HEADER ISOMERASE/DNA 31-DEC-69 3KSA TITLE Detailed structural insight into the DNA cleavage complex of type IIA TITLE 2 topoisomerases (cleaved 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. 3.30 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 D 169 REMARK 465 LYS D 170 REMARK 465 GLY D 171 REMARK 465 LYS D 172 REMARK 465 LYS D 173 DBREF 3KSA D 404 647 UNP Q59961 PARE_STRPN 404 647 SEQRES 1 D 42 PRO LEU TYR LYS MET SER LYS GLY LYS GLY LYS LYS GLU SEQRES 2 D 42 GLU VAL ALA TYR ALA TRP THR ASP GLY GLU LEU GLU GLU SEQRES 3 D 42 LEU ARG LYS GLN PHE GLY LYS GLY ALA THR LEU GLN ARG SEQRES 4 D 42 TYR LYS GLY ATOM 1 N PRO D 541 -53.525 41.146 -24.548 1.00114.90 ATOM 2 CA PRO D 541 -53.434 41.723 -23.202 1.00118.40 ATOM 3 C PRO D 541 -52.359 42.782 -23.076 1.00127.50 ATOM 4 O PRO D 541 -51.352 42.753 -23.791 1.00127.01 ATOM 5 CB PRO D 541 -52.998 40.541 -22.332 1.00117.76 ATOM 6 CG PRO D 541 -53.393 39.369 -23.057 1.00133.47 ATOM 7 CD PRO D 541 -53.369 39.691 -24.531 1.00130.60 ATOM 8 N LEU D 542 -52.574 43.700 -22.143 1.00122.46 ATOM 9 CA LEU D 542 -51.568 44.684 -21.804 1.00118.60 ATOM 10 C LEU D 542 -50.946 44.297 -20.476 1.00118.60 ATOM 11 O LEU D 542 -49.731 44.208 -20.360 1.00113.22 ATOM 12 CB LEU D 542 -52.213 46.054 -21.702 1.00119.63 ATOM 13 CG LEU D 542 -51.333 47.272 -21.951 1.00110.55 ATOM 14 CD1 LEU D 542 -51.606 48.223 -20.803 1.00110.30 ATOM 15 CD2 LEU D 542 -49.846 46.926 -22.035 1.00101.04 ATOM 16 N TYR D 543 -51.801 44.068 -19.481 1.00128.06 ATOM 17 CA TYR D 543 -51.379 43.726 -18.125 1.00125.81 ATOM 18 C TYR D 543 -51.705 42.277 -17.741 1.00128.88 ATOM 19 O TYR D 543 -52.780 41.771 -18.056 1.00133.46 ATOM 20 CB TYR D 543 -52.061 44.661 -17.128 1.00122.20 ATOM 21 CG TYR D 543 -51.707 46.105 -17.309 1.00119.03 ATOM 22 CD1 TYR D 543 -50.410 46.536 -17.155 1.00121.34 ATOM 23 CD2 TYR D 543 -52.675 47.039 -17.618 1.00134.80 ATOM 24 CE1 TYR D 543 -50.077 47.860 -17.318 1.00138.78 ATOM 25 CE2 TYR D 543 -52.353 48.376 -17.777 1.00149.23 ATOM 26 CZ TYR D 543 -51.047 48.782 -17.629 1.00147.53 ATOM 27 OH TYR D 543 -50.702 50.110 -17.799 1.00146.86 ATOM 28 N LYS D 544 -50.772 41.613 -17.063 1.00119.96 ATOM 29 CA LYS D 544 -51.058 40.329 -16.428 1.00123.69 ATOM 30 C LYS D 544 -50.686 40.379 -14.953 1.00118.50 ATOM 31 O LYS D 544 -49.561 40.724 -14.596 1.00116.63 ATOM 32 CB LYS D 544 -50.334 39.165 -17.117 1.00130.24 ATOM 33 CG LYS D 544 -50.821 37.793 -16.631 1.00145.07 ATOM 34 CD LYS D 544 -50.009 36.631 -17.192 1.00146.81 ATOM 35 CE LYS D 544 -48.925 36.203 -16.238 1.00147.50 ATOM 36 NZ LYS D 544 -48.053 37.353 -15.912 1.00154.08 ATOM 37 N MET D 545 -51.629 39.999 -14.101 1.00123.75 ATOM 38 CA MET D 545 -51.444 40.111 -12.665 1.00134.39 ATOM 39 C MET D 545 -51.439 38.709 -12.082 1.00145.35 ATOM 40 O MET D 545 -52.190 37.850 -12.542 1.00146.00 ATOM 41 CB MET D 545 -52.563 40.958 -12.063 1.00129.85 ATOM 42 CG MET D 545 -52.162 41.726 -10.827 1.00128.08 ATOM 43 SD MET D 545 -53.194 43.194 -10.642 1.00164.32 ATOM 44 CE MET D 545 -52.337 44.055 -9.313 1.00180.72 ATOM 45 N SER D 546 -50.562 38.457 -11.113 1.00144.33 ATOM 46 CA SER D 546 -50.438 37.112 -10.552 1.00148.01 ATOM 47 C SER D 546 -50.217 37.114 -9.044 1.00142.60 ATOM 48 O SER D 546 -49.458 37.938 -8.545 1.00143.91 ATOM 49 CB SER D 546 -49.320 36.333 -11.253 1.00153.50 ATOM 50 OG SER D 546 -48.113 37.064 -11.274 1.00162.44 ATOM 51 N LYS D 547 -50.880 36.186 -8.338 1.00155.26 ATOM 52 CA LYS D 547 -50.765 36.033 -6.871 1.00155.32 ATOM 53 C LYS D 547 -50.377 34.614 -6.425 1.00153.65 ATOM 54 O LYS D 547 -49.383 34.038 -6.881 1.00147.49 ATOM 55 CB LYS D 547 -52.069 36.444 -6.153 1.00139.16 ATOM 56 N GLU D 553 -51.086 29.205 -8.282 1.00193.58 ATOM 57 CA GLU D 553 -50.955 30.549 -8.829 1.00193.45 ATOM 58 C GLU D 553 -52.300 31.011 -9.350 1.00208.20 ATOM 59 O GLU D 553 -53.013 30.249 -9.996 1.00221.03 ATOM 60 CB GLU D 553 -49.964 30.562 -9.997 1.00179.25 ATOM 61 N GLU D 554 -52.643 32.263 -9.080 1.00210.60 ATOM 62 CA GLU D 554 -53.855 32.848 -9.641 1.00211.21 ATOM 63 C GLU D 554 -53.461 33.982 -10.583 1.00199.66 ATOM 64 O GLU D 554 -52.668 34.849 -10.228 1.00206.13 ATOM 65 CB GLU D 554 -54.808 33.330 -8.542 1.00214.34 ATOM 66 N VAL D 555 -53.995 33.949 -11.797 1.00176.24 ATOM 67 CA VAL D 555 -53.567 34.865 -12.842 1.00151.92 ATOM 68 C VAL D 555 -54.732 35.432 -13.659 1.00157.61 ATOM 69 O VAL D 555 -55.580 34.700 -14.181 1.00162.76 ATOM 70 CB VAL D 555 -52.561 34.156 -13.763 1.00141.24 ATOM 71 CG1 VAL D 555 -52.384 34.910 -15.120 1.00128.10 ATOM 72 CG2 VAL D 555 -51.239 33.907 -12.999 1.00121.30 ATOM 73 N ALA D 556 -54.754 36.750 -13.771 1.00154.36 ATOM 74 CA ALA D 556 -55.763 37.437 -14.555 1.00149.34 ATOM 75 C ALA D 556 -55.090 38.373 -15.559 1.00143.14 ATOM 76 O ALA D 556 -53.892 38.647 -15.470 1.00127.61 ATOM 77 CB ALA D 556 -56.722 38.190 -13.649 1.00139.17 ATOM 78 N TYR D 557 -55.863 38.828 -16.536 1.00141.18 ATOM 79 CA TYR D 557 -55.360 39.729 -17.554 1.00129.31 ATOM 80 C TYR D 557 -56.222 40.984 -17.649 1.00135.11 ATOM 81 O TYR D 557 -57.441 40.932 -17.483 1.00140.82 ATOM 82 CB TYR D 557 -55.358 39.026 -18.899 1.00126.83 ATOM 83 CG TYR D 557 -54.336 37.928 -19.038 1.00134.46 ATOM 84 CD1 TYR D 557 -54.636 36.619 -18.690 1.00141.36 ATOM 85 CD2 TYR D 557 -53.076 38.194 -19.554 1.00143.09 ATOM 86 CE1 TYR D 557 -53.700 35.601 -18.847 1.00145.16 ATOM 87 CE2 TYR D 557 -52.135 37.187 -19.710 1.00144.95 ATOM 88 CZ TYR D 557 -52.450 35.894 -19.356 1.00146.36 ATOM 89 OH TYR D 557 -51.503 34.905 -19.513 1.00146.67 ATOM 90 N ALA D 558 -55.576 42.107 -17.934 1.00125.96 ATOM 91 CA ALA D 558 -56.257 43.380 -18.106 1.00131.89 ATOM 92 C ALA D 558 -55.932 43.941 -19.482 1.00127.35 ATOM 93 O ALA D 558 -54.907 43.595 -20.069 1.00123.99 ATOM 94 CB ALA D 558 -55.800 44.354 -17.022 1.00141.18 ATOM 95 N TRP D 559 -56.796 44.808 -19.999 1.00134.96 ATOM 96 CA TRP D 559 -56.568 45.373 -21.332 1.00148.43 ATOM 97 C TRP D 559 -56.411 46.892 -21.340 1.00160.77 ATOM 98 O TRP D 559 -55.941 47.465 -22.332 1.00150.28 ATOM 99 CB TRP D 559 -57.676 44.950 -22.304 1.00149.52 ATOM 100 CG TRP D 559 -57.448 43.612 -22.897 1.00141.80 ATOM 101 CD1 TRP D 559 -57.023 43.348 -24.154 1.00136.60 ATOM 102 CD2 TRP D 559 -57.607 42.344 -22.248 1.00151.35 ATOM 103 NE1 TRP D 559 -56.905 41.993 -24.340 1.00140.36 ATOM 104 CE2 TRP D 559 -57.264 41.353 -23.184 1.00149.09 ATOM 105 CE3 TRP D 559 -58.002 41.952 -20.963 1.00158.95 ATOM 106 CZ2 TRP D 559 -57.308 39.994 -22.886 1.00151.74 ATOM 107 CZ3 TRP D 559 -58.043 40.602 -20.665 1.00155.70 ATOM 108 CH2 TRP D 559 -57.699 39.640 -21.624 1.00152.46 ATOM 109 N THR D 560 -56.812 47.531 -20.239 1.00172.96 ATOM 110 CA THR D 560 -56.668 48.976 -20.087 1.00165.28 ATOM 111 C THR D 560 -56.983 49.440 -18.674 1.00177.79 ATOM 112 O THR D 560 -58.021 49.089 -18.112 1.00184.56 ATOM 113 CB THR D 560 -57.549 49.767 -21.086 1.00152.64 ATOM 114 N ASP D 561 -56.057 50.219 -18.121 1.00183.99 ATOM 115 CA ASP D 561 -56.236 50.987 -16.884 1.00193.02 ATOM 116 C ASP D 561 -57.407 50.589 -15.979 1.00189.33 ATOM 117 O ASP D 561 -57.201 50.051 -14.891 1.00190.95 ATOM 118 CB ASP D 561 -56.316 52.472 -17.236 1.00205.15 ATOM 119 CG ASP D 561 -55.524 52.805 -18.488 1.00216.68 ATOM 120 OD1 ASP D 561 -54.363 52.349 -18.601 1.00213.06 ATOM 121 OD2 ASP D 561 -56.071 53.503 -19.370 1.00225.72 ATOM 122 N GLY D 562 -58.628 50.887 -16.410 1.00183.74 ATOM 123 CA GLY D 562 -59.795 50.557 -15.615 1.00194.50 ATOM 124 C GLY D 562 -59.803 49.103 -15.176 1.00198.16 ATOM 125 O GLY D 562 -59.998 48.792 -13.995 1.00189.55 ATOM 126 N GLU D 563 -59.597 48.209 -16.141 1.00204.88 ATOM 127 CA GLU D 563 -59.548 46.774 -15.879 1.00199.54 ATOM 128 C GLU D 563 -58.518 46.478 -14.788 1.00185.52 ATOM 129 O GLU D 563 -58.723 45.614 -13.923 1.00178.80 ATOM 130 CB GLU D 563 -59.240 46.014 -17.182 1.00192.88 ATOM 131 N LEU D 564 -57.412 47.215 -14.840 1.00179.12 ATOM 132 CA LEU D 564 -56.330 47.064 -13.877 1.00167.09 ATOM 133 C LEU D 564 -56.808 47.275 -12.449 1.00158.75 ATOM 134 O LEU D 564 -56.533 46.447 -11.589 1.00158.31 ATOM 135 CB LEU D 564 -55.188 48.038 -14.188 1.00153.99 ATOM 136 CG LEU D 564 -53.827 47.683 -13.592 1.00132.07 ATOM 137 CD1 LEU D 564 -53.776 46.204 -13.251 1.00123.88 ATOM 138 CD2 LEU D 564 -52.691 48.064 -14.540 1.00120.67 ATOM 139 N GLU D 565 -57.526 48.369 -12.200 1.00156.33 ATOM 140 CA GLU D 565 -58.006 48.678 -10.848 1.00169.62 ATOM 141 C GLU D 565 -58.814 47.526 -10.246 1.00186.22 ATOM 142 O GLU D 565 -58.567 47.117 -9.107 1.00180.92 ATOM 143 CB GLU D 565 -58.818 49.982 -10.823 1.00158.81 ATOM 144 N GLU D 566 -59.774 47.014 -11.017 1.00199.84 ATOM 145 CA GLU D 566 -60.605 45.882 -10.598 1.00202.99 ATOM 146 C GLU D 566 -59.775 44.621 -10.335 1.00198.64 ATOM 147 O GLU D 566 -60.000 43.913 -9.347 1.00193.18 ATOM 148 CB GLU D 566 -61.715 45.604 -11.620 1.00196.44 ATOM 149 N LEU D 567 -58.829 44.340 -11.233 1.00191.55 ATOM 150 CA LEU D 567 -57.900 43.224 -11.055 1.00177.75 ATOM 151 C LEU D 567 -57.099 43.364 -9.744 1.00188.41 ATOM 152 O LEU D 567 -56.955 42.400 -8.976 1.00187.95 ATOM 153 CB LEU D 567 -56.980 43.092 -12.282 1.00140.53 ATOM 154 N ARG D 568 -56.590 44.572 -9.497 1.00186.07 ATOM 155 CA ARG D 568 -55.849 44.897 -8.275 1.00169.49 ATOM 156 C ARG D 568 -56.693 44.662 -7.019 1.00179.29 ATOM 157 O ARG D 568 -56.209 44.103 -6.034 1.00175.92 ATOM 158 CB ARG D 568 -55.333 46.348 -8.323 1.00144.38 ATOM 159 N LYS D 569 -57.951 45.097 -7.055 1.00188.65 ATOM 160 CA LYS D 569 -58.872 44.859 -5.946 1.00191.90 ATOM 161 C LYS D 569 -59.007 43.362 -5.678 1.00200.87 ATOM 162 O LYS D 569 -58.916 42.919 -4.532 1.00197.42 ATOM 163 CB LYS D 569 -60.245 45.486 -6.221 1.00183.18 ATOM 164 N GLN D 570 -59.213 42.586 -6.741 1.00208.47 ATOM 165 CA GLN D 570 -59.364 41.136 -6.618 1.00210.09 ATOM 166 C GLN D 570 -58.147 40.475 -5.955 1.00209.76 ATOM 167 O GLN D 570 -58.251 39.883 -4.878 1.00215.58 ATOM 168 CB GLN D 570 -59.646 40.509 -7.992 1.00196.99 ATOM 169 N PHE D 571 -56.992 40.594 -6.595 1.00192.18 ATOM 170 CA PHE D 571 -55.770 39.967 -6.104 1.00182.25 ATOM 171 C PHE D 571 -55.307 40.413 -4.715 1.00195.77 ATOM 172 O PHE D 571 -54.392 39.813 -4.142 1.00192.87 ATOM 173 CB PHE D 571 -54.658 40.216 -7.088 1.00166.36 ATOM 174 CG PHE D 571 -54.721 39.340 -8.277 1.00168.30 ATOM 175 CD1 PHE D 571 -55.688 39.543 -9.238 1.00174.90 ATOM 176 CD2 PHE D 571 -53.808 38.308 -8.438 1.00167.65 ATOM 177 CE1 PHE D 571 -55.743 38.734 -10.352 1.00183.67 ATOM 178 CE2 PHE D 571 -53.856 37.495 -9.541 1.00173.30 ATOM 179 CZ PHE D 571 -54.826 37.704 -10.506 1.00182.46 ATOM 180 N GLY D 572 -55.960 41.435 -4.169 1.00207.80 ATOM 181 CA GLY D 572 -55.405 42.248 -3.098 1.00208.08 ATOM 182 C GLY D 572 -53.906 42.126 -2.883 1.00199.83 ATOM 183 O GLY D 572 -53.139 42.063 -3.842 1.00198.15 ATOM 184 N LYS D 573 -53.478 42.121 -1.626 1.00194.87 ATOM 185 CA LYS D 573 -52.052 42.158 -1.312 1.00184.68 ATOM 186 C LYS D 573 -51.245 41.105 -2.077 1.00180.99 ATOM 187 O LYS D 573 -51.800 40.137 -2.596 1.00186.46 ATOM 188 CB LYS D 573 -51.831 42.020 0.204 1.00174.42 ATOM 189 N GLY D 574 -49.935 41.318 -2.161 1.00171.85 ATOM 190 CA GLY D 574 -49.016 40.300 -2.641 1.00170.69 ATOM 191 C GLY D 574 -48.803 40.231 -4.142 1.00176.62 ATOM 192 O GLY D 574 -47.731 39.842 -4.607 1.00179.01 ATOM 193 N ALA D 575 -49.821 40.609 -4.903 1.00178.33 ATOM 194 CA ALA D 575 -49.792 40.453 -6.355 1.00178.14 ATOM 195 C ALA D 575 -48.635 41.167 -7.058 1.00159.91 ATOM 196 O ALA D 575 -48.294 42.295 -6.727 1.00161.87 ATOM 197 CB ALA D 575 -51.113 40.913 -6.949 1.00193.35 ATOM 198 N THR D 576 -48.036 40.500 -8.037 1.00150.78 ATOM 199 CA THR D 576 -47.138 41.181 -8.959 1.00154.22 ATOM 200 C THR D 576 -47.863 41.449 -10.281 1.00155.55 ATOM 201 O THR D 576 -48.691 40.654 -10.735 1.00153.33 ATOM 202 CB THR D 576 -45.801 40.416 -9.204 1.00155.56 ATOM 203 OG1 THR D 576 -46.063 39.036 -9.467 1.00150.08 ATOM 204 CG2 THR D 576 -44.866 40.527 -7.996 1.00154.48 ATOM 205 N LEU D 577 -47.557 42.591 -10.881 1.00144.93 ATOM 206 CA LEU D 577 -48.210 43.014 -12.107 1.00120.72 ATOM 207 C LEU D 577 -47.156 43.176 -13.169 1.00111.03 ATOM 208 O LEU D 577 -46.090 43.738 -12.923 1.00114.42 ATOM 209 CB LEU D 577 -48.957 44.330 -11.901 1.00117.77 ATOM 210 CG LEU D 577 -49.104 45.258 -13.101 1.00109.12 ATOM 211 CD1 LEU D 577 -49.971 44.636 -14.158 1.00114.59 ATOM 212 CD2 LEU D 577 -49.681 46.580 -12.662 1.00108.82 ATOM 213 N GLN D 578 -47.463 42.676 -14.355 1.00105.44 ATOM 214 CA GLN D 578 -46.531 42.680 -15.460 1.00105.03 ATOM 215 C GLN D 578 -47.221 43.406 -16.597 1.00114.22 ATOM 216 O GLN D 578 -48.420 43.254 -16.790 1.00116.39 ATOM 217 CB GLN D 578 -46.227 41.242 -15.855 1.00120.42 ATOM 218 CG GLN D 578 -44.897 41.020 -16.536 1.00144.06 ATOM 219 CD GLN D 578 -44.786 39.606 -17.079 1.00166.16 ATOM 220 OE1 GLN D 578 -45.510 38.712 -16.647 1.00176.83 ATOM 221 NE2 GLN D 578 -43.888 39.399 -18.034 1.00168.04 ATOM 222 N ARG D 579 -46.483 44.230 -17.327 1.00116.72 ATOM 223 CA ARG D 579 -47.083 44.978 -18.415 1.00109.58 ATOM 224 C ARG D 579 -46.320 44.728 -19.683 1.00108.40 ATOM 225 O ARG D 579 -45.124 45.005 -19.756 1.00120.02 ATOM 226 CB ARG D 579 -47.094 46.466 -18.130 1.00113.12 ATOM 227 CG ARG D 579 -47.578 47.274 -19.315 1.00115.68 ATOM 228 CD ARG D 579 -47.144 48.705 -19.176 1.00120.06 ATOM 229 NE ARG D 579 -46.542 49.171 -20.413 1.00124.38 ATOM 230 CZ ARG D 579 -47.008 50.197 -21.108 1.00119.82 ATOM 231 NH1 ARG D 579 -48.079 50.848 -20.629 1.00111.19 ATOM 232 NH2 ARG D 579 -46.398 50.569 -22.252 1.00 94.22 ATOM 233 N TYR D 580 -47.022 44.201 -20.678 1.00108.52 ATOM 234 CA TYR D 580 -46.408 43.859 -21.949 1.00 98.20 ATOM 235 C TYR D 580 -46.293 45.123 -22.754 1.00112.48 ATOM 236 O TYR D 580 -47.217 45.521 -23.455 1.00125.96 ATOM 237 CB TYR D 580 -47.194 42.760 -22.697 1.00100.63 ATOM 238 CG TYR D 580 -47.397 41.537 -21.842 1.00109.73 ATOM 239 CD1 TYR D 580 -46.344 41.017 -21.108 1.00116.24 ATOM 240 CD2 TYR D 580 -48.638 40.938 -21.719 1.00127.29 ATOM 241 CE1 TYR D 580 -46.503 39.928 -20.285 1.00128.56 ATOM 242 CE2 TYR D 580 -48.812 39.833 -20.894 1.00143.96 ATOM 243 CZ TYR D 580 -47.730 39.332 -20.179 1.00143.33 ATOM 244 OH TYR D 580 -47.851 38.234 -19.350 1.00148.41 ATOM 245 N LYS D 581 -45.149 45.772 -22.608 1.00128.54 ATOM 246 CA LYS D 581 -44.884 47.009 -23.308 1.00146.30 ATOM 247 C LYS D 581 -44.329 46.637 -24.669 1.00126.33 ATOM 248 O LYS D 581 -43.188 46.965 -24.985 1.00139.65 ATOM 249 CB LYS D 581 -43.876 47.853 -22.515 1.00161.82 ATOM 250 N GLY D 582 -45.143 45.947 -25.463 1.00102.59 ATOM 251 CA GLY D 582 -44.677 45.341 -26.698 1.00121.05 ATOM 252 C GLY D 582 -44.902 43.837 -26.712 1.00123.36 ATOM 253 O GLY D 582 -44.787 43.178 -25.684 1.00123.76 TER