HEADER DNA BINDING PROTEIN/DNA 31-DEC-69 6LWO TITLE Crystal structure of human NEIL1(R242, Y244H) bound to duplex DNA TITLE 2 containing 2'-fluoro-2'-deoxy-5,6-dihydrouridine COMPND MOL_ID: 1; COMPND 2 MOLECULE: Endonuclease 8-like 1; COMPND 3 CHAIN: A, D, G; COMPND 4 MUTATION: YES; COMPND 5 EC: 3.2.2.-,4.2.99.18; COMPND 6 ENGINEERED: YES; EXPDTA X-RAY DIFFRACTION REMARK 2 RESOLUTION. 2.51 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 GLU G 247 REMARK 465 SER G 248 REMARK 465 GLY G 249 REMARK 465 GLU G 250 REMARK 465 GLU G 251 REMARK 465 GLY G 264 DBREF 6LWO G 1 295 UNP Q96FI4 NEIL1_HUMAN 1 295 SEQRES 1 G 43 GLU SER GLY GLU GLU ASP PHE ALA ALA PHE ARG ALA TRP SEQRES 2 G 43 LEU ARG CYS TYR GLY MET PRO GLY MET SER SER LEU GLN SEQRES 3 G 43 ASP ARG HIS GLY ARG THR ILE TRP PHE GLN GLY ASP PRO SEQRES 4 G 43 GLY PRO LEU ALA ATOM 1 N ASP G 252 -27.281 12.801 13.855 1.00136.09 ATOM 2 CA ASP G 252 -28.650 12.903 13.271 1.00132.96 ATOM 3 C ASP G 252 -29.372 11.548 13.350 1.00130.01 ATOM 4 O ASP G 252 -30.554 11.527 13.754 1.00129.26 ATOM 5 N PHE G 253 -28.705 10.468 12.922 1.00127.62 ATOM 6 CA PHE G 253 -29.199 9.067 13.018 1.00121.48 ATOM 7 C PHE G 253 -29.366 8.681 14.499 1.00119.45 ATOM 8 O PHE G 253 -30.323 7.952 14.846 1.00117.85 ATOM 9 N ALA G 254 -28.450 9.150 15.352 1.00119.00 ATOM 10 CA ALA G 254 -28.483 8.962 16.823 1.00117.80 ATOM 11 C ALA G 254 -29.688 9.710 17.408 1.00113.03 ATOM 12 O ALA G 254 -30.409 9.119 18.229 1.00112.09 ATOM 13 N ALA G 255 -29.883 10.967 16.992 1.00110.62 ATOM 14 CA ALA G 255 -31.014 11.844 17.378 1.00108.31 ATOM 15 C ALA G 255 -32.344 11.134 17.093 1.00105.49 ATOM 16 O ALA G 255 -33.213 11.109 17.981 1.00104.70 ATOM 17 N PHE G 256 -32.491 10.549 15.902 1.00105.22 ATOM 18 CA PHE G 256 -33.732 9.863 15.457 1.00103.69 ATOM 19 C PHE G 256 -34.012 8.636 16.332 1.00104.81 ATOM 20 O PHE G 256 -35.149 8.497 16.806 1.00102.99 ATOM 21 CB PHE G 256 -33.644 9.458 13.989 1.00102.37 ATOM 22 CG PHE G 256 -34.932 8.907 13.440 1.00102.30 ATOM 23 CD1 PHE G 256 -36.042 9.727 13.268 1.00101.73 ATOM 24 CD2 PHE G 256 -35.036 7.568 13.096 1.00103.44 ATOM 25 CE1 PHE G 256 -37.221 9.220 12.741 1.00 99.46 ATOM 26 CE2 PHE G 256 -36.213 7.068 12.568 1.00101.78 ATOM 27 CZ PHE G 256 -37.293 7.894 12.407 1.00 99.44 ATOM 28 N ARG G 257 -33.001 7.787 16.536 1.00106.69 ATOM 29 CA ARG G 257 -33.107 6.523 17.314 1.00107.91 ATOM 30 C ARG G 257 -33.584 6.858 18.744 1.00109.07 ATOM 31 O ARG G 257 -34.463 6.111 19.272 1.00111.29 ATOM 32 CB ARG G 257 -31.776 5.759 17.228 1.00110.49 ATOM 33 N ALA G 258 -33.087 7.963 19.325 1.00109.39 ATOM 34 CA ALA G 258 -33.406 8.446 20.696 1.00109.45 ATOM 35 C ALA G 258 -34.854 8.963 20.779 1.00105.36 ATOM 36 O ALA G 258 -35.464 8.844 21.840 1.00105.87 ATOM 37 N TRP G 259 -35.371 9.530 19.686 1.00102.66 ATOM 38 CA TRP G 259 -36.765 10.040 19.551 1.00 99.40 ATOM 39 C TRP G 259 -37.767 8.876 19.552 1.00 97.02 ATOM 40 O TRP G 259 -38.845 9.015 20.176 1.00 97.85 ATOM 41 CB TRP G 259 -36.924 10.890 18.276 1.00 96.05 ATOM 42 CG TRP G 259 -38.347 11.284 17.997 1.00 92.94 ATOM 43 CD1 TRP G 259 -39.066 12.289 18.587 1.00 93.30 ATOM 44 CD2 TRP G 259 -39.258 10.640 17.094 1.00 89.18 ATOM 45 NE1 TRP G 259 -40.350 12.319 18.105 1.00 90.57 ATOM 46 CE2 TRP G 259 -40.499 11.311 17.196 1.00 88.84 ATOM 47 CE3 TRP G 259 -39.142 9.572 16.201 1.00 87.62 ATOM 48 CZ2 TRP G 259 -41.608 10.952 16.426 1.00 88.55 ATOM 49 CZ3 TRP G 259 -40.236 9.217 15.438 1.00 85.76 ATOM 50 CH2 TRP G 259 -41.452 9.901 15.545 1.00 86.20 ATOM 51 N LEU G 260 -37.446 7.803 18.831 1.00 95.21 ATOM 52 CA LEU G 260 -38.311 6.604 18.700 1.00 95.54 ATOM 53 C LEU G 260 -38.672 6.088 20.092 1.00 98.75 ATOM 54 O LEU G 260 -37.755 6.021 20.963 1.00104.52 ATOM 55 CB LEU G 260 -37.566 5.517 17.925 1.00 96.20 ATOM 56 CG LEU G 260 -37.453 5.753 16.422 1.00 95.24 ATOM 57 CD1 LEU G 260 -36.530 4.728 15.786 1.00 96.27 ATOM 58 CD2 LEU G 260 -38.823 5.770 15.759 1.00 93.62 ATOM 59 N ARG G 261 -39.939 5.727 20.295 1.00 95.75 ATOM 60 CA ARG G 261 -40.404 5.065 21.545 1.00 96.35 ATOM 61 C ARG G 261 -40.718 3.584 21.279 1.00 99.68 ATOM 62 O ARG G 261 -40.630 2.801 22.235 1.00102.60 ATOM 63 CB ARG G 261 -41.629 5.783 22.110 1.00 92.36 ATOM 64 CG ARG G 261 -41.470 7.292 22.248 1.00 90.06 ATOM 65 CD ARG G 261 -42.758 7.908 22.768 1.00 88.96 ATOM 66 NE ARG G 261 -42.776 9.358 22.653 1.00 88.37 ATOM 67 CZ ARG G 261 -43.638 10.173 23.278 1.00 89.81 ATOM 68 NH1 ARG G 261 -44.587 9.694 24.079 1.00 89.97 ATOM 69 NH2 ARG G 261 -43.548 11.480 23.095 1.00 89.98 ATOM 70 N CYS G 262 -41.022 3.190 20.034 1.00100.22 ATOM 71 CA CYS G 262 -41.578 1.843 19.721 1.00101.71 ATOM 72 C CYS G 262 -40.820 1.143 18.578 1.00101.11 ATOM 73 O CYS G 262 -40.357 0.004 18.804 1.00101.27 ATOM 74 CB CYS G 262 -43.062 1.946 19.384 1.00101.04 ATOM 75 SG CYS G 262 -43.836 0.330 19.110 1.00102.35 ATOM 76 N TYR G 263 -40.733 1.761 17.397 1.00 99.84 ATOM 77 CA TYR G 263 -40.261 1.120 16.136 1.00100.88 ATOM 78 C TYR G 263 -38.880 0.477 16.340 1.00102.20 ATOM 79 O TYR G 263 -37.922 1.222 16.607 1.00101.72 ATOM 80 CB TYR G 263 -40.270 2.122 14.979 1.00 99.26 ATOM 81 CG TYR G 263 -39.665 1.610 13.699 1.00 99.71 ATOM 82 CD1 TYR G 263 -40.393 0.836 12.810 1.00 99.24 ATOM 83 CD2 TYR G 263 -38.342 1.888 13.388 1.00101.73 ATOM 84 CE1 TYR G 263 -39.820 0.353 11.643 1.00100.18 ATOM 85 CE2 TYR G 263 -37.762 1.439 12.213 1.00100.81 ATOM 86 CZ TYR G 263 -38.502 0.664 11.339 1.00100.64 ATOM 87 OH TYR G 263 -37.908 0.212 10.195 1.00101.34 ATOM 88 N MET G 265 -37.495 -0.979 18.903 1.00125.08 ATOM 89 CA MET G 265 -36.933 -0.755 20.261 1.00128.57 ATOM 90 C MET G 265 -36.877 -2.093 20.994 1.00131.40 ATOM 91 O MET G 265 -37.759 -2.940 20.825 1.00131.57 ATOM 92 CB MET G 265 -37.771 0.253 21.068 1.00129.95 ATOM 93 CG MET G 265 -37.102 1.616 21.346 1.00130.36 ATOM 94 SD MET G 265 -35.993 2.263 20.044 1.00131.23 ATOM 95 CE MET G 265 -35.064 3.479 20.980 1.00133.04 ATOM 96 N PRO G 266 -35.845 -2.305 21.844 1.00132.31 ATOM 97 CA PRO G 266 -35.748 -3.546 22.611 1.00135.35 ATOM 98 C PRO G 266 -36.959 -3.755 23.534 1.00134.20 ATOM 99 O PRO G 266 -37.463 -2.778 24.069 1.00133.24 ATOM 100 CB PRO G 266 -34.453 -3.377 23.421 1.00137.95 ATOM 101 N GLY G 267 -37.400 -5.010 23.672 1.00135.82 ATOM 102 CA GLY G 267 -38.568 -5.400 24.484 1.00136.79 ATOM 103 C GLY G 267 -39.900 -5.066 23.827 1.00132.88 ATOM 104 O GLY G 267 -40.911 -5.053 24.557 1.00132.91 ATOM 105 N MET G 268 -39.917 -4.777 22.517 1.00130.02 ATOM 106 CA MET G 268 -41.169 -4.505 21.757 1.00127.66 ATOM 107 C MET G 268 -41.587 -5.745 20.965 1.00125.67 ATOM 108 O MET G 268 -40.690 -6.496 20.561 1.00126.92 ATOM 109 CB MET G 268 -40.987 -3.321 20.805 1.00126.68 ATOM 110 CG MET G 268 -40.894 -1.993 21.533 1.00128.08 ATOM 111 SD MET G 268 -42.499 -1.546 22.278 1.00130.30 ATOM 112 CE MET G 268 -42.001 -0.219 23.380 1.00133.15 ATOM 113 N SER G 269 -42.891 -5.947 20.756 1.00123.25 ATOM 114 CA SER G 269 -43.423 -7.025 19.880 1.00124.23 ATOM 115 C SER G 269 -43.318 -6.567 18.423 1.00122.15 ATOM 116 O SER G 269 -43.239 -5.350 18.201 1.00119.78 ATOM 117 CB SER G 269 -44.842 -7.394 20.234 1.00124.00 ATOM 118 OG SER G 269 -44.873 -8.102 21.463 1.00127.45 ATOM 119 N SER G 270 -43.302 -7.513 17.487 1.00122.11 ATOM 120 CA SER G 270 -43.332 -7.255 16.026 1.00117.97 ATOM 121 C SER G 270 -44.052 -8.422 15.349 1.00120.08 ATOM 122 O SER G 270 -43.810 -9.566 15.758 1.00123.80 ATOM 123 N LEU G 271 -44.922 -8.137 14.378 1.00118.80 ATOM 124 CA LEU G 271 -45.532 -9.161 13.493 1.00119.70 ATOM 125 C LEU G 271 -45.522 -8.622 12.060 1.00116.19 ATOM 126 O LEU G 271 -45.322 -7.403 11.878 1.00110.46 ATOM 127 N GLN G 272 -45.695 -9.511 11.083 1.00119.00 ATOM 128 CA GLN G 272 -45.910 -9.144 9.661 1.00118.25 ATOM 129 C GLN G 272 -47.407 -8.876 9.472 1.00119.20 ATOM 130 O GLN G 272 -48.213 -9.697 9.942 1.00122.05 ATOM 131 CB GLN G 272 -45.399 -10.252 8.736 1.00120.57 ATOM 132 N ASP G 273 -47.765 -7.758 8.834 1.00116.96 ATOM 133 CA ASP G 273 -49.150 -7.500 8.351 1.00118.31 ATOM 134 C ASP G 273 -49.381 -8.339 7.085 1.00121.61 ATOM 135 O ASP G 273 -48.468 -9.106 6.700 1.00120.78 ATOM 136 CB ASP G 273 -49.404 -6.002 8.153 1.00114.96 ATOM 137 CG ASP G 273 -48.503 -5.302 7.142 1.00113.11 ATOM 138 OD1 ASP G 273 -47.909 -5.983 6.274 1.00114.97 ATOM 139 OD2 ASP G 273 -48.411 -4.064 7.224 1.00109.21 ATOM 140 N ARG G 274 -50.547 -8.184 6.454 1.00124.38 ATOM 141 CA ARG G 274 -51.003 -9.026 5.316 1.00128.45 ATOM 142 C ARG G 274 -50.124 -8.779 4.082 1.00129.78 ATOM 143 O ARG G 274 -50.151 -9.643 3.185 1.00136.58 ATOM 144 CB ARG G 274 -52.484 -8.777 5.011 1.00128.53 ATOM 145 N HIS G 275 -49.357 -7.679 4.027 1.00126.90 ATOM 146 CA HIS G 275 -48.491 -7.321 2.866 1.00126.81 ATOM 147 C HIS G 275 -47.004 -7.478 3.221 1.00124.08 ATOM 148 O HIS G 275 -46.162 -6.941 2.487 1.00120.63 ATOM 149 CB HIS G 275 -48.864 -5.915 2.365 1.00126.24 ATOM 150 CG HIS G 275 -50.343 -5.721 2.219 1.00129.97 ATOM 151 ND1 HIS G 275 -51.118 -5.117 3.200 1.00130.93 ATOM 152 CD2 HIS G 275 -51.216 -6.151 1.277 1.00134.22 ATOM 153 CE1 HIS G 275 -52.386 -5.133 2.836 1.00132.31 ATOM 154 NE2 HIS G 275 -52.473 -5.761 1.664 1.00134.24 ATOM 155 N GLY G 276 -46.689 -8.200 4.300 1.00124.37 ATOM 156 CA GLY G 276 -45.314 -8.587 4.670 1.00123.29 ATOM 157 C GLY G 276 -44.509 -7.451 5.287 1.00118.40 ATOM 158 O GLY G 276 -43.280 -7.593 5.345 1.00117.53 ATOM 159 N ARG G 277 -45.148 -6.375 5.757 1.00114.16 ATOM 160 CA ARG G 277 -44.454 -5.238 6.425 1.00109.14 ATOM 161 C ARG G 277 -44.522 -5.420 7.949 1.00107.16 ATOM 162 O ARG G 277 -45.568 -5.859 8.457 1.00107.49 ATOM 163 CB ARG G 277 -45.041 -3.906 5.947 1.00106.72 ATOM 164 CG ARG G 277 -45.030 -3.753 4.434 1.00107.64 ATOM 165 CD ARG G 277 -44.656 -2.367 3.941 1.00104.77 ATOM 166 NE ARG G 277 -43.311 -2.010 4.358 1.00103.15 ATOM 167 CZ ARG G 277 -42.844 -0.771 4.431 1.00102.38 ATOM 168 NH1 ARG G 277 -43.608 0.255 4.100 1.00101.91 ATOM 169 NH2 ARG G 277 -41.616 -0.551 4.864 1.00102.59 ATOM 170 N THR G 278 -43.427 -5.121 8.642 1.00103.64 ATOM 171 CA THR G 278 -43.253 -5.367 10.094 1.00103.30 ATOM 172 C THR G 278 -43.929 -4.235 10.873 1.00100.29 ATOM 173 O THR G 278 -43.546 -3.067 10.653 1.00 96.73 ATOM 174 CB THR G 278 -41.768 -5.502 10.462 1.00103.26 ATOM 175 OG1 THR G 278 -41.211 -6.613 9.758 1.00106.64 ATOM 176 CG2 THR G 278 -41.552 -5.684 11.949 1.00103.87 ATOM 177 N ILE G 279 -44.911 -4.574 11.718 1.00100.48 ATOM 178 CA ILE G 279 -45.553 -3.640 12.691 1.00 98.70 ATOM 179 C ILE G 279 -44.917 -3.887 14.063 1.00100.08 ATOM 180 O ILE G 279 -44.901 -5.048 14.511 1.00102.31 ATOM 181 CB ILE G 279 -47.092 -3.775 12.729 1.00 99.21 ATOM 182 CG1 ILE G 279 -47.722 -2.790 13.721 1.00 97.84 ATOM 183 CG2 ILE G 279 -47.539 -5.202 13.027 1.00102.84 ATOM 184 CD1 ILE G 279 -47.376 -1.337 13.468 1.00 94.58 ATOM 185 N TRP G 280 -44.363 -2.830 14.659 1.00 98.38 ATOM 186 CA TRP G 280 -43.857 -2.803 16.050 1.00 99.26 ATOM 187 C TRP G 280 -44.966 -2.267 16.953 1.00 98.83 ATOM 188 O TRP G 280 -45.640 -1.313 16.556 1.00 96.20 ATOM 189 CB TRP G 280 -42.580 -1.968 16.141 1.00 98.43 ATOM 190 CG TRP G 280 -41.477 -2.553 15.324 1.00 99.61 ATOM 191 CD1 TRP G 280 -41.234 -2.328 14.001 1.00100.34 ATOM 192 CD2 TRP G 280 -40.488 -3.498 15.756 1.00102.89 ATOM 193 NE1 TRP G 280 -40.153 -3.055 13.584 1.00101.85 ATOM 194 CE2 TRP G 280 -39.669 -3.777 14.642 1.00103.34 ATOM 195 CE3 TRP G 280 -40.206 -4.128 16.972 1.00106.37 ATOM 196 CZ2 TRP G 280 -38.589 -4.655 14.709 1.00105.19 ATOM 197 CZ3 TRP G 280 -39.140 -4.997 17.040 1.00109.30 ATOM 198 CH2 TRP G 280 -38.345 -5.259 15.920 1.00108.85 ATOM 199 N PHE G 281 -45.143 -2.879 18.119 1.00102.80 ATOM 200 CA PHE G 281 -46.202 -2.533 19.102 1.00104.34 ATOM 201 C PHE G 281 -45.839 -3.124 20.467 1.00108.15 ATOM 202 O PHE G 281 -44.961 -4.034 20.560 1.00110.21 ATOM 203 CB PHE G 281 -47.569 -3.034 18.630 1.00104.75 ATOM 204 CG PHE G 281 -47.666 -4.531 18.481 1.00108.10 ATOM 205 CD1 PHE G 281 -47.091 -5.174 17.393 1.00108.95 ATOM 206 CD2 PHE G 281 -48.318 -5.302 19.430 1.00110.90 ATOM 207 CE1 PHE G 281 -47.149 -6.556 17.264 1.00112.32 ATOM 208 CE2 PHE G 281 -48.402 -6.678 19.285 1.00114.42 ATOM 209 CZ PHE G 281 -47.818 -7.303 18.206 1.00114.89 ATOM 210 N GLN G 282 -46.489 -2.571 21.496 1.00108.78 ATOM 211 CA GLN G 282 -46.459 -3.058 22.894 1.00110.46 ATOM 212 C GLN G 282 -47.802 -3.739 23.166 1.00112.00 ATOM 213 O GLN G 282 -48.848 -3.167 22.783 1.00108.48 ATOM 214 N GLY G 283 -47.749 -4.941 23.748 1.00115.72 ATOM 215 CA GLY G 283 -48.902 -5.619 24.364 1.00117.87 ATOM 216 C GLY G 283 -49.754 -6.371 23.356 1.00118.13 ATOM 217 O GLY G 283 -49.186 -7.117 22.518 1.00118.18 ATOM 218 N ASP G 284 -51.074 -6.197 23.468 1.00117.92 ATOM 219 CA ASP G 284 -52.104 -7.009 22.757 1.00118.79 ATOM 220 C ASP G 284 -51.953 -6.702 21.260 1.00115.06 ATOM 221 O ASP G 284 -51.870 -5.547 20.827 1.00110.67 ATOM 222 CB ASP G 284 -53.461 -6.900 23.493 1.00120.23 ATOM 223 CG ASP G 284 -54.730 -6.719 22.664 1.00119.92 ATOM 224 OD1 ASP G 284 -54.616 -6.125 21.592 1.00116.60 ATOM 225 OD2 ASP G 284 -55.827 -7.102 23.147 1.00122.77 ATOM 226 N PRO G 285 -51.817 -7.768 20.441 1.00116.90 ATOM 227 CA PRO G 285 -51.781 -7.634 18.983 1.00114.66 ATOM 228 C PRO G 285 -53.115 -7.150 18.388 1.00114.50 ATOM 229 O PRO G 285 -53.058 -6.392 17.438 1.00111.16 ATOM 230 N GLY G 286 -54.263 -7.579 18.939 1.00118.10 ATOM 231 CA GLY G 286 -55.599 -7.157 18.460 1.00119.73 ATOM 232 C GLY G 286 -56.308 -8.225 17.623 1.00124.28 ATOM 233 O GLY G 286 -55.678 -9.168 17.143 1.00127.55 ATOM 234 N PRO G 287 -57.641 -8.097 17.425 1.00126.09 ATOM 235 CA PRO G 287 -58.477 -9.192 16.917 1.00129.95 ATOM 236 C PRO G 287 -58.113 -9.775 15.539 1.00130.32 ATOM 237 O PRO G 287 -58.163 -10.974 15.412 1.00133.51 ATOM 238 CB PRO G 287 -59.893 -8.582 16.856 1.00130.62 ATOM 239 CG PRO G 287 -59.676 -7.075 16.894 1.00126.56 ATOM 240 CD PRO G 287 -58.423 -6.885 17.722 1.00124.40 ATOM 241 N LEU G 288 -57.766 -8.944 14.549 1.00127.66 ATOM 242 CA LEU G 288 -57.560 -9.381 13.134 1.00128.32 ATOM 243 C LEU G 288 -56.092 -9.775 12.889 1.00126.78 ATOM 244 O LEU G 288 -55.644 -9.659 11.726 1.00125.80 ATOM 245 CB LEU G 288 -57.952 -8.247 12.176 1.00125.65 ATOM 246 CG LEU G 288 -59.363 -7.674 12.303 1.00126.25 ATOM 247 CD1 LEU G 288 -59.485 -6.426 11.432 1.00123.20 ATOM 248 CD2 LEU G 288 -60.420 -8.706 11.933 1.00131.10 ATOM 249 N ALA G 289 -55.373 -10.238 13.917 1.00126.44 ATOM 250 CA ALA G 289 -53.914 -10.503 13.888 1.00124.77 ATOM 251 C ALA G 289 -53.556 -11.517 12.794 1.00126.44 ATOM 252 O ALA G 289 -54.287 -12.467 12.548 1.00129.77 ATOM 253 CB ALA G 289 -53.470 -10.974 15.252 1.00126.17 TER