.464 103 H5T T 9 H5T T 9 4.657 -6.820 23.942 104 1H5* C 10 1H5* C 10 -1.462 -9.487 23.542 105 2H5* C 10 2H5* C 10 -2.517 -10.302 22.370 106 H4* C 10 H4' C 10 -3.307 -7.970 22.874 107 H3* C 10 H3' C 10 -2.803 -9.018 20.223 108 H1* C 10 H1' C 10 -2.302 -5.215 21.877 109 1H4 C 10 H41 C 10 3.148 -3.785 18.523 110 2H4 C 10 H42 C 10 2.738 -2.459 19.588 111 H5 C 10 H5 C 10 1.943 -5.920 18.562 112 H6 C 10 H6 C 10 -0.010 -7.075 19.462 113 1H2* C 10 1H2* C 10 -2.171 -6.966 19.294 114 2H2* C 10 2H2* C 10 -3.634 -6.357 20.160 115 1H5* C 11 1H5* C 11 -5.060 -5.053 21.412 116 2H5* C 11 2H5* C 11 -6.679 -5.715 21.113 117 H4* C 11 H4' C 11 -6.973 -3.436 20.733 118 H3* C 11 H3' C 11 -7.008 -5.122 18.494 119 H1* C 11 H1' C 11 -5.762 -1.350 18.758 120 1H4 C 11 H41 C 11 0.647 -2.305 17.366 121 2H4 C 11 H42 C 11 0.333 -0.601 17.124 122 H5 C 11 H5 C 11 -1.090 -3.891 18.003 123 H6 C 11 H6 C 11 -3.461 -4.194 18.287 124 1H2* C 11 1H2* C 11 -5.382 -3.938 17.140 125 2H2* C 11 2H2* C 11 -6.839 -2.724 17.049 126 1H5* +G 12 1H5* +G 12 -8.943 -4.689 15.247 127 2H5* +G 12 2H5* +G 12 -7.547 -3.852 15.889 128 H4* +G 12 H4' +G 12 -9.545 -2.448 14.202 129 H3* +G 12 H3' +G 12 -8.059 -4.537 13.346 130 H1* +G 12 H1' +G 12 -6.984 -0.837 12.838 131 H8 +G 12 H8 +G 12 -4.718 -3.248 14.700 132 H1 +G 12 H1 +G 12 -2.347 2.586 14.240 133 1H2 +G 12 H2* +G 12 -5.412 3.369 12.683 134 1H2* +G 12 1H2* +G 12 -5.982 -3.640 13.117 135 2H2* +G 12 2H2* +G 12 -6.748 -2.847 11.760 136 1H5* C 13 1H5* C 13 -7.713 -3.639 8.149 137 2H5* C 13 2H5* C 13 -6.211 -2.790 8.555 138 H4* C 13 H4' C 13 -8.991 -1.591 8.154 139 H3* C 13 H3' C 13 -6.691 -1.977 6.524 140 H1* C 13 H1' C 13 -7.115 1.430 8.504 141 1H4 C 13 H41 C 13 -1.344 1.237 11.230 142 2H4 C 13 H42 C 13 -1.700 -0.424 11.645 143 H5 C 13 H5 C 13 -3.744 -1.571 10.941 144 H6 C 13 H6 C 13 -5.763 -1.258 9.486 145 1H2* C 13 1H2* C 13 -5.497 -0.083 6.742 146 2H2* C 13 2H2* C 13 -6.945 0.877 6.328 147 1H5* G 14 1H5* G 14 -9.210 1.835 4.654 148 2H5* G 14 2H5* G 14 -9.152 1.342 2.946 149 H4* G 14 H4' G 14 -8.457 3.761 3.451 150 H3* G 14 H3' G 14 -7.550 1.900 1.601 151 H1* G 14 H1' G 14 -5.008 3.923 3.825 152 H8 G 14 H8 G 14 -5.569 0.426 3.552 153 H1 G 14 H1 G 14 -0.736 1.809 7.386 154 1H2 G 14 H21 G 14 -0.627 4.015 7.642 155 2H2 G 14 H22 G 14 -1.745 5.104 6.853 156 1H2* G 14 1H2* G 14 -5.348 1.758 2.054 157 2H2* G 14 2H2* G 14 -5.204 3.499 1.711 158 1H5* G 15 1H5* G 15 -5.553 2.886 0.133 159 2H5* G 15 2H5* G 15 -5.172 4.598 -0.158 160 H4* G 15 H4' G 15 -4.223 3.840 -2.278 161 H3* G 15 H3' G 15 -6.099 1.869 -2.161 162 H1* G 15 H1' G 15 -2.525 1.375 -1.786 163 H8 G 15 H8 G 15 -4.310 0.461 1.457 164 H1 G 15 H1 G 15 1.817 -1.270 1.303 165 1H2 G 15 H21 G 15 1.935 0.508 -1.682 166 2H2 G 15 H22 G 15 2.795 -0.456 -0.503 167 1H2* G 15 1H2* G 15 -5.123 0.612 -0.525 168 2H2* G 15 2H2* G 15 -4.415 0.029 -2.027 169 1H5* A 16 1H5* A 16 -2.644 1.447 -4.027 170 2H5* A 16 2H5* A 16 -1.457 1.986 -5.205 171 H4* A 16 H4' A 16 -1.927 0.296 -6.768 172 H3* A 16 H3' A 16 -4.649 0.660 -5.624 173 H1* A 16 H1' A 16 -1.992 -2.884 -5.703 174 H8 A 16 H8 A 16 -4.631 -1.785 -2.994 175 1H6 A 16 H61 A 16 -1.456 -5.302 0.916 176 2H6 A 16 H62 A 16 -2.900 -4.339 0.695 177 H2 A 16 H2 A 16 0.829 -5.121 -2.953 178 H3T A 16 H3T A 16 -5.091 -0.243 -7.729 179 1H2* A 16 1H2* A 16 -4.954 -1.912 -4.895 180 2H2* A 16 2H2* A 16 -4.382 -2.342 -6.609 181 1H1 TME 1 1H1 TME 1 -2.492 3.881 13.059 182 2H1 TME 1 2H1 TME 1 -3.617 4.859 13.975 183 1H2 TME 1 1H2 TME 1 -3.360 6.221 12.141 184 2H2 TME 1 2H2 TME 1 -4.721 5.262 11.609 185 1H3 TME 1 1H3 TME 1 -3.339 5.017 9.789 186 2H3 TME 1 2H3 TME 1 -2.810 3.639 10.726