0.010396 0.006002 0.000000 0.000000 0.012004 0.000000 0.000000 0.000000 0.003167 0.00000 0.00000 0.00000 Zhou, L. Cheng, X. Connolly, B.A. Dickman, M.J. Hurd, P.J. Hornby, D.P. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 18 90.0 90.0 120.0 96.19 96.19 315.75 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O7 P 347.221 y 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C14 H20 N6 O5 S 384.411 n S-ADENOSYL-L-HOMOCYSTEINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking C9 H13 N2 O7 P 292.182 n 1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)PYRIMIDIN-2(1H)-ONE 2'-DEOXYZEBULARINE-5'-MONOPHOSPHATE DNA linking UK J.MOL.BIOL. JMOBAK 0070 0022-2836 321 591 599 10.1016/S0022-2836(02)00676-9 12206775 ZEBULARINE: A NOVEL DNA METHYLATION INHIBITOR THAT FORMS A COVALENT COMPLEX WITH DNA METHYLTRANSFERASES 2002 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 a parabolic collimating mirror placed upstream of monochromator CCD 1999-09-16 ADSC QUANTUM 4 SINGLE WAVELENGTH M x-ray 1 0.979 1.0 X8C NSLS 0.979 SYNCHROTRON NSLS BEAMLINE X8C 3623.368 5'-D(P*CP*CP*AP*TP*GP*CP*GP*CP*TP*GP*AP*C)-3' 1 syn polymer 3688.401 5'-D(P*GP*TP*CP*AP*GP*(Z)P*GP*CP*AP*TP*GP*G)-3' 1 syn polymer 37042.207 Modification methylase HhaI 2.1.1.73 1 man polymer 384.411 S-ADENOSYL-L-HOMOCYSTEINE 1 syn non-polymer 18.015 water 245 nat water Cytosine-specific methyltransferase HhaI, M.HhaI no no (DC)(DC)(DA)(DT)(DG)(DC)(DG)(DC)(DT)(DG)(DA)(DC) CCATGCGCTGAC C polydeoxyribonucleotide no yes (DG)(DT)(DC)(DA)(DG)Z(DG)(DC)(DA)(DT)(DG)(DG) GTCAGZGCATGG D polydeoxyribonucleotide no no MIEIKDKQLTGLRFIDLFAGLGGFRLALESCGAECVYSNEWDKYAQEVYEMNFGEKPEGDITQVNEKTIPDHDILCAGFP CQAFSISGKQKGFEDSRGTLFFDIARIVREKKPKVVFMENVKNFASHDNGNTLEVVKNTMNELDYSFHAKVLNALDYGIP QKRERIYMICFRNDLNIQNFQFPKPFELNTFVKDLLLPDSEVEHLVIDRKDLVMTNQEIEQTTPKTVRLGIVGKGGQGER IYSTRGIAITLSAYGGGIFAKTGGYLVNGKTRKLHPRECARVMGYPDSYKVHPSTSQAYKQFGNSVVINVLQYIAYNIGS SLNFKPY MIEIKDKQLTGLRFIDLFAGLGGFRLALESCGAECVYSNEWDKYAQEVYEMNFGEKPEGDITQVNEKTIPDHDILCAGFP CQAFSISGKQKGFEDSRGTLFFDIARIVREKKPKVVFMENVKNFASHDNGNTLEVVKNTMNELDYSFHAKVLNALDYGIP QKRERIYMICFRNDLNIQNFQFPKPFELNTFVKDLLLPDSEVEHLVIDRKDLVMTNQEIEQTTPKTVRLGIVGKGGQGER IYSTRGIAITLSAYGGGIFAKTGGYLVNGKTRKLHPRECARVMGYPDSYKVHPSTSQAYKQFGNSVVINVLQYIAYNIGS SLNFKPY A polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n Haemophilus Escherichia sample 726 Haemophilus haemolyticus 562 Escherichia coli 1 3.15 60.91 VAPOR DIFFUSION, HANGING DROP 6.5 PEG 8000, Ca acetate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K 289 -10.504 1 19 C 402 D 433 -1.994 C_DC402:DG433_D 1 -12.054 -0.469 0.093 -0.270 -0.495 1 19 C 403 D 432 -2.225 C_DC403:DG432_D 2 -5.072 -0.156 0.022 -0.271 -2.895 1 20 C 404 D 431 -0.592 C_DA404:DT431_D 3 -2.295 0.536 -0.090 -0.252 8.152 1 20 C 405 D 430 2.052 C_DT405:DA430_D 4 -6.965 0.502 -0.209 -0.277 12.399 1 19 C 406 D 429 -4.878 C_DG406:DC429_D 5 2.513 -0.070 -0.172 -0.277 8.900 1 19 C 407 D 428 -1.808 C_DC407:DG428_D 6 -10.668 0.203 -0.069 -0.270 2.216 1 19 C 409 D 426 -0.259 C_DC409:DG426_D 7 -7.143 0.490 0.110 -0.130 5.038 1 20 C 410 D 425 -5.841 C_DT410:DA425_D 8 -7.318 -0.448 -0.107 -0.137 -0.293 1 19 C 411 D 424 -1.520 C_DG411:DC424_D 9 -0.087 -0.165 -0.109 -0.195 3.628 1 20 C 412 D 423 -2.269 C_DA412:DT423_D 10 -5.258 -0.107 0.034 -0.297 5.235 1 19 C 413 D 422 -3.100 C_DC413:DG422_D 11 -11.853 0.238 0.555 -0.471 3.090 36.016 C C 402 403 7.552 D D 433 432 3.212 4.654 -0.441 -0.502 CC_DC402DC403:DG432DG433_DD 1 2.340 -3.797 35.650 -1.452 1.034 3.395 39.527 C C 403 404 3.982 D D 432 431 3.420 2.689 0.150 -0.319 CC_DC403DA404:DT431DG432_DD 2 2.728 -4.040 39.348 -0.802 0.112 2.973 27.311 C C 404 405 7.517 D D 431 430 3.040 3.537 0.007 -0.277 CC_DA404DT405:DA430DT431_DD 3 1.951 -4.147 27.016 -1.400 0.434 3.366 35.567 C C 405 406 2.989 D D 430 429 3.278 1.823 -0.963 0.515 CC_DT405DG406:DC429DA430_DD 4 -2.939 4.819 35.404 0.573 1.140 3.731 35.345 C C 406 407 -17.177 D D 429 428 3.727 -10.276 1.115 -0.907 CC_DG406DC407:DG428DC429_DD 5 -2.878 4.811 33.744 0.278 -2.333 7.325 52.872 C C 407 409 -2.184 D D 428 426 7.411 -1.940 -0.090 0.677 CC_DC407DC409:DG426DG428_DD 6 6.512 -7.331 52.465 1.043 1.051 3.324 37.393 C C 409 410 4.911 D D 426 425 3.349 3.142 0.016 -0.063 CC_DC409DT410:DA425DG426_DD 7 2.972 -4.646 37.151 -0.521 0.375 3.565 35.972 C C 410 411 5.688 D D 425 424 3.562 3.508 0.688 0.090 CC_DT410DG411:DC424DA425_DD 8 0.555 -0.900 35.802 -0.399 -1.027 3.339 29.766 C C 411 412 9.379 D D 424 423 3.380 4.788 -0.668 -0.327 CC_DG411DA412:DT423DC424_DD 9 -3.313 6.490 29.203 -1.674 0.582 3.014 31.556 C C 412 413 9.591 D D 423 422 3.292 5.171 0.657 -0.551 CC_DA412DC413:DG422DT423_DD 10 -5.165 9.580 30.719 -1.952 -2.146 repository Initial release Version format compliance Version format compliance 1 0 2002-09-18 1 1 2008-04-28 1 2 2011-07-13 CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI/DNA COMPLEX RCSB Y RCSB 2002-06-12 REL SAH S-ADENOSYL-L-HOMOCYSTEINE HOH water SAH 328 4 SAH SAH 328 A HOH 48 5 HOH HOH 48 C HOH 71 5 HOH HOH 71 C HOH 80 5 HOH HOH 80 C HOH 84 5 HOH HOH 84 C HOH 85 5 HOH HOH 85 C HOH 94 5 HOH HOH 94 C HOH 106 5 HOH HOH 106 C HOH 108 5 HOH HOH 108 C HOH 111 5 HOH HOH 111 C HOH 115 5 HOH HOH 115 C HOH 162 5 HOH HOH 162 C HOH 192 5 HOH HOH 192 C HOH 218 5 HOH HOH 218 C HOH 224 5 HOH HOH 224 C HOH 243 5 HOH HOH 243 C HOH 24 5 HOH HOH 24 D HOH 40 5 HOH HOH 40 D HOH 70 5 HOH HOH 70 D HOH 93 5 HOH HOH 93 D HOH 117 5 HOH HOH 117 D HOH 128 5 HOH HOH 128 D HOH 139 5 HOH HOH 139 D HOH 147 5 HOH HOH 147 D HOH 155 5 HOH HOH 155 D HOH 160 5 HOH HOH 160 D HOH 165 5 HOH HOH 165 D HOH 193 5 HOH HOH 193 D HOH 205 5 HOH HOH 205 D HOH 239 5 HOH HOH 239 D HOH 244 5 HOH HOH 244 D HOH 1 5 HOH HOH 329 A HOH 2 5 HOH HOH 330 A HOH 3 5 HOH HOH 331 A HOH 4 5 HOH HOH 332 A HOH 5 5 HOH HOH 333 A HOH 6 5 HOH HOH 334 A HOH 7 5 HOH HOH 335 A HOH 8 5 HOH HOH 336 A HOH 9 5 HOH HOH 337 A HOH 10 5 HOH HOH 338 A HOH 11 5 HOH HOH 339 A HOH 12 5 HOH HOH 340 A HOH 13 5 HOH HOH 341 A HOH 14 5 HOH HOH 342 A HOH 15 5 HOH HOH 343 A HOH 16 5 HOH HOH 344 A HOH 17 5 HOH HOH 345 A HOH 18 5 HOH HOH 346 A HOH 19 5 HOH HOH 347 A HOH 20 5 HOH HOH 348 A HOH 21 5 HOH HOH 349 A HOH 22 5 HOH HOH 350 A HOH 23 5 HOH HOH 351 A HOH 25 5 HOH HOH 352 A HOH 26 5 HOH HOH 353 A HOH 27 5 HOH HOH 354 A HOH 28 5 HOH HOH 355 A HOH 29 5 HOH HOH 356 A HOH 30 5 HOH HOH 357 A HOH 31 5 HOH HOH 358 A HOH 32 5 HOH HOH 359 A HOH 33 5 HOH HOH 360 A HOH 34 5 HOH HOH 361 A HOH 35 5 HOH HOH 362 A HOH 36 5 HOH HOH 363 A HOH 37 5 HOH HOH 364 A HOH 38 5 HOH HOH 365 A HOH 39 5 HOH HOH 366 A HOH 41 5 HOH HOH 367 A HOH 42 5 HOH HOH 368 A HOH 43 5 HOH HOH 369 A HOH 44 5 HOH HOH 370 A HOH 45 5 HOH HOH 371 A HOH 46 5 HOH HOH 372 A HOH 47 5 HOH HOH 373 A HOH 49 5 HOH HOH 374 A HOH 50 5 HOH HOH 375 A HOH 51 5 HOH HOH 376 A HOH 52 5 HOH HOH 377 A HOH 53 5 HOH HOH 378 A HOH 54 5 HOH HOH 379 A HOH 55 5 HOH HOH 380 A HOH 56 5 HOH HOH 381 A HOH 57 5 HOH HOH 382 A HOH 58 5 HOH HOH 383 A HOH 59 5 HOH HOH 384 A HOH 60 5 HOH HOH 385 A HOH 61 5 HOH HOH 386 A HOH 62 5 HOH HOH 387 A HOH 63 5 HOH HOH 388 A HOH 64 5 HOH HOH 389 A HOH 65 5 HOH HOH 390 A HOH 66 5 HOH HOH 391 A HOH 67 5 HOH HOH 392 A HOH 68 5 HOH HOH 393 A HOH 69 5 HOH HOH 394 A HOH 72 5 HOH HOH 395 A HOH 73 5 HOH HOH 396 A HOH 74 5 HOH HOH 397 A HOH 75 5 HOH HOH 398 A HOH 76 5 HOH HOH 399 A HOH 77 5 HOH HOH 400 A HOH 78 5 HOH HOH 401 A HOH 79 5 HOH HOH 402 A HOH 81 5 HOH HOH 403 A HOH 82 5 HOH HOH 404 A HOH 83 5 HOH HOH 405 A HOH 86 5 HOH HOH 406 A HOH 87 5 HOH HOH 407 A HOH 88 5 HOH HOH 408 A HOH 89 5 HOH HOH 409 A HOH 90 5 HOH HOH 410 A HOH 91 5 HOH HOH 411 A HOH 92 5 HOH HOH 412 A HOH 95 5 HOH HOH 413 A HOH 96 5 HOH HOH 414 A HOH 97 5 HOH HOH 415 A HOH 98 5 HOH HOH 416 A HOH 99 5 HOH HOH 417 A HOH 100 5 HOH HOH 418 A HOH 101 5 HOH HOH 419 A HOH 102 5 HOH HOH 420 A HOH 103 5 HOH HOH 421 A HOH 104 5 HOH HOH 422 A HOH 105 5 HOH HOH 423 A HOH 107 5 HOH HOH 424 A HOH 109 5 HOH HOH 425 A HOH 110 5 HOH HOH 426 A HOH 112 5 HOH HOH 427 A HOH 113 5 HOH HOH 428 A HOH 114 5 HOH HOH 429 A HOH 116 5 HOH HOH 430 A HOH 118 5 HOH HOH 431 A HOH 119 5 HOH HOH 432 A HOH 120 5 HOH HOH 433 A HOH 121 5 HOH HOH 434 A HOH 122 5 HOH HOH 435 A HOH 123 5 HOH HOH 436 A HOH 124 5 HOH HOH 437 A HOH 125 5 HOH HOH 438 A HOH 126 5 HOH HOH 439 A HOH 127 5 HOH HOH 440 A HOH 129 5 HOH HOH 441 A HOH 130 5 HOH HOH 442 A HOH 131 5 HOH HOH 443 A HOH 132 5 HOH HOH 444 A HOH 133 5 HOH HOH 445 A HOH 134 5 HOH HOH 446 A HOH 135 5 HOH HOH 447 A HOH 136 5 HOH HOH 448 A HOH 137 5 HOH HOH 449 A HOH 138 5 HOH HOH 450 A HOH 140 5 HOH HOH 451 A HOH 141 5 HOH HOH 452 A HOH 142 5 HOH HOH 453 A HOH 143 5 HOH HOH 454 A HOH 144 5 HOH HOH 455 A HOH 145 5 HOH HOH 456 A HOH 146 5 HOH HOH 457 A HOH 148 5 HOH HOH 458 A HOH 149 5 HOH HOH 459 A HOH 150 5 HOH HOH 460 A HOH 151 5 HOH HOH 461 A HOH 152 5 HOH HOH 462 A HOH 153 5 HOH HOH 463 A HOH 154 5 HOH HOH 464 A HOH 156 5 HOH HOH 465 A HOH 157 5 HOH HOH 466 A HOH 158 5 HOH HOH 467 A HOH 159 5 HOH HOH 468 A HOH 161 5 HOH HOH 469 A HOH 163 5 HOH HOH 470 A HOH 164 5 HOH HOH 471 A HOH 166 5 HOH HOH 472 A HOH 167 5 HOH HOH 473 A HOH 168 5 HOH HOH 474 A HOH 169 5 HOH HOH 475 A HOH 170 5 HOH HOH 476 A HOH 171 5 HOH HOH 477 A HOH 172 5 HOH HOH 478 A HOH 173 5 HOH HOH 479 A HOH 174 5 HOH HOH 480 A HOH 175 5 HOH HOH 481 A HOH 176 5 HOH HOH 482 A HOH 177 5 HOH HOH 483 A HOH 178 5 HOH HOH 484 A HOH 179 5 HOH HOH 485 A HOH 180 5 HOH HOH 486 A HOH 181 5 HOH HOH 487 A HOH 182 5 HOH HOH 488 A HOH 183 5 HOH HOH 489 A HOH 184 5 HOH HOH 490 A HOH 185 5 HOH HOH 491 A HOH 186 5 HOH HOH 492 A HOH 187 5 HOH HOH 493 A HOH 188 5 HOH HOH 494 A HOH 189 5 HOH HOH 495 A HOH 190 5 HOH HOH 496 A HOH 191 5 HOH HOH 497 A HOH 194 5 HOH HOH 498 A HOH 195 5 HOH HOH 499 A HOH 196 5 HOH HOH 500 A HOH 197 5 HOH HOH 501 A HOH 198 5 HOH HOH 502 A HOH 199 5 HOH HOH 503 A HOH 200 5 HOH HOH 504 A HOH 201 5 HOH HOH 505 A HOH 202 5 HOH HOH 506 A HOH 203 5 HOH HOH 507 A HOH 204 5 HOH HOH 508 A HOH 206 5 HOH HOH 509 A HOH 207 5 HOH HOH 510 A HOH 208 5 HOH HOH 511 A HOH 209 5 HOH HOH 512 A HOH 210 5 HOH HOH 513 A HOH 211 5 HOH HOH 514 A HOH 212 5 HOH HOH 515 A HOH 213 5 HOH HOH 516 A HOH 214 5 HOH HOH 517 A HOH 215 5 HOH HOH 518 A HOH 216 5 HOH HOH 519 A HOH 217 5 HOH HOH 520 A HOH 219 5 HOH HOH 521 A HOH 220 5 HOH HOH 522 A HOH 221 5 HOH HOH 523 A HOH 222 5 HOH HOH 524 A HOH 223 5 HOH HOH 525 A HOH 225 5 HOH HOH 526 A HOH 226 5 HOH HOH 527 A HOH 227 5 HOH HOH 528 A HOH 228 5 HOH HOH 529 A HOH 229 5 HOH HOH 530 A HOH 230 5 HOH HOH 531 A HOH 231 5 HOH HOH 532 A HOH 232 5 HOH HOH 533 A HOH 233 5 HOH HOH 534 A HOH 235 5 HOH HOH 535 A HOH 236 5 HOH HOH 536 A HOH 237 5 HOH HOH 537 A HOH 238 5 HOH HOH 538 A HOH 240 5 HOH HOH 539 A HOH 241 5 HOH HOH 540 A HOH 242 5 HOH HOH 541 A HOH 245 5 HOH HOH 542 A HOH 246 5 HOH HOH 543 A C 402 n 1 DC 402 C C 403 n 2 DC 403 C A 404 n 3 DA 404 C T 405 n 4 DT 405 C G 406 n 5 DG 406 C C 407 n 6 DC 407 C G 408 n 7 DG 408 C C 409 n 8 DC 409 C T 410 n 9 DT 410 C G 411 n 10 DG 411 C A 412 n 11 DA 412 C C 413 n 12 DC 413 C G 422 n 1 DG 422 D T 423 n 2 DT 423 D C 424 n 3 DC 424 D A 425 n 4 DA 425 D G 426 n 5 DG 426 D Z 427 n 6 Z 427 D G 428 n 7 DG 428 D C 429 n 8 DC 429 D A 430 n 9 DA 430 D T 431 n 10 DT 431 D G 432 n 11 DG 432 D G 433 n 12 DG 433 D MET 1 n 1 MET 1 A ILE 2 n 2 ILE 2 A GLU 3 n 3 GLU 3 A ILE 4 n 4 ILE 4 A LYS 5 n 5 LYS 5 A ASP 6 n 6 ASP 6 A LYS 7 n 7 LYS 7 A GLN 8 n 8 GLN 8 A LEU 9 n 9 LEU 9 A THR 10 n 10 THR 10 A GLY 11 n 11 GLY 11 A LEU 12 n 12 LEU 12 A ARG 13 n 13 ARG 13 A PHE 14 n 14 PHE 14 A ILE 15 n 15 ILE 15 A ASP 16 n 16 ASP 16 A LEU 17 n 17 LEU 17 A PHE 18 n 18 PHE 18 A ALA 19 n 19 ALA 19 A GLY 20 n 20 GLY 20 A LEU 21 n 21 LEU 21 A GLY 22 n 22 GLY 22 A GLY 23 n 23 GLY 23 A PHE 24 n 24 PHE 24 A ARG 25 n 25 ARG 25 A LEU 26 n 26 LEU 26 A ALA 27 n 27 ALA 27 A LEU 28 n 28 LEU 28 A GLU 29 n 29 GLU 29 A SER 30 n 30 SER 30 A CYS 31 n 31 CYS 31 A GLY 32 n 32 GLY 32 A ALA 33 n 33 ALA 33 A GLU 34 n 34 GLU 34 A CYS 35 n 35 CYS 35 A VAL 36 n 36 VAL 36 A TYR 37 n 37 TYR 37 A SER 38 n 38 SER 38 A ASN 39 n 39 ASN 39 A GLU 40 n 40 GLU 40 A TRP 41 n 41 TRP 41 A ASP 42 n 42 ASP 42 A LYS 43 n 43 LYS 43 A TYR 44 n 44 TYR 44 A ALA 45 n 45 ALA 45 A GLN 46 n 46 GLN 46 A GLU 47 n 47 GLU 47 A VAL 48 n 48 VAL 48 A TYR 49 n 49 TYR 49 A GLU 50 n 50 GLU 50 A MET 51 n 51 MET 51 A ASN 52 n 52 ASN 52 A PHE 53 n 53 PHE 53 A GLY 54 n 54 GLY 54 A GLU 55 n 55 GLU 55 A LYS 56 n 56 LYS 56 A PRO 57 n 57 PRO 57 A GLU 58 n 58 GLU 58 A GLY 59 n 59 GLY 59 A ASP 60 n 60 ASP 60 A ILE 61 n 61 ILE 61 A THR 62 n 62 THR 62 A GLN 63 n 63 GLN 63 A VAL 64 n 64 VAL 64 A ASN 65 n 65 ASN 65 A GLU 66 n 66 GLU 66 A LYS 67 n 67 LYS 67 A THR 68 n 68 THR 68 A ILE 69 n 69 ILE 69 A PRO 70 n 70 PRO 70 A ASP 71 n 71 ASP 71 A HIS 72 n 72 HIS 72 A ASP 73 n 73 ASP 73 A ILE 74 n 74 ILE 74 A LEU 75 n 75 LEU 75 A CYS 76 n 76 CYS 76 A ALA 77 n 77 ALA 77 A GLY 78 n 78 GLY 78 A PHE 79 n 79 PHE 79 A PRO 80 n 80 PRO 80 A CYS 81 n 81 CYS 81 A GLN 82 n 82 GLN 82 A ALA 83 n 83 ALA 83 A PHE 84 n 84 PHE 84 A SER 85 n 85 SER 85 A ILE 86 n 86 ILE 86 A SER 87 n 87 SER 87 A GLY 88 n 88 GLY 88 A LYS 89 n 89 LYS 89 A GLN 90 n 90 GLN 90 A LYS 91 n 91 LYS 91 A GLY 92 n 92 GLY 92 A PHE 93 n 93 PHE 93 A GLU 94 n 94 GLU 94 A ASP 95 n 95 ASP 95 A SER 96 n 96 SER 96 A ARG 97 n 97 ARG 97 A GLY 98 n 98 GLY 98 A THR 99 n 99 THR 99 A LEU 100 n 100 LEU 100 A PHE 101 n 101 PHE 101 A PHE 102 n 102 PHE 102 A ASP 103 n 103 ASP 103 A ILE 104 n 104 ILE 104 A ALA 105 n 105 ALA 105 A ARG 106 n 106 ARG 106 A ILE 107 n 107 ILE 107 A VAL 108 n 108 VAL 108 A ARG 109 n 109 ARG 109 A GLU 110 n 110 GLU 110 A LYS 111 n 111 LYS 111 A LYS 112 n 112 LYS 112 A PRO 113 n 113 PRO 113 A LYS 114 n 114 LYS 114 A VAL 115 n 115 VAL 115 A VAL 116 n 116 VAL 116 A PHE 117 n 117 PHE 117 A MET 118 n 118 MET 118 A GLU 119 n 119 GLU 119 A ASN 120 n 120 ASN 120 A VAL 121 n 121 VAL 121 A LYS 122 n 122 LYS 122 A ASN 123 n 123 ASN 123 A PHE 124 n 124 PHE 124 A ALA 125 n 125 ALA 125 A SER 126 n 126 SER 126 A HIS 127 n 127 HIS 127 A ASP 128 n 128 ASP 128 A ASN 129 n 129 ASN 129 A GLY 130 n 130 GLY 130 A ASN 131 n 131 ASN 131 A THR 132 n 132 THR 132 A LEU 133 n 133 LEU 133 A GLU 134 n 134 GLU 134 A VAL 135 n 135 VAL 135 A VAL 136 n 136 VAL 136 A LYS 137 n 137 LYS 137 A ASN 138 n 138 ASN 138 A THR 139 n 139 THR 139 A MET 140 n 140 MET 140 A ASN 141 n 141 ASN 141 A GLU 142 n 142 GLU 142 A LEU 143 n 143 LEU 143 A ASP 144 n 144 ASP 144 A TYR 145 n 145 TYR 145 A SER 146 n 146 SER 146 A PHE 147 n 147 PHE 147 A HIS 148 n 148 HIS 148 A ALA 149 n 149 ALA 149 A LYS 150 n 150 LYS 150 A VAL 151 n 151 VAL 151 A LEU 152 n 152 LEU 152 A ASN 153 n 153 ASN 153 A ALA 154 n 154 ALA 154 A LEU 155 n 155 LEU 155 A ASP 156 n 156 ASP 156 A TYR 157 n 157 TYR 157 A GLY 158 n 158 GLY 158 A ILE 159 n 159 ILE 159 A PRO 160 n 160 PRO 160 A GLN 161 n 161 GLN 161 A LYS 162 n 162 LYS 162 A ARG 163 n 163 ARG 163 A GLU 164 n 164 GLU 164 A ARG 165 n 165 ARG 165 A ILE 166 n 166 ILE 166 A TYR 167 n 167 TYR 167 A MET 168 n 168 MET 168 A ILE 169 n 169 ILE 169 A CYS 170 n 170 CYS 170 A PHE 171 n 171 PHE 171 A ARG 172 n 172 ARG 172 A ASN 173 n 173 ASN 173 A ASP 174 n 174 ASP 174 A LEU 175 n 175 LEU 175 A ASN 176 n 176 ASN 176 A ILE 177 n 177 ILE 177 A GLN 178 n 178 GLN 178 A ASN 179 n 179 ASN 179 A PHE 180 n 180 PHE 180 A GLN 181 n 181 GLN 181 A PHE 182 n 182 PHE 182 A PRO 183 n 183 PRO 183 A LYS 184 n 184 LYS 184 A PRO 185 n 185 PRO 185 A PHE 186 n 186 PHE 186 A GLU 187 n 187 GLU 187 A LEU 188 n 188 LEU 188 A ASN 189 n 189 ASN 189 A THR 190 n 190 THR 190 A PHE 191 n 191 PHE 191 A VAL 192 n 192 VAL 192 A LYS 193 n 193 LYS 193 A ASP 194 n 194 ASP 194 A LEU 195 n 195 LEU 195 A LEU 196 n 196 LEU 196 A LEU 197 n 197 LEU 197 A PRO 198 n 198 PRO 198 A ASP 199 n 199 ASP 199 A SER 200 n 200 SER 200 A GLU 201 n 201 GLU 201 A VAL 202 n 202 VAL 202 A GLU 203 n 203 GLU 203 A HIS 204 n 204 HIS 204 A LEU 205 n 205 LEU 205 A VAL 206 n 206 VAL 206 A ILE 207 n 207 ILE 207 A ASP 208 n 208 ASP 208 A ARG 209 n 209 ARG 209 A LYS 210 n 210 LYS 210 A ASP 211 n 211 ASP 211 A LEU 212 n 212 LEU 212 A VAL 213 n 213 VAL 213 A MET 214 n 214 MET 214 A THR 215 n 215 THR 215 A ASN 216 n 216 ASN 216 A GLN 217 n 217 GLN 217 A GLU 218 n 218 GLU 218 A ILE 219 n 219 ILE 219 A GLU 220 n 220 GLU 220 A GLN 221 n 221 GLN 221 A THR 222 n 222 THR 222 A THR 223 n 223 THR 223 A PRO 224 n 224 PRO 224 A LYS 225 n 225 LYS 225 A THR 226 n 226 THR 226 A VAL 227 n 227 VAL 227 A ARG 228 n 228 ARG 228 A LEU 229 n 229 LEU 229 A GLY 230 n 230 GLY 230 A ILE 231 n 231 ILE 231 A VAL 232 n 232 VAL 232 A GLY 233 n 233 GLY 233 A LYS 234 n 234 LYS 234 A GLY 235 n 235 GLY 235 A GLY 236 n 236 GLY 236 A GLN 237 n 237 GLN 237 A GLY 238 n 238 GLY 238 A GLU 239 n 239 GLU 239 A ARG 240 n 240 ARG 240 A ILE 241 n 241 ILE 241 A TYR 242 n 242 TYR 242 A SER 243 n 243 SER 243 A THR 244 n 244 THR 244 A ARG 245 n 245 ARG 245 A GLY 246 n 246 GLY 246 A ILE 247 n 247 ILE 247 A ALA 248 n 248 ALA 248 A ILE 249 n 249 ILE 249 A THR 250 n 250 THR 250 A LEU 251 n 251 LEU 251 A SER 252 n 252 SER 252 A ALA 253 n 253 ALA 253 A TYR 254 n 254 TYR 254 A GLY 255 n 255 GLY 255 A GLY 256 n 256 GLY 256 A GLY 257 n 257 GLY 257 A ILE 258 n 258 ILE 258 A PHE 259 n 259 PHE 259 A ALA 260 n 260 ALA 260 A LYS 261 n 261 LYS 261 A THR 262 n 262 THR 262 A GLY 263 n 263 GLY 263 A GLY 264 n 264 GLY 264 A TYR 265 n 265 TYR 265 A LEU 266 n 266 LEU 266 A VAL 267 n 267 VAL 267 A ASN 268 n 268 ASN 268 A GLY 269 n 269 GLY 269 A LYS 270 n 270 LYS 270 A THR 271 n 271 THR 271 A ARG 272 n 272 ARG 272 A LYS 273 n 273 LYS 273 A LEU 274 n 274 LEU 274 A HIS 275 n 275 HIS 275 A PRO 276 n 276 PRO 276 A ARG 277 n 277 ARG 277 A GLU 278 n 278 GLU 278 A CYS 279 n 279 CYS 279 A ALA 280 n 280 ALA 280 A ARG 281 n 281 ARG 281 A VAL 282 n 282 VAL 282 A MET 283 n 283 MET 283 A GLY 284 n 284 GLY 284 A TYR 285 n 285 TYR 285 A PRO 286 n 286 PRO 286 A ASP 287 n 287 ASP 287 A SER 288 n 288 SER 288 A TYR 289 n 289 TYR 289 A LYS 290 n 290 LYS 290 A VAL 291 n 291 VAL 291 A HIS 292 n 292 HIS 292 A PRO 293 n 293 PRO 293 A SER 294 n 294 SER 294 A THR 295 n 295 THR 295 A SER 296 n 296 SER 296 A GLN 297 n 297 GLN 297 A ALA 298 n 298 ALA 298 A TYR 299 n 299 TYR 299 A LYS 300 n 300 LYS 300 A GLN 301 n 301 GLN 301 A PHE 302 n 302 PHE 302 A GLY 303 n 303 GLY 303 A ASN 304 n 304 ASN 304 A SER 305 n 305 SER 305 A VAL 306 n 306 VAL 306 A VAL 307 n 307 VAL 307 A ILE 308 n 308 ILE 308 A ASN 309 n 309 ASN 309 A VAL 310 n 310 VAL 310 A LEU 311 n 311 LEU 311 A GLN 312 n 312 GLN 312 A TYR 313 n 313 TYR 313 A ILE 314 n 314 ILE 314 A ALA 315 n 315 ALA 315 A TYR 316 n 316 TYR 316 A ASN 317 n 317 ASN 317 A ILE 318 n 318 ILE 318 A GLY 319 n 319 GLY 319 A SER 320 n 320 SER 320 A SER 321 n 321 SER 321 A LEU 322 n 322 LEU 322 A ASN 323 n 323 ASN 323 A PHE 324 n 324 PHE 324 A LYS 325 n 325 LYS 325 A PRO 326 n 326 PRO 326 A TYR 327 n 327 TYR 327 A author_defined_assembly 3 trimeric D Z 427 ZEBULARINE B Z 6 DC 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 A O TYR 37 C O TYR 37 A N ASP 16 C N ASP 16 A N ILE 15 C N ILE 15 A O CYS 76 C O CYS 76 A N LEU 75 C N LEU 75 A O VAL 115 C O VAL 115 A N ASN 120 C N ASN 120 A O ILE 166 C O ILE 166 A O ILE 169 C O ILE 169 A N HIS 148 C N HIS 148 A N GLY 230 C N GLY 230 A O ILE 241 C O ILE 241 A N TYR 242 C N TYR 242 A O GLY 264 C O GLY 264 A N VAL 267 C N VAL 267 A O LYS 270 C O LYS 270 1 A HOH 526 G HOH 1 A CG LYS 43 C CG LYS 43 1 Y 1 A CD LYS 43 C CD LYS 43 1 Y 1 A CE LYS 43 C CE LYS 43 1 Y 1 A NZ LYS 43 C NZ LYS 43 1 Y 1 A CG LYS 184 C CG LYS 184 1 Y 1 A CD LYS 184 C CD LYS 184 1 Y 1 A CE LYS 184 C CE LYS 184 1 Y 1 A NZ LYS 184 C NZ LYS 184 1 Y 1 A CG1 ILE 207 C CG1 ILE 207 1 Y 1 A CG2 ILE 207 C CG2 ILE 207 1 Y 1 A CD1 ILE 207 C CD1 ILE 207 1 Y 1 A CG GLN 217 C CG GLN 217 1 Y 1 A CD GLN 217 C CD GLN 217 1 Y 1 A OE1 GLN 217 C OE1 GLN 217 1 Y 1 A NE2 GLN 217 C NE2 GLN 217 1 Y 1 C DC 413 0.070 SIDE CHAIN 1 D DG 422 0.064 SIDE CHAIN 1 D DC 424 0.077 SIDE CHAIN 1 6.88 1.10 109.80 116.68 C C C C5' C4' O4' DC DC DC 409 409 409 N 1 -7.28 1.00 110.10 102.82 C C C C1' O4' C4' DC DC DC 409 409 409 N 1 A ASP 16 -106.93 78.64 1 A ASP 60 -0.96 99.75 1 A ALA 77 -162.49 109.78 1 A LYS 112 38.69 63.11 1 A ASP 144 77.38 48.92 1 A MET 214 -69.92 88.11 1 A LYS 261 69.60 -12.86 1 A THR 262 -131.97 -31.09 1 A SER 305 -77.50 -169.43 31.1 0.04 1.04 0.00 0.04 0.00 -0.07 0.2430000 0.1770000 2.50 39.7 1938 19591 19591 98.1 Random 1 THROUGHOUT 2.0 MOLECULAR REPLACEMENT PDB entry 9MHT 0.24 39.7 0.26 2.50 39.7 245 3379 26 491 2617 0.011 1.5 26.2 1.47 0.3290000 0.019 0.2680000 2.66 312 96.3 2.5 39.7 1M0E 19591 -3.0 -3.0 1 98.1 2.50 2.61 96.3 data reduction DENZO data scaling SCALEPACK phasing AMoRE refinement X-PLOR 3.851 Modification methylase HhaI/DNA Complex ZEBULARINE: A NOVEL DNA METHYLATION INHIBITOR THAT FORMS A COVALENT COMPLEX WITH DNA METHYLTRANSFERASE 1 N N 2 N N 3 N N 4 N N 5 N N 5 N N 5 N N A GLY 22 C GLY 22 HELX_P A SER 30 C SER 30 1 1 9 A ASP 42 C ASP 42 HELX_P A GLY 54 C GLY 54 1 2 13 A ASP 60 C ASP 60 HELX_P A VAL 64 C VAL 64 5 3 5 A ASN 65 C ASN 65 HELX_P A ILE 69 C ILE 69 5 4 5 A LYS 91 C LYS 91 HELX_P A ASP 95 C ASP 95 5 5 5 A THR 99 C THR 99 HELX_P A LYS 112 C LYS 112 1 6 14 A LYS 122 C LYS 122 HELX_P A HIS 127 C HIS 127 1 7 6 A GLY 130 C GLY 130 HELX_P A LEU 143 C LEU 143 1 8 14 A LEU 155 C LEU 155 HELX_P A GLY 158 C GLY 158 5 9 4 A ASN 173 C ASN 173 HELX_P A ASN 176 C ASN 176 5 10 4 A PHE 191 C PHE 191 HELX_P A LEU 196 C LEU 196 1 11 6 A PRO 198 C PRO 198 HELX_P A VAL 206 C VAL 206 5 12 9 A HIS 275 C HIS 275 HELX_P A MET 283 C MET 283 1 13 9 A SER 294 C SER 294 HELX_P A SER 305 C SER 305 1 14 12 A VAL 307 C VAL 307 HELX_P A PHE 324 C PHE 324 1 15 18 covale 1.836 D Z 427 B C6 Z 6 1_555 A CYS 81 C SG CYS 81 1_555 covale 1.589 D DG 426 B O3' DG 5 1_555 D Z 427 B P Z 6 1_555 covale 1.598 D Z 427 B O3' Z 6 1_555 D DG 428 B P DG 7 1_555 hydrog WATSON-CRICK C DC 402 A N3 DC 1 1_555 D DG 433 B N1 DG 12 1_555 hydrog WATSON-CRICK C DC 402 A N4 DC 1 1_555 D DG 433 B O6 DG 12 1_555 hydrog WATSON-CRICK C DC 402 A O2 DC 1 1_555 D DG 433 B N2 DG 12 1_555 hydrog WATSON-CRICK C DC 403 A N3 DC 2 1_555 D DG 432 B N1 DG 11 1_555 hydrog WATSON-CRICK C DC 403 A N4 DC 2 1_555 D DG 432 B O6 DG 11 1_555 hydrog WATSON-CRICK C DC 403 A O2 DC 2 1_555 D DG 432 B N2 DG 11 1_555 hydrog WATSON-CRICK C DA 404 A N1 DA 3 1_555 D DT 431 B N3 DT 10 1_555 hydrog WATSON-CRICK C DA 404 A N6 DA 3 1_555 D DT 431 B O4 DT 10 1_555 hydrog WATSON-CRICK C DT 405 A N3 DT 4 1_555 D DA 430 B N1 DA 9 1_555 hydrog WATSON-CRICK C DT 405 A O4 DT 4 1_555 D DA 430 B N6 DA 9 1_555 hydrog WATSON-CRICK C DG 406 A N1 DG 5 1_555 D DC 429 B N3 DC 8 1_555 hydrog WATSON-CRICK C DG 406 A N2 DG 5 1_555 D DC 429 B O2 DC 8 1_555 hydrog WATSON-CRICK C DG 406 A O6 DG 5 1_555 D DC 429 B N4 DC 8 1_555 hydrog WATSON-CRICK C DC 407 A N3 DC 6 1_555 D DG 428 B N1 DG 7 1_555 hydrog WATSON-CRICK C DC 407 A N4 DC 6 1_555 D DG 428 B O6 DG 7 1_555 hydrog WATSON-CRICK C DC 407 A O2 DC 6 1_555 D DG 428 B N2 DG 7 1_555 hydrog WATSON-CRICK C DC 409 A N3 DC 8 1_555 D DG 426 B N1 DG 5 1_555 hydrog WATSON-CRICK C DC 409 A N4 DC 8 1_555 D DG 426 B O6 DG 5 1_555 hydrog WATSON-CRICK C DC 409 A O2 DC 8 1_555 D DG 426 B N2 DG 5 1_555 hydrog WATSON-CRICK C DT 410 A N3 DT 9 1_555 D DA 425 B N1 DA 4 1_555 hydrog WATSON-CRICK C DT 410 A O4 DT 9 1_555 D DA 425 B N6 DA 4 1_555 hydrog WATSON-CRICK C DG 411 A N1 DG 10 1_555 D DC 424 B N3 DC 3 1_555 hydrog WATSON-CRICK C DG 411 A N2 DG 10 1_555 D DC 424 B O2 DC 3 1_555 hydrog WATSON-CRICK C DG 411 A O6 DG 10 1_555 D DC 424 B N4 DC 3 1_555 hydrog WATSON-CRICK C DA 412 A N1 DA 11 1_555 D DT 423 B N3 DT 2 1_555 hydrog WATSON-CRICK C DA 412 A N6 DA 11 1_555 D DT 423 B O4 DT 2 1_555 hydrog WATSON-CRICK C DC 413 A N3 DC 12 1_555 D DG 422 B N1 DG 1 1_555 hydrog WATSON-CRICK C DC 413 A N4 DC 12 1_555 D DG 422 B O6 DG 1 1_555 hydrog WATSON-CRICK C DC 413 A O2 DC 12 1_555 D DG 422 B N2 DG 1 1_555 TRANSFERASE/DNA Protein-DNA covalent complex, Mechanism based DNA methylation inhibitors, Zebularine, TRANSFERASE-DNA COMPLEX MTH1_HAEHA UNP 3 1 P05102 MIEIKDKQLTGLRFIDLFAGLGGFRLALESCGAECVYSNEWDKYAQEVYEMNFGEKPEGDITQVNEKTIPDHDILCAGFP CQAFSISGKQKGFEDSRGTLFFDIARIVREKKPKVVFMENVKNFASHDNGNTLEVVKNTMNELDYSFHAKVLNALDYGIP QKRERIYMICFRNDLNIQNFQFPKPFELNTFVKDLLLPDSEVEHLVIDRKDLVMTNQEIEQTTPKTVRLGIVGKGGQGER IYSTRGIAITLSAYGGGIFAKTGGYLVNGKTRKLHPRECARVMGYPDSYKVHPSTSQAYKQFGNSVVINVLQYIAYNIGS SLNFKPY 1M0E PDB 1 1M0E 1M0E PDB 2 1M0E 1 327 1M0E 1 327 P05102 A 1 1 327 402 413 1M0E 402 413 1M0E C 2 1 12 422 433 1M0E 422 433 1M0E D 3 1 12 6 4 parallel parallel parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel A GLU 34 C GLU 34 A SER 38 C SER 38 A ARG 13 C ARG 13 A LEU 17 C LEU 17 A ILE 74 C ILE 74 A GLY 78 C GLY 78 A VAL 115 C VAL 115 A VAL 121 C VAL 121 A GLU 164 C GLU 164 A PHE 171 C PHE 171 A HIS 148 C HIS 148 A ASN 153 C ASN 153 A ARG 228 C ARG 228 A ILE 231 C ILE 231 A ARG 240 C ARG 240 A SER 243 C SER 243 A GLY 264 C GLY 264 A VAL 267 C VAL 267 A LYS 270 C LYS 270 A ARG 272 C ARG 272 BINDING SITE FOR RESIDUE SAH A 328 Software 21 A PHE 18 C PHE 18 21 1_555 A ALA 19 C ALA 19 21 1_555 A GLY 20 C GLY 20 21 1_555 A LEU 21 C LEU 21 21 1_555 A GLY 23 C GLY 23 21 1_555 A ASN 39 C ASN 39 21 1_555 A GLU 40 C GLU 40 21 1_555 A TRP 41 C TRP 41 21 1_555 A ASP 60 C ASP 60 21 1_555 A ILE 61 C ILE 61 21 1_555 A GLY 78 C GLY 78 21 1_555 A ASN 304 C ASN 304 21 1_555 A SER 305 C SER 305 21 1_555 A VAL 306 C VAL 306 21 1_555 A HOH 335 G HOH 21 1_555 A HOH 348 G HOH 21 1_555 A HOH 350 G HOH 21 1_555 A HOH 357 G HOH 21 1_555 A HOH 361 G HOH 21 1_555 A HOH 369 G HOH 21 1_555 A HOH 374 G HOH 21 1_555 155 H 3 2