HEADER DNA BINDING PROTEIN/DNA 31-DEC-69 6LWM TITLE Crystal structure of human NEIL1(K242) bound to duplex DNA containing TITLE 2 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 EC: 3.2.2.-,4.2.99.18; COMPND 5 ENGINEERED: YES; EXPDTA X-RAY DIFFRACTION REMARK 2 RESOLUTION. 2.67 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 A 247 REMARK 465 SER A 248 REMARK 465 GLY A 249 DBREF 6LWM A 1 295 UNP Q96FI4 NEIL1_HUMAN 1 295 SEQRES 1 A 44 GLU SER GLY GLU GLU ASP PHE ALA ALA PHE ARG ALA TRP SEQRES 2 A 44 LEU ARG CYS TYR GLY MET PRO GLY MET SER SER LEU GLN SEQRES 3 A 44 ASP ARG HIS GLY ARG THR ILE TRP PHE GLN GLY ASP PRO SEQRES 4 A 44 GLY PRO LEU ALA PRO ATOM 1 N ASP G 252 -27.170 12.981 12.233 1.00145.47 ATOM 2 CA ASP G 252 -28.168 13.066 13.335 1.00143.85 ATOM 3 C ASP G 252 -29.102 11.841 13.315 1.00140.67 ATOM 4 O ASP G 252 -30.286 12.018 13.651 1.00138.23 ATOM 5 CB ASP G 252 -28.962 14.371 13.230 1.00141.98 ATOM 6 N PHE G 253 -28.594 10.657 12.940 1.00139.23 ATOM 7 CA PHE G 253 -29.316 9.355 12.954 1.00133.61 ATOM 8 C PHE G 253 -29.444 8.845 14.401 1.00133.41 ATOM 9 O PHE G 253 -30.460 8.173 14.714 1.00132.11 ATOM 10 N ALA G 254 -28.448 9.146 15.249 1.00130.62 ATOM 11 CA ALA G 254 -28.456 8.864 16.707 1.00130.07 ATOM 12 C ALA G 254 -29.599 9.640 17.387 1.00126.13 ATOM 13 O ALA G 254 -30.315 9.051 18.222 1.00122.31 ATOM 14 CB ALA G 254 -27.113 9.211 17.313 1.00133.42 ATOM 15 N ALA G 255 -29.752 10.923 17.045 1.00123.63 ATOM 16 CA ALA G 255 -30.842 11.806 17.524 1.00122.63 ATOM 17 C ALA G 255 -32.197 11.166 17.203 1.00118.77 ATOM 18 O ALA G 255 -33.028 11.048 18.108 1.00119.53 ATOM 19 CB ALA G 255 -30.717 13.179 16.910 1.00122.72 ATOM 20 N PHE G 256 -32.400 10.719 15.968 1.00118.29 ATOM 21 CA PHE G 256 -33.649 10.049 15.527 1.00117.78 ATOM 22 C PHE G 256 -33.882 8.773 16.351 1.00119.02 ATOM 23 O PHE G 256 -35.003 8.588 16.885 1.00117.45 ATOM 24 CB PHE G 256 -33.606 9.755 14.031 1.00117.14 ATOM 25 CG PHE G 256 -34.872 9.123 13.520 1.00117.26 ATOM 26 CD1 PHE G 256 -36.045 9.860 13.413 1.00117.68 ATOM 27 CD2 PHE G 256 -34.897 7.781 13.170 1.00118.45 ATOM 28 CE1 PHE G 256 -37.215 9.268 12.948 1.00115.83 ATOM 29 CE2 PHE G 256 -36.065 7.195 12.713 1.00117.27 ATOM 30 CZ PHE G 256 -37.215 7.939 12.617 1.00114.91 ATOM 31 N ARG G 257 -32.867 7.910 16.446 1.00121.90 ATOM 32 CA ARG G 257 -32.938 6.605 17.165 1.00125.72 ATOM 33 C ARG G 257 -33.435 6.816 18.622 1.00124.85 ATOM 34 O ARG G 257 -34.263 5.951 19.169 1.00126.75 ATOM 35 CB ARG G 257 -31.569 5.906 17.136 1.00131.48 ATOM 36 CG ARG G 257 -31.165 5.298 15.796 1.00134.26 ATOM 37 CD ARG G 257 -31.866 4.006 15.372 1.00136.80 ATOM 38 NE ARG G 257 -31.309 2.792 15.974 1.00142.18 ATOM 39 CZ ARG G 257 -31.987 1.867 16.672 1.00144.79 ATOM 40 NH1 ARG G 257 -33.297 1.957 16.878 1.00142.06 ATOM 41 NH2 ARG G 257 -31.334 0.823 17.157 1.00146.91 ATOM 42 N ALA G 258 -32.955 7.904 19.251 1.00123.55 ATOM 43 CA ALA G 258 -33.256 8.317 20.646 1.00123.97 ATOM 44 C ALA G 258 -34.708 8.804 20.784 1.00118.90 ATOM 45 O ALA G 258 -35.297 8.580 21.854 1.00114.93 ATOM 46 CB ALA G 258 -32.287 9.397 21.063 1.00126.55 ATOM 47 N TRP G 259 -35.240 9.463 19.745 1.00115.63 ATOM 48 CA TRP G 259 -36.633 9.989 19.667 1.00111.10 ATOM 49 C TRP G 259 -37.627 8.817 19.647 1.00107.11 ATOM 50 O TRP G 259 -38.677 8.905 20.333 1.00106.49 ATOM 51 CB TRP G 259 -36.815 10.895 18.436 1.00108.88 ATOM 52 CG TRP G 259 -38.235 11.319 18.172 1.00107.05 ATOM 53 CD1 TRP G 259 -38.907 12.369 18.733 1.00106.79 ATOM 54 CD2 TRP G 259 -39.164 10.712 17.252 1.00105.00 ATOM 55 NE1 TRP G 259 -40.183 12.444 18.240 1.00105.55 ATOM 56 CE2 TRP G 259 -40.377 11.434 17.340 1.00104.45 ATOM 57 CE3 TRP G 259 -39.091 9.621 16.376 1.00103.26 ATOM 58 CZ2 TRP G 259 -41.503 11.092 16.589 1.00105.19 ATOM 59 CZ3 TRP G 259 -40.197 9.292 15.622 1.00103.19 ATOM 60 CH2 TRP G 259 -41.386 10.020 15.729 1.00104.64 ATOM 61 N LEU G 260 -37.322 7.784 18.860 1.00103.96 ATOM 62 CA LEU G 260 -38.198 6.595 18.712 1.00103.43 ATOM 63 C LEU G 260 -38.563 6.088 20.110 1.00104.73 ATOM 64 O LEU G 260 -37.656 5.978 20.953 1.00110.51 ATOM 65 CB LEU G 260 -37.463 5.518 17.911 1.00103.94 ATOM 66 CG LEU G 260 -37.275 5.827 16.424 1.00104.18 ATOM 67 CD1 LEU G 260 -36.381 4.788 15.755 1.00104.90 ATOM 68 CD2 LEU G 260 -38.617 5.935 15.707 1.00102.87 ATOM 69 N ARG G 261 -39.841 5.810 20.353 1.00100.56 ATOM 70 CA ARG G 261 -40.318 5.182 21.611 1.00100.92 ATOM 71 C ARG G 261 -40.681 3.715 21.358 1.00103.83 ATOM 72 O ARG G 261 -40.656 2.946 22.310 1.00106.70 ATOM 73 CB ARG G 261 -41.533 5.919 22.172 1.00 97.89 ATOM 74 CG ARG G 261 -41.405 7.436 22.214 1.00 96.21 ATOM 75 CD ARG G 261 -42.580 8.059 22.939 1.00 95.55 ATOM 76 NE ARG G 261 -42.560 9.512 22.884 1.00 94.51 ATOM 77 CZ ARG G 261 -43.436 10.309 23.501 1.00 95.03 ATOM 78 NH1 ARG G 261 -44.417 9.810 24.238 1.00 94.85 ATOM 79 NH2 ARG G 261 -43.327 11.620 23.384 1.00 95.87 ATOM 80 N CYS G 262 -40.951 3.319 20.113 1.00105.81 ATOM 81 CA CYS G 262 -41.465 1.959 19.813 1.00108.20 ATOM 82 C CYS G 262 -40.698 1.285 18.664 1.00109.30 ATOM 83 O CYS G 262 -40.231 0.148 18.850 1.00108.94 ATOM 84 CB CYS G 262 -42.955 2.010 19.505 1.00107.36 ATOM 85 SG CYS G 262 -43.646 0.349 19.292 1.00109.82 ATOM 86 N TYR G 263 -40.623 1.920 17.493 1.00111.51 ATOM 87 CA TYR G 263 -40.086 1.301 16.248 1.00114.44 ATOM 88 C TYR G 263 -38.632 0.856 16.487 1.00118.21 ATOM 89 O TYR G 263 -37.757 1.713 16.722 1.00114.24 ATOM 90 CB TYR G 263 -40.235 2.253 15.055 1.00112.56 ATOM 91 CG TYR G 263 -39.606 1.752 13.778 1.00112.59 ATOM 92 CD1 TYR G 263 -40.261 0.849 12.955 1.00111.79 ATOM 93 CD2 TYR G 263 -38.327 2.152 13.418 1.00112.96 ATOM 94 CE1 TYR G 263 -39.667 0.374 11.799 1.00111.34 ATOM 95 CE2 TYR G 263 -37.721 1.690 12.262 1.00111.11 ATOM 96 CZ TYR G 263 -38.394 0.799 11.450 1.00111.56 ATOM 97 OH TYR G 263 -37.780 0.348 10.316 1.00113.72 ATOM 98 N GLY G 264 -38.405 -0.467 16.470 1.00124.18 ATOM 99 CA GLY G 264 -37.072 -1.093 16.568 1.00126.15 ATOM 100 C GLY G 264 -36.480 -1.035 17.971 1.00131.57 ATOM 101 O GLY G 264 -35.257 -1.254 18.082 1.00135.68 ATOM 102 N MET G 265 -37.288 -0.793 19.014 1.00130.80 ATOM 103 CA MET G 265 -36.781 -0.623 20.405 1.00133.01 ATOM 104 C MET G 265 -36.693 -1.976 21.109 1.00133.96 ATOM 105 O MET G 265 -37.570 -2.826 20.972 1.00132.35 ATOM 106 CB MET G 265 -37.661 0.334 21.227 1.00133.93 ATOM 107 CG MET G 265 -37.133 1.772 21.308 1.00132.92 ATOM 108 SD MET G 265 -35.779 2.040 20.127 1.00131.98 ATOM 109 CE MET G 265 -35.283 3.709 20.539 1.00132.97 ATOM 110 N PRO G 266 -35.641 -2.187 21.930 1.00135.52 ATOM 111 CA PRO G 266 -35.536 -3.405 22.731 1.00137.98 ATOM 112 C PRO G 266 -36.799 -3.581 23.588 1.00135.46 ATOM 113 O PRO G 266 -37.341 -2.589 24.024 1.00133.27 ATOM 114 CB PRO G 266 -34.277 -3.193 23.589 1.00141.39 ATOM 115 CG PRO G 266 -33.989 -1.700 23.502 1.00139.33 ATOM 116 CD PRO G 266 -34.529 -1.250 22.160 1.00135.84 ATOM 117 N GLY G 267 -37.252 -4.827 23.757 1.00135.43 ATOM 118 CA GLY G 267 -38.419 -5.196 24.582 1.00135.69 ATOM 119 C GLY G 267 -39.754 -4.825 23.951 1.00130.68 ATOM 120 O GLY G 267 -40.754 -4.808 24.677 1.00131.32 ATOM 121 N MET G 268 -39.789 -4.537 22.648 1.00127.13 ATOM 122 CA MET G 268 -41.052 -4.243 21.914 1.00124.51 ATOM 123 C MET G 268 -41.460 -5.486 21.119 1.00125.14 ATOM 124 O MET G 268 -40.574 -6.239 20.714 1.00126.90 ATOM 125 CB MET G 268 -40.878 -3.051 20.968 1.00119.79 ATOM 126 N SER G 269 -42.753 -5.694 20.896 1.00125.09 ATOM 127 CA SER G 269 -43.286 -6.764 20.016 1.00125.25 ATOM 128 C SER G 269 -43.001 -6.383 18.555 1.00122.92 ATOM 129 O SER G 269 -42.739 -5.182 18.293 1.00119.67 ATOM 130 CB SER G 269 -44.767 -6.970 20.264 1.00124.32 ATOM 131 OG SER G 269 -45.063 -8.339 20.463 1.00126.20 ATOM 132 N SER G 270 -43.046 -7.356 17.645 1.00122.67 ATOM 133 CA SER G 270 -42.969 -7.130 16.179 1.00119.04 ATOM 134 C SER G 270 -43.530 -8.336 15.423 1.00121.30 ATOM 135 O SER G 270 -42.949 -9.420 15.557 1.00124.96 ATOM 136 N LEU G 271 -44.600 -8.151 14.638 1.00121.34 ATOM 137 CA LEU G 271 -45.156 -9.173 13.715 1.00121.95 ATOM 138 C LEU G 271 -45.266 -8.556 12.309 1.00119.87 ATOM 139 O LEU G 271 -44.970 -7.347 12.144 1.00115.66 ATOM 140 N GLN G 272 -45.631 -9.375 11.326 1.00122.14 ATOM 141 CA GLN G 272 -45.822 -8.939 9.922 1.00122.66 ATOM 142 C GLN G 272 -47.300 -8.587 9.724 1.00124.38 ATOM 143 O GLN G 272 -48.147 -9.377 10.154 1.00126.87 ATOM 144 N ASP G 273 -47.606 -7.448 9.095 1.00122.74 ATOM 145 CA ASP G 273 -48.956 -7.197 8.508 1.00124.34 ATOM 146 C ASP G 273 -49.127 -8.098 7.267 1.00125.93 ATOM 147 O ASP G 273 -48.209 -8.879 6.954 1.00122.63 ATOM 148 CB ASP G 273 -49.190 -5.710 8.205 1.00121.91 ATOM 149 CG ASP G 273 -48.173 -5.098 7.254 1.00120.48 ATOM 150 OD1 ASP G 273 -47.207 -5.767 6.974 1.00123.24 ATOM 151 OD2 ASP G 273 -48.372 -3.975 6.778 1.00119.48 ATOM 152 N ARG G 274 -50.278 -7.996 6.604 1.00128.78 ATOM 153 CA ARG G 274 -50.690 -8.881 5.484 1.00133.81 ATOM 154 C ARG G 274 -49.792 -8.635 4.267 1.00135.69 ATOM 155 O ARG G 274 -49.728 -9.533 3.424 1.00145.92 ATOM 156 CB ARG G 274 -52.170 -8.677 5.141 1.00133.31 ATOM 157 N HIS G 275 -49.098 -7.497 4.179 1.00132.28 ATOM 158 CA HIS G 275 -48.258 -7.127 3.004 1.00131.93 ATOM 159 C HIS G 275 -46.765 -7.358 3.281 1.00129.25 ATOM 160 O HIS G 275 -45.949 -6.886 2.483 1.00126.47 ATOM 161 CB HIS G 275 -48.563 -5.686 2.574 1.00131.32 ATOM 162 CG HIS G 275 -50.014 -5.451 2.309 1.00134.19 ATOM 163 ND1 HIS G 275 -50.724 -6.175 1.366 1.00137.85 ATOM 164 CD2 HIS G 275 -50.903 -4.612 2.883 1.00134.24 ATOM 165 CE1 HIS G 275 -51.981 -5.779 1.360 1.00138.64 ATOM 166 NE2 HIS G 275 -52.118 -4.820 2.280 1.00135.66 ATOM 167 N GLY G 276 -46.421 -8.071 4.356 1.00129.93 ATOM 168 CA GLY G 276 -45.033 -8.473 4.669 1.00128.36 ATOM 169 C GLY G 276 -44.213 -7.367 5.324 1.00124.08 ATOM 170 O GLY G 276 -42.999 -7.567 5.485 1.00122.65 ATOM 171 N ARG G 277 -44.837 -6.260 5.743 1.00120.25 ATOM 172 CA ARG G 277 -44.161 -5.133 6.448 1.00115.39 ATOM 173 C ARG G 277 -44.279 -5.320 7.974 1.00112.48 ATOM 174 O ARG G 277 -45.337 -5.766 8.455 1.00113.82 ATOM 175 CB ARG G 277 -44.724 -3.798 5.947 1.00112.60 ATOM 176 CG ARG G 277 -44.657 -3.649 4.432 1.00112.58 ATOM 177 CD ARG G 277 -44.420 -2.237 3.959 1.00109.81 ATOM 178 NE ARG G 277 -43.132 -1.760 4.431 1.00109.36 ATOM 179 CZ ARG G 277 -42.789 -0.479 4.547 1.00109.33 ATOM 180 NH1 ARG G 277 -43.639 0.474 4.203 1.00110.27 ATOM 181 NH2 ARG G 277 -41.596 -0.153 5.013 1.00108.34 ATOM 182 N THR G 278 -43.199 -5.028 8.700 1.00108.95 ATOM 183 CA THR G 278 -43.045 -5.356 10.140 1.00109.64 ATOM 184 C THR G 278 -43.657 -4.202 10.928 1.00107.04 ATOM 185 O THR G 278 -43.232 -3.065 10.697 1.00104.76 ATOM 186 CB THR G 278 -41.584 -5.622 10.534 1.00107.93 ATOM 187 N ILE G 279 -44.637 -4.506 11.785 1.00108.60 ATOM 188 CA ILE G 279 -45.238 -3.558 12.772 1.00107.62 ATOM 189 C ILE G 279 -44.600 -3.809 14.150 1.00109.81 ATOM 190 O ILE G 279 -44.650 -4.969 14.639 1.00114.31 ATOM 191 CB ILE G 279 -46.780 -3.657 12.804 1.00107.02 ATOM 192 CG1 ILE G 279 -47.387 -2.640 13.775 1.00106.75 ATOM 193 CG2 ILE G 279 -47.267 -5.070 13.112 1.00108.95 ATOM 194 CD1 ILE G 279 -46.975 -1.192 13.535 1.00104.61 ATOM 195 N TRP G 280 -43.992 -2.768 14.729 1.00107.99 ATOM 196 CA TRP G 280 -43.524 -2.739 16.138 1.00108.24 ATOM 197 C TRP G 280 -44.645 -2.188 17.033 1.00109.13 ATOM 198 O TRP G 280 -45.358 -1.251 16.615 1.00108.43 ATOM 199 CB TRP G 280 -42.213 -1.959 16.254 1.00106.53 ATOM 200 CG TRP G 280 -41.096 -2.615 15.494 1.00106.22 ATOM 201 CD1 TRP G 280 -40.811 -2.458 14.168 1.00103.53 ATOM 202 CD2 TRP G 280 -40.142 -3.576 15.997 1.00108.11 ATOM 203 N PHE G 281 -44.816 -2.777 18.217 1.00112.11 ATOM 204 CA PHE G 281 -45.938 -2.498 19.149 1.00112.56 ATOM 205 C PHE G 281 -45.604 -2.965 20.580 1.00117.06 ATOM 206 O PHE G 281 -44.550 -3.636 20.835 1.00118.89 ATOM 207 CB PHE G 281 -47.191 -3.195 18.623 1.00110.82 ATOM 208 N GLN G 282 -46.483 -2.595 21.509 1.00117.33 ATOM 209 CA GLN G 282 -46.469 -3.051 22.920 1.00118.94 ATOM 210 C GLN G 282 -47.849 -3.651 23.188 1.00120.33 ATOM 211 O GLN G 282 -48.845 -3.005 22.799 1.00116.94 ATOM 212 N GLY G 283 -47.899 -4.858 23.770 1.00123.47 ATOM 213 CA GLY G 283 -49.104 -5.429 24.405 1.00124.47 ATOM 214 C GLY G 283 -49.999 -6.210 23.448 1.00124.46 ATOM 215 O GLY G 283 -49.479 -6.907 22.540 1.00123.85 ATOM 216 N ASP G 284 -51.314 -6.139 23.695 1.00124.80 ATOM 217 CA ASP G 284 -52.395 -6.760 22.881 1.00125.05 ATOM 218 C ASP G 284 -52.002 -6.602 21.410 1.00121.77 ATOM 219 O ASP G 284 -51.717 -5.493 20.959 1.00116.42 ATOM 220 CB ASP G 284 -53.756 -6.132 23.249 1.00125.49 ATOM 221 CG ASP G 284 -55.008 -6.755 22.628 1.00127.26 ATOM 222 OD1 ASP G 284 -54.933 -7.924 22.231 1.00131.03 ATOM 223 OD2 ASP G 284 -56.066 -6.069 22.563 1.00125.84 ATOM 224 N PRO G 285 -51.864 -7.717 20.657 1.00122.87 ATOM 225 CA PRO G 285 -51.797 -7.644 19.197 1.00119.99 ATOM 226 C PRO G 285 -53.071 -7.052 18.561 1.00118.93 ATOM 227 O PRO G 285 -52.938 -6.296 17.614 1.00115.84 ATOM 228 N GLY G 286 -54.256 -7.418 19.072 1.00120.35 ATOM 229 CA GLY G 286 -55.565 -7.001 18.523 1.00119.34 ATOM 230 C GLY G 286 -56.297 -8.147 17.818 1.00122.39 ATOM 231 O GLY G 286 -55.686 -9.148 17.446 1.00124.24 ATOM 232 N PRO G 287 -57.630 -8.023 17.604 1.00123.37 ATOM 233 CA PRO G 287 -58.431 -9.124 17.058 1.00126.36 ATOM 234 C PRO G 287 -58.055 -9.625 15.650 1.00127.49 ATOM 235 O PRO G 287 -58.060 -10.821 15.461 1.00128.80 ATOM 236 N LEU G 288 -57.734 -8.718 14.710 1.00126.37 ATOM 237 CA LEU G 288 -57.634 -9.001 13.242 1.00125.38 ATOM 238 C LEU G 288 -56.190 -9.384 12.872 1.00125.11 ATOM 239 O LEU G 288 -55.750 -9.014 11.763 1.00125.50 ATOM 240 CB LEU G 288 -58.101 -7.767 12.457 1.00121.25 ATOM 241 N ALA G 289 -55.494 -10.121 13.744 1.00125.24 ATOM 242 CA ALA G 289 -54.099 -10.578 13.553 1.00123.50 ATOM 243 C ALA G 289 -53.981 -11.368 12.244 1.00124.26 ATOM 244 O ALA G 289 -52.882 -11.765 11.868 1.00124.16 ATOM 245 CB ALA G 289 -53.692 -11.428 14.729 1.00125.52 TER