HEADER DNA BINDING PROTEIN/DNA 31-DEC-69 6A57 TITLE Structure of histone demethylase REF6 complexed with DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: Lysine-specific demethylase REF6; COMPND 3 CHAIN: A; COMPND 4 EC: 1.14.11.-; COMPND 5 FRAGMENT: Ig gamma-1 chain C ; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 3; COMPND 8 DNA COMPND 9 (5'-D(*GP*GP*AP*CP*AP*AP*AP*AP*CP*AP*GP*AP*GP*AP*AP*A)-3'); COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES; EXPDTA X-RAY DIFFRACTION REMARK 2 RESOLUTION. 2.70 ANGSTORMS DBREF 6A57 A 1223 1360 UNP Q9STM3 REF6_ARATH 1223 1360 DBREF 6A57 C 21 36 PDB 6A57 6A57 21 36 SEQRES 1 A 30 ARG PRO LEU LYS CYS PRO TRP LYS GLY CYS LYS MET THR SEQRES 2 A 30 PHE LYS TRP ALA TRP SER ARG THR GLU HIS ILE ARG VAL SEQRES 3 A 30 HIS THR GLY ALA ATOM 1 N ARG A1294 -48.938 12.258 21.324 1.00 40.49 ATOM 2 CA ARG A1294 -49.148 12.876 20.021 1.00 37.20 ATOM 3 C ARG A1294 -49.462 14.370 20.237 1.00 35.43 ATOM 4 O ARG A1294 -50.636 14.764 20.275 1.00 34.02 ATOM 5 CB ARG A1294 -50.296 12.162 19.299 1.00 36.74 ATOM 6 CG ARG A1294 -50.079 10.665 19.136 1.00 35.90 ATOM 7 CD ARG A1294 -51.293 9.965 18.543 1.00 35.18 ATOM 8 NE ARG A1294 -51.451 10.219 17.112 1.00 34.63 ATOM 9 CZ ARG A1294 -50.711 9.675 16.145 1.00 33.52 ATOM 10 NH1 ARG A1294 -49.720 8.828 16.424 1.00 33.31 ATOM 11 NH2 ARG A1294 -50.957 9.993 14.881 1.00 33.00 ATOM 12 N PRO A1295 -48.413 15.204 20.401 1.00 33.99 ATOM 13 CA PRO A1295 -48.587 16.626 20.761 1.00 34.33 ATOM 14 C PRO A1295 -49.335 17.481 19.735 1.00 34.90 ATOM 15 O PRO A1295 -50.166 18.305 20.113 1.00 35.90 ATOM 16 CB PRO A1295 -47.149 17.142 20.898 1.00 34.23 ATOM 17 CG PRO A1295 -46.293 15.934 20.995 1.00 34.50 ATOM 18 CD PRO A1295 -46.991 14.853 20.244 1.00 33.96 ATOM 19 N LEU A1296 -49.028 17.280 18.455 1.00 35.33 ATOM 20 CA LEU A1296 -49.588 18.078 17.361 1.00 34.26 ATOM 21 C LEU A1296 -51.050 17.706 17.089 1.00 34.75 ATOM 22 O LEU A1296 -51.384 16.531 17.015 1.00 32.71 ATOM 23 CB LEU A1296 -48.746 17.881 16.095 1.00 32.98 ATOM 24 CG LEU A1296 -47.349 18.522 15.983 1.00 32.15 ATOM 25 CD1 LEU A1296 -46.737 18.998 17.289 1.00 31.67 ATOM 26 CD2 LEU A1296 -46.392 17.563 15.296 1.00 31.98 ATOM 27 N LYS A1297 -51.893 18.729 16.930 1.00 37.82 ATOM 28 CA LYS A1297 -53.343 18.591 16.751 1.00 40.87 ATOM 29 C LYS A1297 -53.766 19.141 15.392 1.00 40.24 ATOM 30 O LYS A1297 -53.078 19.987 14.820 1.00 42.03 ATOM 31 CB LYS A1297 -54.083 19.394 17.827 1.00 44.80 ATOM 32 CG LYS A1297 -53.686 19.083 19.268 1.00 49.87 ATOM 33 CD LYS A1297 -54.548 17.988 19.885 1.00 54.07 ATOM 34 CE LYS A1297 -54.099 17.652 21.304 1.00 56.71 ATOM 35 NZ LYS A1297 -52.950 16.699 21.341 1.00 57.72 ATOM 36 N CYS A1298 -54.902 18.671 14.883 1.00 38.18 ATOM 37 CA CYS A1298 -55.522 19.270 13.706 1.00 36.54 ATOM 38 C CYS A1298 -56.457 20.356 14.201 1.00 37.11 ATOM 39 O CYS A1298 -57.270 20.087 15.085 1.00 37.20 ATOM 40 CB CYS A1298 -56.325 18.248 12.905 1.00 35.52 ATOM 41 SG CYS A1298 -57.090 18.950 11.422 1.00 32.67 ATOM 42 N PRO A1299 -56.363 21.574 13.631 1.00 37.28 ATOM 43 CA PRO A1299 -57.183 22.696 14.086 1.00 37.04 ATOM 44 C PRO A1299 -58.613 22.782 13.525 1.00 37.77 ATOM 45 O PRO A1299 -59.339 23.702 13.901 1.00 37.95 ATOM 46 CB PRO A1299 -56.372 23.906 13.631 1.00 37.29 ATOM 47 CG PRO A1299 -55.739 23.445 12.377 1.00 37.76 ATOM 48 CD PRO A1299 -55.391 22.004 12.609 1.00 37.66 ATOM 49 N TRP A1300 -59.030 21.863 12.652 1.00 38.54 ATOM 50 CA TRP A1300 -60.412 21.890 12.144 1.00 39.45 ATOM 51 C TRP A1300 -61.397 21.432 13.230 1.00 40.45 ATOM 52 O TRP A1300 -61.071 20.563 14.036 1.00 40.83 ATOM 53 CB TRP A1300 -60.566 21.093 10.829 1.00 40.12 ATOM 54 CG TRP A1300 -60.673 21.992 9.609 1.00 40.54 ATOM 55 CD1 TRP A1300 -61.794 22.228 8.856 1.00 41.02 ATOM 56 CD2 TRP A1300 -59.632 22.797 9.036 1.00 40.47 ATOM 57 NE1 TRP A1300 -61.510 23.122 7.846 1.00 41.00 ATOM 58 CE2 TRP A1300 -60.192 23.487 7.933 1.00 40.33 ATOM 59 CE3 TRP A1300 -58.277 22.997 9.341 1.00 41.41 ATOM 60 CZ2 TRP A1300 -59.447 24.366 7.138 1.00 40.57 ATOM 61 CZ3 TRP A1300 -57.532 23.874 8.549 1.00 41.23 ATOM 62 CH2 TRP A1300 -58.123 24.546 7.459 1.00 40.89 ATOM 63 N LYS A1301 -62.594 22.027 13.224 1.00 42.44 ATOM 64 CA LYS A1301 -63.546 21.979 14.355 1.00 43.39 ATOM 65 C LYS A1301 -63.807 20.584 14.917 1.00 44.78 ATOM 66 O LYS A1301 -63.419 20.289 16.054 1.00 49.85 ATOM 67 CB LYS A1301 -64.887 22.628 13.975 1.00 42.13 ATOM 68 N GLY A1302 -64.445 19.727 14.128 1.00 42.96 ATOM 69 CA GLY A1302 -64.820 18.394 14.597 1.00 42.66 ATOM 70 C GLY A1302 -63.760 17.315 14.419 1.00 43.51 ATOM 71 O GLY A1302 -64.039 16.141 14.670 1.00 45.03 ATOM 72 N CYS A1303 -62.550 17.696 13.999 1.00 42.07 ATOM 73 CA CYS A1303 -61.509 16.736 13.644 1.00 41.29 ATOM 74 C CYS A1303 -60.622 16.398 14.843 1.00 42.01 ATOM 75 O CYS A1303 -59.932 17.266 15.376 1.00 41.15 ATOM 76 CB CYS A1303 -60.663 17.291 12.497 1.00 40.12 ATOM 77 SG CYS A1303 -59.545 16.089 11.756 1.00 36.73 ATOM 78 N LYS A1304 -60.635 15.126 15.243 1.00 44.48 ATOM 79 CA LYS A1304 -59.871 14.649 16.410 1.00 46.57 ATOM 80 C LYS A1304 -58.446 14.169 16.086 1.00 44.17 ATOM 81 O LYS A1304 -57.700 13.832 17.008 1.00 43.57 ATOM 82 CB LYS A1304 -60.651 13.539 17.155 1.00 49.74 ATOM 83 CG LYS A1304 -61.268 13.959 18.491 1.00 52.95 ATOM 84 CD LYS A1304 -62.280 15.098 18.397 1.00 55.26 ATOM 85 CE LYS A1304 -63.524 14.724 17.597 1.00 59.73 ATOM 86 NZ LYS A1304 -64.232 13.515 18.113 1.00 61.48 ATOM 87 N MET A1305 -58.067 14.147 14.804 1.00 42.02 ATOM 88 CA MET A1305 -56.737 13.674 14.384 1.00 41.19 ATOM 89 C MET A1305 -55.601 14.328 15.163 1.00 37.87 ATOM 90 O MET A1305 -55.662 15.516 15.487 1.00 37.01 ATOM 91 CB MET A1305 -56.501 13.906 12.880 1.00 44.62 ATOM 92 CG MET A1305 -56.854 12.732 11.981 1.00 47.15 ATOM 93 SD MET A1305 -55.768 11.309 12.199 1.00 53.60 ATOM 94 CE MET A1305 -54.159 11.944 11.774 1.00 51.48 ATOM 95 N THR A1306 -54.578 13.533 15.459 1.00 35.06 ATOM 96 CA THR A1306 -53.383 14.007 16.147 1.00 34.37 ATOM 97 C THR A1306 -52.154 13.403 15.503 1.00 32.62 ATOM 98 O THR A1306 -52.247 12.398 14.808 1.00 32.90 ATOM 99 CB THR A1306 -53.385 13.599 17.625 1.00 34.80 ATOM 100 OG1 THR A1306 -53.484 12.172 17.717 1.00 36.16 ATOM 101 CG2 THR A1306 -54.553 14.238 18.361 1.00 34.57 ATOM 102 N PHE A1307 -51.005 14.020 15.752 1.00 31.63 ATOM 103 CA PHE A1307 -49.757 13.660 15.082 1.00 31.51 ATOM 104 C PHE A1307 -48.581 13.758 16.025 1.00 31.31 ATOM 105 O PHE A1307 -48.639 14.453 17.042 1.00 32.09 ATOM 106 CB PHE A1307 -49.498 14.592 13.892 1.00 31.93 ATOM 107 CG PHE A1307 -50.715 14.845 13.057 1.00 32.16 ATOM 108 CD1 PHE A1307 -51.015 14.021 11.985 1.00 31.31 ATOM 109 CD2 PHE A1307 -51.587 15.882 13.376 1.00 31.82 ATOM 110 CE1 PHE A1307 -52.142 14.247 11.226 1.00 32.17 ATOM 111 CE2 PHE A1307 -52.728 16.101 12.628 1.00 32.51 ATOM 112 CZ PHE A1307 -53.008 15.282 11.551 1.00 32.13 ATOM 113 N LYS A1308 -47.523 13.042 15.674 1.00 30.16 ATOM 114 CA LYS A1308 -46.229 13.198 16.301 1.00 30.10 ATOM 115 C LYS A1308 -45.302 14.050 15.449 1.00 28.58 ATOM 116 O LYS A1308 -44.319 14.566 15.960 1.00 29.70 ATOM 117 CB LYS A1308 -45.576 11.830 16.505 1.00 30.98 ATOM 118 CG LYS A1308 -46.413 10.829 17.280 1.00 31.28 ATOM 119 CD LYS A1308 -45.636 9.532 17.438 1.00 31.94 ATOM 120 CE LYS A1308 -46.461 8.449 18.114 1.00 32.66 ATOM 121 NZ LYS A1308 -45.663 7.204 18.301 1.00 33.26 ATOM 122 N TRP A1309 -45.599 14.169 14.157 1.00 27.76 ATOM 123 CA TRP A1309 -44.698 14.775 13.174 1.00 26.60 ATOM 124 C TRP A1309 -45.396 15.926 12.460 1.00 26.03 ATOM 125 O TRP A1309 -46.578 15.830 12.098 1.00 23.56 ATOM 126 CB TRP A1309 -44.288 13.747 12.130 1.00 26.59 ATOM 127 CG TRP A1309 -43.513 12.595 12.651 1.00 27.14 ATOM 128 CD1 TRP A1309 -43.929 11.289 12.744 1.00 27.22 ATOM 129 CD2 TRP A1309 -42.173 12.623 13.131 1.00 27.53 ATOM 130 NE1 TRP A1309 -42.924 10.509 13.260 1.00 27.08 ATOM 131 CE2 TRP A1309 -41.836 11.302 13.512 1.00 27.24 ATOM 132 CE3 TRP A1309 -41.221 13.637 13.284 1.00 27.93 ATOM 133 CZ2 TRP A1309 -40.591 10.972 14.041 1.00 27.71 ATOM 134 CZ3 TRP A1309 -39.973 13.304 13.809 1.00 28.53 ATOM 135 CH2 TRP A1309 -39.671 11.978 14.177 1.00 28.13 ATOM 136 N ALA A1310 -44.648 17.008 12.248 1.00 26.85 ATOM 137 CA ALA A1310 -45.191 18.229 11.645 1.00 27.58 ATOM 138 C ALA A1310 -45.663 18.014 10.201 1.00 27.89 ATOM 139 O ALA A1310 -46.745 18.489 9.826 1.00 26.68 ATOM 140 CB ALA A1310 -44.162 19.349 11.701 1.00 27.37 ATOM 141 N TRP A1311 -44.864 17.302 9.401 1.00 27.97 ATOM 142 CA TRP A1311 -45.228 17.084 8.002 1.00 28.68 ATOM 143 C TRP A1311 -46.593 16.376 7.856 1.00 28.50 ATOM 144 O TRP A1311 -47.424 16.809 7.052 1.00 29.01 ATOM 145 CB TRP A1311 -44.112 16.380 7.204 1.00 29.44 ATOM 146 CG TRP A1311 -44.388 16.420 5.736 1.00 30.88 ATOM 147 CD1 TRP A1311 -44.620 15.355 4.910 1.00 31.50 ATOM 148 CD2 TRP A1311 -44.532 17.591 4.925 1.00 31.82 ATOM 149 NE1 TRP A1311 -44.878 15.788 3.634 1.00 31.16 ATOM 150 CE2 TRP A1311 -44.840 17.157 3.615 1.00 31.50 ATOM 151 CE3 TRP A1311 -44.436 18.966 5.177 1.00 32.28 ATOM 152 CZ2 TRP A1311 -45.041 18.047 2.560 1.00 31.16 ATOM 153 CZ3 TRP A1311 -44.639 19.853 4.124 1.00 32.53 ATOM 154 CH2 TRP A1311 -44.939 19.385 2.830 1.00 31.65 ATOM 155 N SER A1312 -46.842 15.336 8.650 1.00 27.56 ATOM 156 CA SER A1312 -48.143 14.652 8.623 1.00 28.19 ATOM 157 C SER A1312 -49.289 15.622 8.821 1.00 28.27 ATOM 158 O SER A1312 -50.280 15.562 8.093 1.00 29.18 ATOM 159 CB SER A1312 -48.243 13.549 9.688 1.00 29.13 ATOM 160 OG SER A1312 -47.465 12.406 9.358 1.00 29.77 ATOM 161 N ARG A1313 -49.146 16.510 9.804 1.00 28.64 ATOM 162 CA ARG A1313 -50.146 17.552 10.083 1.00 29.36 ATOM 163 C ARG A1313 -50.377 18.487 8.881 1.00 29.23 ATOM 164 O ARG A1313 -51.518 18.771 8.517 1.00 28.46 ATOM 165 CB ARG A1313 -49.716 18.376 11.301 1.00 30.08 ATOM 166 CG ARG A1313 -50.735 19.381 11.806 1.00 30.89 ATOM 167 CD ARG A1313 -50.245 20.047 13.088 1.00 32.33 ATOM 168 NE ARG A1313 -51.116 21.149 13.476 1.00 32.91 ATOM 169 CZ ARG A1313 -51.129 22.359 12.909 1.00 34.15 ATOM 170 NH1 ARG A1313 -50.290 22.671 11.919 1.00 33.45 ATOM 171 NH2 ARG A1313 -52.001 23.275 13.341 1.00 35.56 ATOM 172 N THR A1314 -49.287 18.955 8.276 1.00 29.35 ATOM 173 CA THR A1314 -49.352 19.897 7.157 1.00 29.32 ATOM 174 C THR A1314 -50.150 19.323 5.988 1.00 28.89 ATOM 175 O THR A1314 -51.068 19.968 5.489 1.00 28.17 ATOM 176 CB THR A1314 -47.930 20.278 6.696 1.00 30.24 ATOM 177 OG1 THR A1314 -47.306 21.062 7.719 1.00 30.12 ATOM 178 CG2 THR A1314 -47.944 21.068 5.382 1.00 30.56 ATOM 179 N GLU A1315 -49.797 18.107 5.575 1.00 28.99 ATOM 180 CA GLU A1315 -50.476 17.431 4.469 1.00 28.71 ATOM 181 C GLU A1315 -51.902 17.022 4.840 1.00 28.61 ATOM 182 O GLU A1315 -52.792 17.075 3.991 1.00 29.13 ATOM 183 CB GLU A1315 -49.685 16.210 3.990 1.00 28.94 ATOM 184 CG GLU A1315 -48.283 16.525 3.468 1.00 29.57 ATOM 185 CD GLU A1315 -47.798 15.544 2.401 1.00 29.76 ATOM 186 OE1 GLU A1315 -47.606 14.344 2.727 1.00 29.04 ATOM 187 OE2 GLU A1315 -47.583 15.982 1.243 1.00 29.27 ATOM 188 N HIS A1316 -52.124 16.624 6.093 1.00 27.48 ATOM 189 CA HIS A1316 -53.475 16.277 6.546 1.00 27.82 ATOM 190 C HIS A1316 -54.457 17.439 6.440 1.00 28.58 ATOM 191 O HIS A1316 -55.629 17.231 6.120 1.00 28.78 ATOM 192 CB HIS A1316 -53.481 15.744 7.987 1.00 27.45 ATOM 193 CG HIS A1316 -54.838 15.759 8.627 1.00 26.95 ATOM 194 ND1 HIS A1316 -55.694 14.683 8.586 1.00 26.69 ATOM 195 CD2 HIS A1316 -55.490 16.730 9.313 1.00 26.83 ATOM 196 CE1 HIS A1316 -56.810 14.985 9.226 1.00 26.79 ATOM 197 NE2 HIS A1316 -56.712 16.222 9.676 1.00 26.07 ATOM 198 N ILE A1317 -53.999 18.653 6.734 1.00 29.35 ATOM 199 CA ILE A1317 -54.893 19.813 6.697 1.00 30.38 ATOM 200 C ILE A1317 -55.486 19.994 5.297 1.00 29.83 ATOM 201 O ILE A1317 -56.635 20.411 5.165 1.00 28.84 ATOM 202 CB ILE A1317 -54.201 21.100 7.209 1.00 31.01 ATOM 203 CG1 ILE A1317 -53.976 20.989 8.722 1.00 31.66 ATOM 204 CG2 ILE A1317 -55.050 22.334 6.919 1.00 31.21 ATOM 205 CD1 ILE A1317 -52.946 21.946 9.289 1.00 31.89 ATOM 206 N ARG A1318 -54.719 19.638 4.267 1.00 30.62 ATOM 207 CA ARG A1318 -55.198 19.721 2.886 1.00 30.23 ATOM 208 C ARG A1318 -56.490 18.945 2.644 1.00 30.35 ATOM 209 O ARG A1318 -57.308 19.364 1.833 1.00 30.72 ATOM 210 CB ARG A1318 -54.134 19.251 1.906 1.00 29.28 ATOM 211 CG ARG A1318 -52.933 20.165 1.818 1.00 28.12 ATOM 212 CD ARG A1318 -51.843 19.521 0.995 1.00 27.20 ATOM 213 NE ARG A1318 -50.547 20.114 1.295 1.00 26.37 ATOM 214 CZ ARG A1318 -49.375 19.486 1.213 1.00 27.14 ATOM 215 NH1 ARG A1318 -49.284 18.208 0.833 1.00 27.26 ATOM 216 NH2 ARG A1318 -48.265 20.147 1.516 1.00 28.06 ATOM 217 N VAL A1319 -56.673 17.831 3.351 1.00 30.69 ATOM 218 CA VAL A1319 -57.932 17.074 3.292 1.00 31.90 ATOM 219 C VAL A1319 -59.133 17.979 3.567 1.00 33.12 ATOM 220 O VAL A1319 -60.166 17.834 2.920 1.00 34.63 ATOM 221 CB VAL A1319 -57.944 15.884 4.282 1.00 31.88 ATOM 222 CG1 VAL A1319 -59.338 15.282 4.432 1.00 32.52 ATOM 223 CG2 VAL A1319 -56.966 14.813 3.832 1.00 32.04 ATOM 224 N HIS A1320 -58.989 18.896 4.524 1.00 34.30 ATOM 225 CA HIS A1320 -60.056 19.847 4.873 1.00 34.89 ATOM 226 C HIS A1320 -60.168 20.988 3.860 1.00 34.98 ATOM 227 O HIS A1320 -61.277 21.312 3.417 1.00 34.75 ATOM 228 CB HIS A1320 -59.845 20.419 6.285 1.00 34.83 ATOM 229 CG HIS A1320 -59.841 19.378 7.361 1.00 34.53 ATOM 230 ND1 HIS A1320 -60.969 18.666 7.711 1.00 34.48 ATOM 231 CD2 HIS A1320 -58.846 18.925 8.160 1.00 34.33 ATOM 232 CE1 HIS A1320 -60.668 17.817 8.678 1.00 34.46 ATOM 233 NE2 HIS A1320 -59.386 17.951 8.968 1.00 34.59 ATOM 234 N THR A1321 -59.025 21.577 3.498 1.00 34.37 ATOM 235 CA THR A1321 -58.983 22.740 2.606 1.00 34.29 ATOM 236 C THR A1321 -59.243 22.393 1.143 1.00 36.07 ATOM 237 O THR A1321 -59.622 23.262 0.360 1.00 39.46 ATOM 238 CB THR A1321 -57.615 23.454 2.635 1.00 33.72 ATOM 239 OG1 THR A1321 -56.632 22.640 1.992 1.00 32.89 ATOM 240 CG2 THR A1321 -57.176 23.759 4.055 1.00 33.80 ATOM 241 N GLY A1322 -58.987 21.145 0.763 1.00 36.27 ATOM 242 CA GLY A1322 -59.092 20.717 -0.628 1.00 35.56 ATOM 243 C GLY A1322 -57.892 21.035 -1.511 1.00 35.23 ATOM 244 O GLY A1322 -57.875 20.622 -2.665 1.00 36.78 ATOM 245 N ALA A1323 -56.876 21.724 -0.990 1.00 34.44 ATOM 246 CA ALA A1323 -55.746 22.187 -1.810 1.00 34.37 ATOM 247 C ALA A1323 -54.988 21.059 -2.526 1.00 35.12 ATOM 248 O ALA A1323 -54.918 19.922 -2.034 1.00 34.25 ATOM 249 CB ALA A1323 -54.777 22.993 -0.960 1.00 34.07 ATOM 250 ZN ZN A1403 -58.190 17.276 10.500 1.00 33.83 ATOM 251 C1 GOL A 102 -45.051 22.924 -1.108 1.00 54.74 ATOM 252 O1 GOL A 102 -46.056 22.991 -0.093 1.00 52.35 ATOM 253 C2 GOL A 102 -45.119 24.182 -1.980 1.00 56.91 ATOM 254 O2 GOL A 102 -44.798 23.866 -3.348 1.00 56.69 ATOM 255 C3 GOL A 102 -44.187 25.274 -1.432 1.00 55.75 ATOM 256 O3 GOL A 102 -42.802 24.930 -1.574 1.00 53.89 TER