HEADER ISOMERASE/DNA 31-DEC-69 3KSB TITLE Detailed structural insight into the DNA cleavage complex of type IIA TITLE 2 topoisomerases (re-sealed form) COMPND MOL_ID: 2; COMPND 2 MOLECULE: DNA topoisomerase 4 subunit B; COMPND 3 CHAIN: C, D; COMPND 4 EC: 5.99.1.-; COMPND 5 FRAGMENT: residues ; COMPND 6 ENGINEERED: YES; EXPDTA X-RAY DIFFRACTION REMARK 2 RESOLUTION. 3.50 ANGSTORMS REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY C 169 REMARK 465 LYS C 170 REMARK 465 GLY C 171 DBREF 3KSB C 404 647 UNP Q59961 PARE_STRPN 404 647 SEQRES 1 C 42 PRO LEU TYR LYS MET SER LYS GLY LYS GLY LYS LYS GLU SEQRES 2 C 42 GLU VAL ALA TYR ALA TRP THR ASP GLY GLU LEU GLU GLU SEQRES 3 C 42 LEU ARG LYS GLN PHE GLY LYS GLY ALA THR LEU GLN ARG SEQRES 4 C 42 TYR LYS GLY ATOM 1 N PRO C 541 -4.855 60.144 -24.710 1.00122.98 ATOM 2 CA PRO C 541 -4.925 59.544 -23.374 1.00132.62 ATOM 3 C PRO C 541 -5.972 58.455 -23.295 1.00139.13 ATOM 4 O PRO C 541 -6.913 58.437 -24.094 1.00140.21 ATOM 5 CB PRO C 541 -5.445 60.678 -22.501 1.00137.54 ATOM 6 CG PRO C 541 -5.267 61.893 -23.265 1.00141.04 ATOM 7 CD PRO C 541 -4.962 61.600 -24.691 1.00128.51 ATOM 8 N LEU C 542 -5.810 57.561 -22.328 1.00139.93 ATOM 9 CA LEU C 542 -6.822 56.555 -22.049 1.00137.31 ATOM 10 C LEU C 542 -7.485 56.839 -20.706 1.00131.19 ATOM 11 O LEU C 542 -8.711 56.772 -20.580 1.00115.49 ATOM 12 CB LEU C 542 -6.192 55.170 -22.032 1.00135.81 ATOM 13 CG LEU C 542 -7.162 54.019 -22.277 1.00130.32 ATOM 14 CD1 LEU C 542 -6.929 52.968 -21.212 1.00122.82 ATOM 15 CD2 LEU C 542 -8.614 54.510 -22.257 1.00137.98 ATOM 16 N TYR C 543 -6.653 57.145 -19.711 1.00135.81 ATOM 17 CA TYR C 543 -7.096 57.447 -18.352 1.00139.53 ATOM 18 C TYR C 543 -6.734 58.882 -17.952 1.00140.55 ATOM 19 O TYR C 543 -5.644 59.358 -18.255 1.00152.18 ATOM 20 CB TYR C 543 -6.435 56.478 -17.365 1.00143.74 ATOM 21 CG TYR C 543 -6.775 55.031 -17.558 1.00139.79 ATOM 22 CD1 TYR C 543 -8.037 54.570 -17.299 1.00144.08 ATOM 23 CD2 TYR C 543 -5.829 54.130 -17.980 1.00148.98 ATOM 24 CE1 TYR C 543 -8.365 53.248 -17.475 1.00157.91 ATOM 25 CE2 TYR C 543 -6.144 52.798 -18.152 1.00165.81 ATOM 26 CZ TYR C 543 -7.422 52.357 -17.897 1.00166.85 ATOM 27 OH TYR C 543 -7.775 51.027 -18.064 1.00167.24 ATOM 28 N LYS C 544 -7.650 59.567 -17.275 1.00138.54 ATOM 29 CA LYS C 544 -7.357 60.860 -16.646 1.00139.52 ATOM 30 C LYS C 544 -7.727 60.817 -15.158 1.00133.81 ATOM 31 O LYS C 544 -8.850 60.454 -14.783 1.00118.40 ATOM 32 CB LYS C 544 -8.043 62.051 -17.368 1.00112.68 ATOM 33 N MET C 545 -6.785 61.204 -14.311 1.00139.76 ATOM 34 CA MET C 545 -6.969 61.051 -12.875 1.00161.25 ATOM 35 C MET C 545 -6.925 62.413 -12.190 1.00163.30 ATOM 36 O MET C 545 -6.128 63.270 -12.571 1.00175.11 ATOM 37 CB MET C 545 -5.906 60.104 -12.330 1.00129.61 ATOM 38 N SER C 546 -7.799 62.627 -11.208 1.00148.98 ATOM 39 CA SER C 546 -7.915 63.945 -10.576 1.00149.41 ATOM 40 C SER C 546 -8.078 63.945 -9.046 1.00155.85 ATOM 41 O SER C 546 -8.847 63.158 -8.496 1.00162.00 ATOM 42 CB SER C 546 -9.048 64.749 -11.226 1.00143.06 ATOM 43 OG SER C 546 -10.061 63.901 -11.746 1.00147.20 ATOM 44 N LYS C 547 -7.351 64.844 -8.375 1.00167.87 ATOM 45 CA LYS C 547 -7.459 65.040 -6.921 1.00186.45 ATOM 46 C LYS C 547 -7.809 66.488 -6.571 1.00185.12 ATOM 47 O LYS C 547 -8.681 67.104 -7.194 1.00177.07 ATOM 48 CB LYS C 547 -6.163 64.638 -6.171 1.00157.63 ATOM 49 N LYS C 551 -11.834 74.562 -7.051 1.00213.04 ATOM 50 CA LYS C 551 -10.924 75.611 -7.499 1.00218.87 ATOM 51 C LYS C 551 -9.537 75.055 -7.811 1.00224.34 ATOM 52 O LYS C 551 -9.004 75.261 -8.903 1.00206.22 ATOM 53 CB LYS C 551 -10.826 76.683 -6.416 1.00218.16 ATOM 54 N LYS C 552 -8.956 74.354 -6.841 1.00238.76 ATOM 55 CA LYS C 552 -7.644 73.741 -7.016 1.00238.34 ATOM 56 C LYS C 552 -7.787 72.275 -7.401 1.00225.46 ATOM 57 O LYS C 552 -8.428 71.495 -6.694 1.00224.80 ATOM 58 CB LYS C 552 -6.804 73.869 -5.745 1.00249.19 ATOM 59 N GLU C 553 -7.187 71.911 -8.531 1.00209.84 ATOM 60 CA GLU C 553 -7.257 70.551 -9.051 1.00193.45 ATOM 61 C GLU C 553 -5.881 70.061 -9.475 1.00214.00 ATOM 62 O GLU C 553 -5.050 70.840 -9.933 1.00227.09 ATOM 63 CB GLU C 553 -8.193 70.478 -10.260 1.00163.50 ATOM 64 N GLU C 554 -5.642 68.766 -9.315 1.00227.21 ATOM 65 CA GLU C 554 -4.433 68.140 -9.839 1.00235.15 ATOM 66 C GLU C 554 -4.839 67.012 -10.784 1.00222.89 ATOM 67 O GLU C 554 -5.669 66.173 -10.439 1.00238.59 ATOM 68 CB GLU C 554 -3.515 67.641 -8.715 1.00244.49 ATOM 69 N VAL C 555 -4.273 67.010 -11.986 1.00192.51 ATOM 70 CA VAL C 555 -4.711 66.092 -13.030 1.00165.65 ATOM 71 C VAL C 555 -3.548 65.452 -13.784 1.00165.94 ATOM 72 O VAL C 555 -2.539 66.093 -14.083 1.00165.81 ATOM 73 CB VAL C 555 -5.654 66.830 -13.993 1.00156.18 ATOM 74 CG1 VAL C 555 -5.842 66.064 -15.332 1.00123.53 ATOM 75 CG2 VAL C 555 -6.979 67.184 -13.262 1.00129.58 ATOM 76 N ALA C 556 -3.701 64.172 -14.083 1.00170.65 ATOM 77 CA ALA C 556 -2.701 63.435 -14.837 1.00175.93 ATOM 78 C ALA C 556 -3.353 62.677 -15.991 1.00161.46 ATOM 79 O ALA C 556 -4.579 62.555 -16.054 1.00148.16 ATOM 80 CB ALA C 556 -1.934 62.484 -13.920 1.00181.85 ATOM 81 N TYR C 557 -2.526 62.207 -16.918 1.00156.28 ATOM 82 CA TYR C 557 -2.992 61.361 -18.004 1.00146.23 ATOM 83 C TYR C 557 -2.158 60.087 -18.070 1.00137.45 ATOM 84 O TYR C 557 -0.937 60.124 -17.910 1.00134.23 ATOM 85 CB TYR C 557 -2.931 62.127 -19.326 1.00144.07 ATOM 86 CG TYR C 557 -3.955 63.250 -19.438 1.00160.98 ATOM 87 CD1 TYR C 557 -3.591 64.587 -19.302 1.00162.74 ATOM 88 CD2 TYR C 557 -5.290 62.973 -19.687 1.00173.28 ATOM 89 CE1 TYR C 557 -4.530 65.613 -19.426 1.00155.42 ATOM 90 CE2 TYR C 557 -6.229 63.990 -19.799 1.00171.87 ATOM 91 CZ TYR C 557 -5.841 65.299 -19.671 1.00164.18 ATOM 92 OH TYR C 557 -6.784 66.283 -19.785 1.00174.09 ATOM 93 N ALA C 558 -2.833 58.963 -18.292 1.00131.96 ATOM 94 CA ALA C 558 -2.179 57.666 -18.458 1.00133.89 ATOM 95 C ALA C 558 -2.543 57.081 -19.820 1.00140.55 ATOM 96 O ALA C 558 -3.606 57.390 -20.377 1.00139.10 ATOM 97 CB ALA C 558 -2.589 56.698 -17.345 1.00121.39 ATOM 98 N TRP C 559 -1.664 56.243 -20.362 1.00142.27 ATOM 99 CA TRP C 559 -1.867 55.742 -21.720 1.00155.11 ATOM 100 C TRP C 559 -2.077 54.229 -21.790 1.00161.78 ATOM 101 O TRP C 559 -2.551 53.708 -22.805 1.00147.14 ATOM 102 CB TRP C 559 -0.720 56.205 -22.644 1.00164.41 ATOM 103 CG TRP C 559 -0.923 57.589 -23.148 1.00157.48 ATOM 104 CD1 TRP C 559 -1.389 57.941 -24.367 1.00149.91 ATOM 105 CD2 TRP C 559 -0.723 58.811 -22.424 1.00166.61 ATOM 106 NE1 TRP C 559 -1.489 59.306 -24.459 1.00155.34 ATOM 107 CE2 TRP C 559 -1.086 59.863 -23.277 1.00162.79 ATOM 108 CE3 TRP C 559 -0.278 59.112 -21.136 1.00180.25 ATOM 109 CZ2 TRP C 559 -1.012 61.198 -22.893 1.00165.29 ATOM 110 CZ3 TRP C 559 -0.212 60.442 -20.754 1.00182.81 ATOM 111 CH2 TRP C 559 -0.577 61.466 -21.631 1.00171.82 ATOM 112 N THR C 560 -1.728 53.540 -20.704 1.00181.24 ATOM 113 CA THR C 560 -1.981 52.106 -20.563 1.00181.96 ATOM 114 C THR C 560 -1.818 51.659 -19.112 1.00199.08 ATOM 115 O THR C 560 -1.203 52.352 -18.298 1.00202.07 ATOM 116 CB THR C 560 -1.075 51.238 -21.472 1.00148.69 ATOM 117 N ASP C 561 -2.367 50.486 -18.812 1.00206.18 ATOM 118 CA ASP C 561 -2.404 49.935 -17.456 1.00208.36 ATOM 119 C ASP C 561 -1.151 50.209 -16.625 1.00201.63 ATOM 120 O ASP C 561 -1.249 50.622 -15.470 1.00205.93 ATOM 121 CB ASP C 561 -2.715 48.434 -17.519 1.00212.05 ATOM 122 CG ASP C 561 -3.691 48.084 -18.650 1.00214.30 ATOM 123 OD1 ASP C 561 -4.586 48.898 -18.981 1.00200.71 ATOM 124 OD2 ASP C 561 -3.557 46.984 -19.216 1.00226.59 ATOM 125 N GLY C 562 0.021 49.967 -17.204 1.00192.71 ATOM 126 CA GLY C 562 1.265 50.223 -16.505 1.00199.73 ATOM 127 C GLY C 562 1.289 51.627 -15.932 1.00211.09 ATOM 128 O GLY C 562 1.470 51.823 -14.725 1.00205.45 ATOM 129 N GLU C 563 1.094 52.606 -16.811 1.00216.99 ATOM 130 CA GLU C 563 1.092 54.016 -16.431 1.00214.02 ATOM 131 C GLU C 563 0.206 54.275 -15.215 1.00213.44 ATOM 132 O GLU C 563 0.522 55.108 -14.364 1.00213.70 ATOM 133 CB GLU C 563 0.663 54.879 -17.633 1.00201.54 ATOM 134 N LEU C 564 -0.907 53.551 -15.144 1.00209.95 ATOM 135 CA LEU C 564 -1.918 53.788 -14.120 1.00198.98 ATOM 136 C LEU C 564 -1.381 53.656 -12.702 1.00208.62 ATOM 137 O LEU C 564 -1.583 54.550 -11.885 1.00220.18 ATOM 138 CB LEU C 564 -3.121 52.849 -14.319 1.00177.45 ATOM 139 CG LEU C 564 -4.490 53.405 -13.906 1.00157.14 ATOM 140 CD1 LEU C 564 -4.390 54.890 -13.576 1.00156.18 ATOM 141 CD2 LEU C 564 -5.582 53.148 -14.972 1.00135.48 ATOM 142 N GLU C 565 -0.687 52.556 -12.416 1.00207.75 ATOM 143 CA GLU C 565 -0.251 52.266 -11.047 1.00209.78 ATOM 144 C GLU C 565 0.510 53.432 -10.406 1.00223.94 ATOM 145 O GLU C 565 0.201 53.836 -9.282 1.00218.15 ATOM 146 CB GLU C 565 0.554 50.965 -10.985 1.00199.85 ATOM 147 N GLU C 566 1.497 53.967 -11.125 1.00240.38 ATOM 148 CA GLU C 566 2.283 55.112 -10.654 1.00248.91 ATOM 149 C GLU C 566 1.422 56.357 -10.442 1.00248.75 ATOM 150 O GLU C 566 1.626 57.105 -9.483 1.00249.65 ATOM 151 CB GLU C 566 3.444 55.428 -11.602 1.00245.54 ATOM 152 N LEU C 567 0.480 56.582 -11.357 1.00241.85 ATOM 153 CA LEU C 567 -0.471 57.689 -11.249 1.00231.45 ATOM 154 C LEU C 567 -1.317 57.578 -9.974 1.00238.46 ATOM 155 O LEU C 567 -1.474 58.551 -9.228 1.00242.78 ATOM 156 CB LEU C 567 -1.363 57.753 -12.500 1.00204.22 ATOM 157 N ARG C 568 -1.859 56.385 -9.736 1.00227.79 ATOM 158 CA ARG C 568 -2.644 56.107 -8.537 1.00208.86 ATOM 159 C ARG C 568 -1.821 56.319 -7.268 1.00208.92 ATOM 160 O ARG C 568 -2.282 56.955 -6.320 1.00207.28 ATOM 161 CB ARG C 568 -3.196 54.676 -8.574 1.00192.36 ATOM 162 N LYS C 569 -0.604 55.781 -7.252 1.00212.39 ATOM 163 CA LYS C 569 0.289 55.952 -6.110 1.00212.96 ATOM 164 C LYS C 569 0.532 57.433 -5.850 1.00222.88 ATOM 165 O LYS C 569 0.504 57.883 -4.705 1.00227.17 ATOM 166 CB LYS C 569 1.606 55.185 -6.288 1.00199.40 ATOM 167 N GLN C 570 0.765 58.188 -6.920 1.00224.15 ATOM 168 CA GLN C 570 0.994 59.624 -6.810 1.00228.46 ATOM 169 C GLN C 570 -0.196 60.339 -6.170 1.00234.10 ATOM 170 O GLN C 570 -0.070 60.954 -5.110 1.00245.83 ATOM 171 CB GLN C 570 1.270 60.217 -8.193 1.00217.42 ATOM 172 N PHE C 571 -1.351 60.238 -6.818 1.00219.54 ATOM 173 CA PHE C 571 -2.570 60.914 -6.377 1.00212.12 ATOM 174 C PHE C 571 -3.072 60.562 -4.976 1.00218.22 ATOM 175 O PHE C 571 -4.001 61.200 -4.473 1.00209.48 ATOM 176 CB PHE C 571 -3.667 60.632 -7.367 1.00204.04 ATOM 177 CG PHE C 571 -3.737 61.624 -8.445 1.00199.52 ATOM 178 CD1 PHE C 571 -2.904 61.522 -9.543 1.00197.06 ATOM 179 CD2 PHE C 571 -4.627 62.680 -8.358 1.00196.30 ATOM 180 CE1 PHE C 571 -2.968 62.457 -10.559 1.00197.66 ATOM 181 CE2 PHE C 571 -4.702 63.614 -9.359 1.00196.61 ATOM 182 CZ PHE C 571 -3.867 63.509 -10.471 1.00198.18 ATOM 183 N GLY C 572 -2.436 59.579 -4.343 1.00239.36 ATOM 184 CA GLY C 572 -3.022 58.841 -3.234 1.00247.36 ATOM 185 C GLY C 572 -4.528 58.984 -3.078 1.00241.37 ATOM 186 O GLY C 572 -5.253 59.057 -4.073 1.00251.26 ATOM 187 N LYS C 573 -5.006 58.996 -1.837 1.00223.38 ATOM 188 CA LYS C 573 -6.444 58.987 -1.574 1.00222.42 ATOM 189 C LYS C 573 -7.210 60.052 -2.362 1.00234.83 ATOM 190 O LYS C 573 -6.621 60.976 -2.925 1.00247.87 ATOM 191 CB LYS C 573 -6.727 59.134 -0.074 1.00224.02 ATOM 192 N GLY C 574 -8.530 59.899 -2.411 1.00227.83 ATOM 193 CA GLY C 574 -9.407 60.933 -2.932 1.00216.65 ATOM 194 C GLY C 574 -9.498 61.057 -4.440 1.00201.49 ATOM 195 O GLY C 574 -10.355 61.775 -4.951 1.00206.39 ATOM 196 N ALA C 575 -8.625 60.362 -5.160 1.00189.47 ATOM 197 CA ALA C 575 -8.597 60.468 -6.620 1.00185.22 ATOM 198 C ALA C 575 -9.887 60.008 -7.303 1.00162.37 ATOM 199 O ALA C 575 -10.646 59.202 -6.766 1.00166.35 ATOM 200 CB ALA C 575 -7.401 59.706 -7.205 1.00190.22 ATOM 201 N THR C 576 -10.131 60.543 -8.490 1.00146.40 ATOM 202 CA THR C 576 -11.169 60.021 -9.367 1.00152.21 ATOM 203 C THR C 576 -10.510 59.662 -10.695 1.00154.42 ATOM 204 O THR C 576 -9.743 60.450 -11.252 1.00152.58 ATOM 205 CB THR C 576 -12.360 61.051 -9.595 1.00174.91 ATOM 206 OG1 THR C 576 -11.915 62.384 -9.335 1.00178.99 ATOM 207 CG2 THR C 576 -13.604 60.772 -8.695 1.00149.20 ATOM 208 N LEU C 577 -10.802 58.468 -11.199 1.00152.24 ATOM 209 CA LEU C 577 -10.186 58.007 -12.435 1.00141.51 ATOM 210 C LEU C 577 -11.229 57.914 -13.524 1.00135.19 ATOM 211 O LEU C 577 -12.300 57.344 -13.331 1.00138.09 ATOM 212 CB LEU C 577 -9.489 56.656 -12.253 1.00124.27 ATOM 213 CG LEU C 577 -9.334 55.734 -13.461 1.00120.03 ATOM 214 CD1 LEU C 577 -8.903 56.472 -14.665 1.00116.93 ATOM 215 CD2 LEU C 577 -8.313 54.684 -13.170 1.00124.36 ATOM 216 N GLN C 578 -10.899 58.484 -14.672 1.00116.09 ATOM 217 CA GLN C 578 -11.813 58.521 -15.789 1.00118.63 ATOM 218 C GLN C 578 -11.164 57.761 -16.933 1.00111.11 ATOM 219 O GLN C 578 -9.963 57.864 -17.147 1.00112.13 ATOM 220 CB GLN C 578 -12.082 59.956 -16.186 1.00127.66 ATOM 221 CG GLN C 578 -13.430 60.176 -16.813 1.00162.32 ATOM 222 CD GLN C 578 -13.595 61.603 -17.257 1.00186.52 ATOM 223 OE1 GLN C 578 -12.786 62.460 -16.908 1.00197.74 ATOM 224 NE2 GLN C 578 -14.635 61.872 -18.034 1.00191.72 ATOM 225 N ARG C 579 -11.938 56.962 -17.650 1.00126.64 ATOM 226 CA ARG C 579 -11.356 56.154 -18.709 1.00124.40 ATOM 227 C ARG C 579 -12.121 56.357 -19.994 1.00118.65 ATOM 228 O ARG C 579 -13.336 56.156 -20.043 1.00128.81 ATOM 229 CB ARG C 579 -11.348 54.688 -18.325 1.00136.28 ATOM 230 CG ARG C 579 -10.851 53.812 -19.413 1.00138.74 ATOM 231 CD ARG C 579 -11.473 52.466 -19.281 1.00143.71 ATOM 232 NE ARG C 579 -12.047 52.050 -20.552 1.00143.15 ATOM 233 CZ ARG C 579 -11.503 51.119 -21.327 1.00128.68 ATOM 234 NH1 ARG C 579 -10.370 50.507 -20.908 1.00107.57 ATOM 235 NH2 ARG C 579 -12.103 50.799 -22.496 1.00108.50 ATOM 236 N TYR C 580 -11.404 56.756 -21.037 1.00116.43 ATOM 237 CA TYR C 580 -12.052 57.136 -22.277 1.00130.51 ATOM 238 C TYR C 580 -12.318 55.903 -23.116 1.00142.40 ATOM 239 O TYR C 580 -11.423 55.367 -23.770 1.00139.50 ATOM 240 CB TYR C 580 -11.230 58.199 -23.031 1.00134.51 ATOM 241 CG TYR C 580 -11.039 59.467 -22.225 1.00128.57 ATOM 242 CD1 TYR C 580 -12.085 59.985 -21.476 1.00138.77 ATOM 243 CD2 TYR C 580 -9.824 60.120 -22.188 1.00132.30 ATOM 244 CE1 TYR C 580 -11.940 61.111 -20.717 1.00155.56 ATOM 245 CE2 TYR C 580 -9.663 61.254 -21.432 1.00153.87 ATOM 246 CZ TYR C 580 -10.732 61.750 -20.693 1.00168.44 ATOM 247 OH TYR C 580 -10.612 62.890 -19.918 1.00183.62 ATOM 248 N LYS C 581 -13.564 55.444 -23.062 1.00159.87 ATOM 249 CA LYS C 581 -13.984 54.245 -23.773 1.00168.70 ATOM 250 C LYS C 581 -14.104 54.521 -25.265 1.00152.42 ATOM 251 O LYS C 581 -14.791 53.801 -25.982 1.00154.51 ATOM 252 CB LYS C 581 -15.333 53.748 -23.226 1.00171.83 ATOM 253 N GLY C 582 -13.412 55.558 -25.722 1.00123.36 ATOM 254 CA GLY C 582 -13.591 56.096 -27.061 1.00139.33 ATOM 255 C GLY C 582 -13.427 57.610 -27.045 1.00150.32 ATOM 256 O GLY C 582 -13.671 58.254 -26.023 1.00158.13 TER