0.007746 0.004472 0.000000 -0.000000 0.008944 0.000000 0.000000 -0.000000 0.011839 0.000000 0.000000 0.000000 Chen, B. Gan, J. Yang, C.G. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.000 90.000 120.000 129.099 129.099 84.466 C11 H18 N3 O7 P S 367.315 2'-deoxy-N-(2-sulfanylethyl)cytidine 5'-(dihydrogen phosphate) non-polymer 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 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 Mg 2 24.305 MAGNESIUM ION non-polymer C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE 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 N 1 N P N 2 N O N 3 N O N 4 N O N 5 N C N 6 R C N 7 N O N 8 S C N 9 N O N 10 N C N 11 R C N 12 N N N 13 N C N 14 N O N 15 N N N 16 N C N 17 N N N 18 N C N 19 N C N 20 N S N 21 N C N 22 N C N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N H N 40 N O N 41 N H N 42 N N N 43 S C N 44 N C N 45 N O N 46 N C N 47 N O N 48 N H N 49 N H N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H N 55 N N N 56 S C N 57 N C N 58 N O N 59 N C N 60 N C N 61 N C N 62 N N N 63 N C N 64 N N N 65 N N N 66 N O N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N H N 75 N H N 76 N H N 77 N H N 78 N H N 79 N H N 80 N H N 81 N H N 82 N N N 83 S C N 84 N C N 85 N O N 86 N C N 87 N C N 88 N O N 89 N N N 90 N O N 91 N H N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N N N 100 S C N 101 N C N 102 N O N 103 N C N 104 N C N 105 N O N 106 N O N 107 N O N 108 N H N 109 N H N 110 N H N 111 N H N 112 N H N 113 N H N 114 N H N 115 N N N 116 R C N 117 N C N 118 N O N 119 N C N 120 N S N 121 N O N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H N 129 N O N 130 N P N 131 N O N 132 N O N 133 N O N 134 N C N 135 R C N 136 N O N 137 S C N 138 N O N 139 N C N 140 R C Y 141 N N Y 142 N C Y 143 N N Y 144 N C Y 145 N C N 146 N N Y 147 N N Y 148 N C Y 149 N N Y 150 N C N 151 N H N 152 N H N 153 N H N 154 N H N 155 N H N 156 N H N 157 N H N 158 N H N 159 N H N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N O N 166 N P N 167 N O N 168 N O N 169 N O N 170 N C N 171 R C N 172 N O N 173 S C N 174 N O N 175 N C N 176 R C N 177 N N N 178 N C N 179 N O N 180 N N N 181 N C N 182 N N N 183 N C N 184 N C N 185 N H N 186 N H N 187 N H N 188 N H N 189 N H N 190 N H N 191 N H N 192 N H N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N H N 199 N O N 200 N P N 201 N O N 202 N O N 203 N O N 204 N C N 205 R C N 206 N O N 207 S C N 208 N O N 209 N C N 210 R C Y 211 N N Y 212 N C Y 213 N N Y 214 N C N 215 N C N 216 N O N 217 N N N 218 N C N 219 N N N 220 N N Y 221 N C N 222 N H N 223 N H N 224 N H N 225 N H N 226 N H N 227 N H N 228 N H N 229 N H N 230 N H N 231 N H N 232 N H N 233 N H N 234 N H N 235 N H N 236 N O N 237 N P N 238 N O N 239 N O N 240 N O N 241 N C N 242 R C N 243 N O N 244 S C N 245 N O N 246 N C N 247 R C N 248 N N N 249 N C N 250 N O N 251 N N N 252 N C N 253 N O N 254 N C N 255 N C N 256 N C N 257 N H N 258 N H N 259 N H N 260 N H N 261 N H N 262 N H N 263 N H N 264 N H N 265 N H N 266 N H N 267 N H N 268 N H N 269 N H N 270 N H N 271 N H N 272 N N N 273 S C N 274 N C N 275 N O N 276 N C N 277 N C N 278 N C N 279 N O N 280 N N N 281 N O N 282 N H N 283 N H N 284 N H N 285 N H N 286 N H N 287 N H N 288 N H N 289 N H N 290 N H N 291 N H N 292 N N N 293 S C N 294 N C N 295 N O N 296 N C N 297 N C N 298 N C N 299 N O N 300 N O N 301 N O N 302 N H N 303 N H N 304 N H N 305 N H N 306 N H N 307 N H N 308 N H N 309 N H N 310 N H N 311 N N N 312 N C N 313 N C N 314 N O N 315 N O N 316 N H N 317 N H N 318 N H N 319 N H N 320 N H N 321 N N N 322 S C N 323 N C N 324 N O N 325 N C Y 326 N C Y 327 N N Y 328 N C Y 329 N C Y 330 N N N 331 N O N 332 N H N 333 N H N 334 N H N 335 N H N 336 N H N 337 N H N 338 N H N 339 N H N 340 N H N 341 N H N 342 N N N 343 S C N 344 N C N 345 N O N 346 S C N 347 N C N 348 N C N 349 N C N 350 N O N 351 N H N 352 N H N 353 N H N 354 N H N 355 N H N 356 N H N 357 N H N 358 N H N 359 N H N 360 N H N 361 N H N 362 N H N 363 N H N 364 N N N 365 S C N 366 N C N 367 N O N 368 N C N 369 N C N 370 N C N 371 N C N 372 N O N 373 N H N 374 N H N 375 N H N 376 N H N 377 N H N 378 N H N 379 N H N 380 N H N 381 N H N 382 N H N 383 N H N 384 N H N 385 N H N 386 N N N 387 S C N 388 N C N 389 N O N 390 N C N 391 N C N 392 N C N 393 N C N 394 N N N 395 N O N 396 N H N 397 N H N 398 N H N 399 N H N 400 N H N 401 N H N 402 N H N 403 N H N 404 N H N 405 N H N 406 N H N 407 N H N 408 N H N 409 N H N 410 N H N 411 N N N 412 S C N 413 N C N 414 N O N 415 N C N 416 N C N 417 N S N 418 N C N 419 N O N 420 N H N 421 N H N 422 N H N 423 N H N 424 N H N 425 N H N 426 N H N 427 N H N 428 N H N 429 N H N 430 N H N 431 N MG N 432 N N N 433 S C N 434 N C N 435 N O N 436 N C Y 437 N C Y 438 N C Y 439 N C Y 440 N C Y 441 N C Y 442 N C N 443 N O N 444 N H N 445 N H N 446 N H N 447 N H N 448 N H N 449 N H N 450 N H N 451 N H N 452 N H N 453 N H N 454 N H N 455 N N N 456 S C N 457 N C N 458 N O N 459 N C N 460 N C N 461 N C N 462 N O N 463 N H N 464 N H N 465 N H N 466 N H N 467 N H N 468 N H N 469 N H N 470 N H N 471 N H N 472 N N N 473 S C N 474 N C N 475 N O N 476 N C N 477 N O N 478 N O N 479 N H N 480 N H N 481 N H N 482 N H N 483 N H N 484 N H N 485 N H N 486 N N N 487 S C N 488 N C N 489 N O N 490 R C N 491 N O N 492 N C N 493 N O N 494 N H N 495 N H N 496 N H N 497 N H N 498 N H N 499 N H N 500 N H N 501 N H N 502 N H N 503 N N N 504 S C N 505 N C N 506 N O N 507 N C Y 508 N C Y 509 N C Y 510 N C Y 511 N N Y 512 N C Y 513 N C Y 514 N C Y 515 N C Y 516 N C N 517 N O N 518 N H N 519 N H N 520 N H N 521 N H N 522 N H N 523 N H N 524 N H N 525 N H N 526 N H N 527 N H N 528 N H N 529 N H N 530 N N N 531 S C N 532 N C N 533 N O N 534 N C Y 535 N C Y 536 N C Y 537 N C Y 538 N C Y 539 N C Y 540 N C N 541 N O N 542 N O N 543 N H N 544 N H N 545 N H N 546 N H N 547 N H N 548 N H N 549 N H N 550 N H N 551 N H N 552 N H N 553 N H N 554 N N N 555 S C N 556 N C N 557 N O N 558 N C N 559 N C N 560 N C N 561 N O N 562 N H N 563 N H N 564 N H N 565 N H N 566 N H N 567 N H N 568 N H N 569 N H N 570 N H N 571 N H N 572 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N doub N 6 N sing N 7 N sing N 8 N doub N 9 N doub N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N doub N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N doub N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N doub N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N doub N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N doub N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N doub N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N doub N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N doub N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N doub N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N doub N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing Y 148 N sing Y 149 N sing Y 150 N doub N 151 N sing Y 152 N sing Y 153 N sing Y 154 N doub N 155 N sing Y 156 N doub N 157 N sing N 158 N sing Y 159 N sing Y 160 N doub N 161 N sing Y 162 N sing N 163 N sing N 164 N sing N 165 N doub N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N doub N 189 N sing N 190 N doub N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N doub N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N doub N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N sing N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N sing N 214 N sing N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N sing N 220 N sing Y 221 N sing Y 222 N sing Y 223 N doub N 224 N sing Y 225 N sing N 226 N sing Y 227 N doub N 228 N doub N 229 N sing N 230 N sing N 231 N sing N 232 N sing N 233 N doub N 234 N sing N 235 N sing N 236 N sing N 237 N sing N 238 N sing N 239 N doub N 240 N sing N 241 N sing N 242 N sing N 243 N sing N 244 N sing N 245 N sing N 246 N sing N 247 N sing N 248 N sing N 249 N sing N 250 N sing N 251 N sing N 252 N sing N 253 N sing N 254 N sing N 255 N sing N 256 N sing N 257 N sing N 258 N sing N 259 N sing N 260 N sing N 261 N sing N 262 N doub N 263 N sing N 264 N sing N 265 N sing N 266 N doub N 267 N sing N 268 N sing N 269 N doub N 270 N sing N 271 N sing N 272 N sing N 273 N sing N 274 N sing N 275 N sing N 276 N sing N 277 N sing N 278 N sing N 279 N sing N 280 N doub N 281 N sing N 282 N sing N 283 N sing N 284 N sing N 285 N sing N 286 N sing N 287 N sing N 288 N doub N 289 N sing N 290 N sing N 291 N sing N 292 N sing N 293 N sing N 294 N sing N 295 N sing N 296 N sing N 297 N sing N 298 N sing N 299 N doub N 300 N sing N 301 N sing N 302 N sing N 303 N sing N 304 N sing N 305 N sing N 306 N sing N 307 N doub N 308 N sing N 309 N sing N 310 N sing N 311 N sing N 312 N sing N 313 N sing N 314 N sing N 315 N sing N 316 N sing N 317 N doub N 318 N sing N 319 N sing N 320 N sing N 321 N sing N 322 N sing N 323 N sing N 324 N sing N 325 N sing N 326 N doub N 327 N sing N 328 N sing N 329 N sing N 330 N sing Y 331 N sing Y 332 N doub Y 333 N doub N 334 N sing Y 335 N sing N 336 N sing Y 337 N sing N 338 N sing N 339 N sing N 340 N sing N 341 N sing N 342 N sing N 343 N sing N 344 N sing N 345 N sing N 346 N sing N 347 N doub N 348 N sing N 349 N sing N 350 N sing N 351 N sing N 352 N sing N 353 N sing N 354 N sing N 355 N sing N 356 N sing N 357 N sing N 358 N sing N 359 N sing N 360 N sing N 361 N sing N 362 N sing N 363 N sing N 364 N sing N 365 N sing N 366 N sing N 367 N sing N 368 N doub N 369 N sing N 370 N sing N 371 N sing N 372 N sing N 373 N sing N 374 N sing N 375 N sing N 376 N sing N 377 N sing N 378 N sing N 379 N sing N 380 N sing N 381 N sing N 382 N sing N 383 N sing N 384 N sing N 385 N sing N 386 N sing N 387 N sing N 388 N sing N 389 N doub N 390 N sing N 391 N sing N 392 N sing N 393 N sing N 394 N sing N 395 N sing N 396 N sing N 397 N sing N 398 N sing N 399 N sing N 400 N sing N 401 N sing N 402 N sing N 403 N sing N 404 N sing N 405 N sing N 406 N sing N 407 N sing N 408 N sing N 409 N sing N 410 N sing N 411 N sing N 412 N sing N 413 N doub N 414 N sing N 415 N sing N 416 N sing N 417 N sing N 418 N sing N 419 N sing N 420 N sing N 421 N sing N 422 N sing N 423 N sing N 424 N sing N 425 N sing N 426 N sing N 427 N sing N 428 N sing N 429 N sing N 430 N sing N 431 N sing N 432 N doub N 433 N sing N 434 N sing N 435 N sing N 436 N sing Y 437 N doub Y 438 N sing Y 439 N sing N 440 N sing Y 441 N doub N 442 N sing Y 443 N doub N 444 N sing Y 445 N sing N 446 N sing N 447 N sing N 448 N sing N 449 N sing N 450 N sing N 451 N sing N 452 N sing N 453 N sing N 454 N sing N 455 N doub N 456 N sing N 457 N sing N 458 N sing N 459 N sing N 460 N sing N 461 N sing N 462 N sing N 463 N sing N 464 N sing N 465 N sing N 466 N sing N 467 N sing N 468 N sing N 469 N sing N 470 N sing N 471 N sing N 472 N doub N 473 N sing N 474 N sing N 475 N sing N 476 N sing N 477 N sing N 478 N sing N 479 N sing N 480 N sing N 481 N sing N 482 N sing N 483 N sing N 484 N sing N 485 N doub N 486 N sing N 487 N sing N 488 N sing N 489 N sing N 490 N sing N 491 N sing N 492 N sing N 493 N sing N 494 N sing N 495 N sing N 496 N sing N 497 N sing N 498 N sing N 499 N sing N 500 N sing N 501 N doub N 502 N sing N 503 N sing N 504 N sing N 505 N sing Y 506 N doub Y 507 N sing Y 508 N sing N 509 N sing Y 510 N doub Y 511 N sing Y 512 N sing N 513 N sing Y 514 N sing Y 515 N doub N 516 N sing Y 517 N doub N 518 N sing Y 519 N sing N 520 N sing N 521 N sing N 522 N sing N 523 N sing N 524 N sing N 525 N sing N 526 N sing N 527 N sing N 528 N sing N 529 N doub N 530 N sing N 531 N sing N 532 N sing N 533 N sing Y 534 N doub Y 535 N sing Y 536 N sing N 537 N sing Y 538 N doub N 539 N sing Y 540 N doub N 541 N sing Y 542 N sing N 543 N sing N 544 N sing N 545 N sing N 546 N sing N 547 N sing N 548 N sing N 549 N sing N 550 N sing N 551 N sing N 552 N sing N 553 N doub N 554 N sing N 555 N sing N 556 N sing N 557 N sing N 558 N sing N 559 N sing N 560 N sing N 561 N sing N 562 N sing N 563 N sing N 564 N sing CN Sci China Chem 1674-7291 57 307 313 10.1007/s11426-013-5029-z The complex structures of ALKBH2 mutants cross-linked to dsDNA reveal the conformational swing of β-hairpin 2014 10.2210/pdb4mgt/pdb pdb_00004mgt 100 1 CCD 2010-02-10 ADSC QUANTUM 315r Si (111) SINGLE WAVELENGTH M x-ray 1 0.9794 1.0 369194 0.101 1.06 2.600 50.000 13363 99.40 27.60 BL17U SSRF 0.9794 SYNCHROTRON SSRF BEAMLINE BL17U 23238.545 Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2 1.14.11.33 UNP residues 56-258 R110A 1 man polymer 4313.831 DNA1 1 syn polymer 3993.676 DNA2 1 syn polymer 24.305 MAGNESIUM ION 1 syn non-polymer Alkylated DNA repair protein alkB homolog 2, DNA oxidative demethylase ALKBH2, Oxy DC1 no no MSWRHIRAEGLDSSYTVLFGKAEADEIFQELEKEVEYFTGALARVQVFGKWHSVPAKQATYGDAGLTYTFSGLTLSPKPW IPVLERIRDHVSGVTGQTFNFVLINRYKDGSDHICEHRDDERELAPGSPIASVSFGASRDFVFRHKDSRGKSPSRRVAVV RLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFRKILLG MSWRHIRAEGLDSSYTVLFGKAEADEIFQELEKEVEYFTGALARVQVFGKWHSVPAKQATYGDAGLTYTFSGLTLSPKPW IPVLERIRDHVSGVTGQTFNFVLINRYKDGSDHICEHRDDERELAPGSPIASVSFGASRDFVFRHKDSRGKSPSRRVAVV RLPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFRKILLG A polypeptide(L) no no (DT)(DC)(DG)(DA)(DC)(DA)(DG)(DT)(DG)(DA)(DG)(DA)(DC)(DA) TCGACAGTGAGACA B polydeoxyribonucleotide no yes (DT)(DG)(DT)(DC)(DT)(DC)(DA)(2YR)(DT)(DG)(DT)(DC)(DG) TGTCTCAXTGTCG C polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n human sample ALKBH2, ABH2 9606 Homo sapiens 562 Escherichia coli 1 3.23 61.88 VAPOR DIFFUSION, HANGING DROP 6.5 12% PEG 5000, 100mM sodium chloride, 50mM Magnesium chloride, 100mM cacodylate, pH 6.5, vapor diffusion, hanging drop, temperature 277K 277 software chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model struct_conn struct_conn_type struct_ref_seq_dif struct_site repository Initial release Non-polymer description Refinement description Data collection Database references Derived calculations Refinement description 1 0 2014-02-26 1 1 2014-05-28 1 2 2017-11-15 1 3 2023-09-20 _software.classification _software.contact_author _software.contact_author_email _software.date _software.language _software.location _software.name _software.type _software.version _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.conn_type_id _struct_conn.id _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn_type.id _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id N RCSB Y RCSB 2013-08-28 REL REL 0.047 1.091 99.70 29.70 0.070 1.001 100.00 32.00 0.083 1.091 99.90 33.00 0.124 1.046 100.00 33.30 0.195 1.131 99.90 33.40 0.296 1.100 99.80 32.40 0.430 1.006 99.90 29.50 0.604 1.005 99.70 24.40 0.830 0.994 99.30 17.00 0.894 1.046 95.10 9.70 MG MAGNESIUM ION Synthesis sample Synthesis sample 3S5A PDB ENTRY 3S5A PDB experimental model MG 301 4 MG MG 301 A MET 55 n 1 MET 55 A SER 56 n 2 SER 56 A TRP 57 n 3 TRP 57 A ARG 58 n 4 ARG 58 A HIS 59 n 5 HIS 59 A ILE 60 n 6 ILE 60 A ARG 61 n 7 ARG 61 A ALA 62 n 8 ALA 62 A GLU 63 n 9 GLU 63 A GLY 64 n 10 GLY 64 A LEU 65 n 11 LEU 65 A ASP 66 n 12 ASP 66 A SER 67 n 13 SER 67 A SER 68 n 14 SER 68 A TYR 69 n 15 TYR 69 A THR 70 n 16 THR 70 A VAL 71 n 17 VAL 71 A LEU 72 n 18 LEU 72 A PHE 73 n 19 PHE 73 A GLY 74 n 20 GLY 74 A LYS 75 n 21 LYS 75 A ALA 76 n 22 ALA 76 A GLU 77 n 23 GLU 77 A ALA 78 n 24 ALA 78 A ASP 79 n 25 ASP 79 A GLU 80 n 26 GLU 80 A ILE 81 n 27 ILE 81 A PHE 82 n 28 PHE 82 A GLN 83 n 29 GLN 83 A GLU 84 n 30 GLU 84 A LEU 85 n 31 LEU 85 A GLU 86 n 32 GLU 86 A LYS 87 n 33 LYS 87 A GLU 88 n 34 GLU 88 A VAL 89 n 35 VAL 89 A GLU 90 n 36 GLU 90 A TYR 91 n 37 TYR 91 A PHE 92 n 38 PHE 92 A THR 93 n 39 THR 93 A GLY 94 n 40 GLY 94 A ALA 95 n 41 ALA 95 A LEU 96 n 42 LEU 96 A ALA 97 n 43 ALA 97 A ARG 98 n 44 ARG 98 A VAL 99 n 45 VAL 99 A GLN 100 n 46 GLN 100 A VAL 101 n 47 VAL 101 A PHE 102 n 48 PHE 102 A GLY 103 n 49 GLY 103 A LYS 104 n 50 LYS 104 A TRP 105 n 51 TRP 105 A HIS 106 n 52 HIS 106 A SER 107 n 53 SER 107 A VAL 108 n 54 VAL 108 A PRO 109 n 55 PRO 109 A ALA 110 n 56 ALA 110 A LYS 111 n 57 LYS 111 A GLN 112 n 58 GLN 112 A ALA 113 n 59 ALA 113 A THR 114 n 60 THR 114 A TYR 115 n 61 TYR 115 A GLY 116 n 62 GLY 116 A ASP 117 n 63 ASP 117 A ALA 118 n 64 ALA 118 A GLY 119 n 65 GLY 119 A LEU 120 n 66 LEU 120 A THR 121 n 67 THR 121 A TYR 122 n 68 TYR 122 A THR 123 n 69 THR 123 A PHE 124 n 70 PHE 124 A SER 125 n 71 SER 125 A GLY 126 n 72 GLY 126 A LEU 127 n 73 LEU 127 A THR 128 n 74 THR 128 A LEU 129 n 75 LEU 129 A SER 130 n 76 SER 130 A PRO 131 n 77 PRO 131 A LYS 132 n 78 LYS 132 A PRO 133 n 79 PRO 133 A TRP 134 n 80 TRP 134 A ILE 135 n 81 ILE 135 A PRO 136 n 82 PRO 136 A VAL 137 n 83 VAL 137 A LEU 138 n 84 LEU 138 A GLU 139 n 85 GLU 139 A ARG 140 n 86 ARG 140 A ILE 141 n 87 ILE 141 A ARG 142 n 88 ARG 142 A ASP 143 n 89 ASP 143 A HIS 144 n 90 HIS 144 A VAL 145 n 91 VAL 145 A SER 146 n 92 SER 146 A GLY 147 n 93 GLY 147 A VAL 148 n 94 VAL 148 A THR 149 n 95 THR 149 A GLY 150 n 96 GLY 150 A GLN 151 n 97 GLN 151 A THR 152 n 98 THR 152 A PHE 153 n 99 PHE 153 A ASN 154 n 100 ASN 154 A PHE 155 n 101 PHE 155 A VAL 156 n 102 VAL 156 A LEU 157 n 103 LEU 157 A ILE 158 n 104 ILE 158 A ASN 159 n 105 ASN 159 A ARG 160 n 106 ARG 160 A TYR 161 n 107 TYR 161 A LYS 162 n 108 LYS 162 A ASP 163 n 109 ASP 163 A GLY 164 n 110 GLY 164 A SER 165 n 111 SER 165 A ASP 166 n 112 ASP 166 A HIS 167 n 113 HIS 167 A ILE 168 n 114 ILE 168 A CYS 169 n 115 CYS 169 A GLU 170 n 116 GLU 170 A HIS 171 n 117 HIS 171 A ARG 172 n 118 ARG 172 A ASP 173 n 119 ASP 173 A ASP 174 n 120 ASP 174 A GLU 175 n 121 GLU 175 A ARG 176 n 122 ARG 176 A GLU 177 n 123 GLU 177 A LEU 178 n 124 LEU 178 A ALA 179 n 125 ALA 179 A n 126 180 A n 127 181 A SER 182 n 128 SER 182 A PRO 183 n 129 PRO 183 A ILE 184 n 130 ILE 184 A ALA 185 n 131 ALA 185 A SER 186 n 132 SER 186 A VAL 187 n 133 VAL 187 A SER 188 n 134 SER 188 A PHE 189 n 135 PHE 189 A GLY 190 n 136 GLY 190 A ALA 191 n 137 ALA 191 A SER 192 n 138 SER 192 A ARG 193 n 139 ARG 193 A ASP 194 n 140 ASP 194 A PHE 195 n 141 PHE 195 A VAL 196 n 142 VAL 196 A PHE 197 n 143 PHE 197 A ARG 198 n 144 ARG 198 A HIS 199 n 145 HIS 199 A LYS 200 n 146 LYS 200 A ASP 201 n 147 ASP 201 A SER 202 n 148 SER 202 A n 149 203 A n 150 204 A n 151 205 A n 152 206 A PRO 207 n 153 PRO 207 A SER 208 n 154 SER 208 A ARG 209 n 155 ARG 209 A ARG 210 n 156 ARG 210 A VAL 211 n 157 VAL 211 A ALA 212 n 158 ALA 212 A VAL 213 n 159 VAL 213 A VAL 214 n 160 VAL 214 A ARG 215 n 161 ARG 215 A LEU 216 n 162 LEU 216 A PRO 217 n 163 PRO 217 A LEU 218 n 164 LEU 218 A ALA 219 n 165 ALA 219 A HIS 220 n 166 HIS 220 A GLY 221 n 167 GLY 221 A SER 222 n 168 SER 222 A LEU 223 n 169 LEU 223 A LEU 224 n 170 LEU 224 A MET 225 n 171 MET 225 A MET 226 n 172 MET 226 A ASN 227 n 173 ASN 227 A HIS 228 n 174 HIS 228 A PRO 229 n 175 PRO 229 A THR 230 n 176 THR 230 A ASN 231 n 177 ASN 231 A THR 232 n 178 THR 232 A HIS 233 n 179 HIS 233 A TRP 234 n 180 TRP 234 A TYR 235 n 181 TYR 235 A HIS 236 n 182 HIS 236 A SER 237 n 183 SER 237 A LEU 238 n 184 LEU 238 A PRO 239 n 185 PRO 239 A VAL 240 n 186 VAL 240 A ARG 241 n 187 ARG 241 A LYS 242 n 188 LYS 242 A LYS 243 n 189 LYS 243 A VAL 244 n 190 VAL 244 A LEU 245 n 191 LEU 245 A ALA 246 n 192 ALA 246 A PRO 247 n 193 PRO 247 A ARG 248 n 194 ARG 248 A VAL 249 n 195 VAL 249 A ASN 250 n 196 ASN 250 A LEU 251 n 197 LEU 251 A THR 252 n 198 THR 252 A PHE 253 n 199 PHE 253 A ARG 254 n 200 ARG 254 A LYS 255 n 201 LYS 255 A ILE 256 n 202 ILE 256 A LEU 257 n 203 LEU 257 A LEU 258 n 204 LEU 258 A GLY 259 n 205 GLY 259 A DT 10 n 1 DT 10 B DC 11 n 2 DC 11 B DG 12 n 3 DG 12 B DA 13 n 4 DA 13 B DC 14 n 5 DC 14 B DA 15 n 6 DA 15 B DG 16 n 7 DG 16 B DT 17 n 8 DT 17 B DG 18 n 9 DG 18 B DA 19 n 10 DA 19 B DG 20 n 11 DG 20 B DA 21 n 12 DA 21 B DC 22 n 13 DC 22 B DA 23 n 14 DA 23 B DT 28 n 1 DT 28 C DG 29 n 2 DG 29 C DT 30 n 3 DT 30 C DC 31 n 4 DC 31 C DT 32 n 5 DT 32 C DC 33 n 6 DC 33 C DA 34 n 7 DA 34 C 2YR 35 n 8 2YR 35 C DT 36 n 9 DT 36 C DG 37 n 10 DG 37 C DT 38 n 11 DT 38 C DC 39 n 12 DC 39 C DG 40 n 13 DG 40 C 2.2961 0.3991 -0.4412 2.0276 0.0611 0.8263 0.0754 -0.0527 0.1947 0.0060 0.1311 -0.0687 -0.0854 0.0888 -0.2065 0.0893 -0.0461 0.0924 0.1134 -0.0157 0.1436 refined 38.5321 -35.7958 -3.9841 X-RAY DIFFRACTION 4.0321 -2.0794 2.9621 4.0644 -3.6353 10.5692 -0.0510 -0.2312 0.2087 0.2772 0.2095 -0.2432 -0.4956 -0.1955 -0.1585 0.1365 -0.1077 0.0864 0.1490 -0.1156 0.1155 refined 48.5332 -18.5380 6.0190 X-RAY DIFFRACTION 5.2287 -0.5377 0.8077 4.0922 -2.4960 6.3168 0.0461 0.0436 -0.0745 0.2201 0.0913 0.0400 -0.9046 0.3679 -0.1374 0.3126 -0.1964 0.1069 0.2411 -0.1934 0.1853 refined 50.5074 -18.0512 6.0938 X-RAY DIFFRACTION A 55 A 259 X-RAY DIFFRACTION 1 B 10 B 23 X-RAY DIFFRACTION 2 C 28 C 40 X-RAY DIFFRACTION 3 author_and_software_defined_assembly PISA 3 trimeric 3030 -25 14140 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 N ILE 60 A N ILE 6 A O SER 67 A O SER 13 A N THR 70 A N THR 16 A O LEU 223 A O LEU 169 A O LEU 224 A O LEU 170 A N SER 186 A N SER 132 A N PHE 189 A N PHE 135 A O VAL 249 A O VAL 195 A O ARG 248 A O ARG 194 A N TYR 161 A N TYR 107 A O ILE 158 A O ILE 104 A N ALA 113 A N ALA 59 A N GLY 116 A N GLY 62 A O LYS 132 A O LYS 78 A N VAL 101 A N VAL 47 A O LYS 104 A O LYS 50 A N PHE 124 A N PHE 70 A O LEU 127 A O LEU 73 A N HIS 171 A N HIS 117 A O HIS 236 A O HIS 182 A O TYR 235 A O TYR 181 A N ARG 198 A N ARG 144 A N ARG 193 A N ARG 139 A O LEU 218 A O LEU 164 1 A PRO 180 A PRO 126 1 Y 1 A GLY 181 A GLY 127 1 Y 1 A ARG 203 A ARG 149 1 Y 1 A GLY 204 A GLY 150 1 Y 1 A LYS 205 A LYS 151 1 Y 1 A SER 206 A SER 152 1 Y 1 A GLU 63 -58.53 102.07 1 A ASP 173 -45.06 157.40 1 A HIS 228 -35.14 137.32 1 A PRO 229 -105.67 44.09 118.400 70.637 20.000 0.4100 0.4100 -0.0000 0.4100 -0.0000 -1.3500 0.9340 0.9060 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY 0.2759 0.2306 0.2330 2.6000 30.0000 649 13849 13200 4.9000 99.3800 1.000 0.400 21.8690 0.2170 RANDOM 1 THROUGHOUT 0.000 MOLECULAR REPLACEMENT 0.4480 0.3060 0.8000 0.8000 1.2000 PDB ENTRY 3S5A MAXIMUM LIKELIHOOD MASK 2.6000 30.0000 0 2151 1 550 1600 0.010 0.017 2271 0.001 0.020 1886 1.398 1.710 3180 0.954 3.000 4345 6.590 5.000 200 31.566 21.923 78 18.169 15.000 274 14.535 15.000 16 0.082 0.200 324 0.007 0.020 2167 0.001 0.020 550 0.4870 0.3980 2.6670 44 858 902 20 95.0500 2.60 50.00 4MGT 13880 13760 1.5 1.8 1 99.2 2.60 2.69 1 95.1 2.69 2.80 1 99.3 2.80 2.93 1 99.7 2.93 3.08 1 99.9 3.08 3.28 1 99.8 3.28 3.53 1 99.9 data reduction Zbyszek Otwinowski hkl@hkl-xray.com http://www.hkl-xray.com/ DENZO package data scaling Zbyszek Otwinowski hkl@hkl-xray.com http://www.hkl-xray.com/ SCALEPACK package phasing Alexei Vaguine alexei@ysbl.york.ac.uk Fortran_77 http://www.ccp4.ac.uk/dist/html/molrep.html MOLREP program refinement Garib N. Murshudov garib@ysbl.york.ac.uk Fortran_77 http://www.ccp4.ac.uk/dist/html/refmac5.html REFMAC program 5.7.0029 data extraction PDB deposit@deposit.rcsb.org April 22, 2011 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.11 ALKBH2 R110A cross-linked to undamaged dsDNA 1 N N 2 N N 3 N N 4 N N A GLY 74 A GLY 20 HELX_P A VAL 89 A VAL 35 1 1 16 A ILE 81 A ILE 27 HELX_P A GLY 150 A GLY 96 1 2 70 A ASP 174 A ASP 120 HELX_P A LEU 178 A LEU 124 5 3 5 A PRO 229 A PRO 175 HELX_P A HIS 233 A HIS 179 1 4 5 covale 2.101 one A CYS 169 A SG CYS 115 1_555 C 2YR 35 C S 2YR 8 1_555 covale 1.603 both C DA 34 C O3' DA 7 1_555 C 2YR 35 C P 2YR 8 1_555 covale 1.596 both C 2YR 35 C O3' 2YR 8 1_555 C DT 36 C P DT 9 1_555 metalc 2.360 A ASP 173 A OD1 ASP 119 1_555 A MG 301 D MG MG 1_555 hydrog WATSON-CRICK B DC 11 B N3 DC 2 1_555 C DG 40 C N1 DG 13 1_555 hydrog WATSON-CRICK B DC 11 B N4 DC 2 1_555 C DG 40 C O6 DG 13 1_555 hydrog WATSON-CRICK B DC 11 B O2 DC 2 1_555 C DG 40 C N2 DG 13 1_555 hydrog WATSON-CRICK B DG 12 B N1 DG 3 1_555 C DC 39 C N3 DC 12 1_555 hydrog WATSON-CRICK B DG 12 B N2 DG 3 1_555 C DC 39 C O2 DC 12 1_555 hydrog WATSON-CRICK B DG 12 B O6 DG 3 1_555 C DC 39 C N4 DC 12 1_555 hydrog WATSON-CRICK B DA 13 B N1 DA 4 1_555 C DT 38 C N3 DT 11 1_555 hydrog WATSON-CRICK B DA 13 B N6 DA 4 1_555 C DT 38 C O4 DT 11 1_555 hydrog WATSON-CRICK B DC 14 B N3 DC 5 1_555 C DG 37 C N1 DG 10 1_555 hydrog WATSON-CRICK B DC 14 B N4 DC 5 1_555 C DG 37 C O6 DG 10 1_555 hydrog WATSON-CRICK B DC 14 B O2 DC 5 1_555 C DG 37 C N2 DG 10 1_555 hydrog WATSON-CRICK B DA 15 B N1 DA 6 1_555 C DT 36 C N3 DT 9 1_555 hydrog WATSON-CRICK B DA 15 B N6 DA 6 1_555 C DT 36 C O4 DT 9 1_555 hydrog WATSON-CRICK B DT 17 B N3 DT 8 1_555 C DA 34 C N1 DA 7 1_555 hydrog WATSON-CRICK B DT 17 B O4 DT 8 1_555 C DA 34 C N6 DA 7 1_555 hydrog WATSON-CRICK B DG 18 B N1 DG 9 1_555 C DC 33 C N3 DC 6 1_555 hydrog WATSON-CRICK B DG 18 B N2 DG 9 1_555 C DC 33 C O2 DC 6 1_555 hydrog WATSON-CRICK B DG 18 B O6 DG 9 1_555 C DC 33 C N4 DC 6 1_555 hydrog WATSON-CRICK B DA 19 B N1 DA 10 1_555 C DT 32 C N3 DT 5 1_555 hydrog WATSON-CRICK B DA 19 B N6 DA 10 1_555 C DT 32 C O4 DT 5 1_555 hydrog WATSON-CRICK B DG 20 B N1 DG 11 1_555 C DC 31 C N3 DC 4 1_555 hydrog WATSON-CRICK B DG 20 B N2 DG 11 1_555 C DC 31 C O2 DC 4 1_555 hydrog WATSON-CRICK B DG 20 B O6 DG 11 1_555 C DC 31 C N4 DC 4 1_555 hydrog WATSON-CRICK B DA 21 B N1 DA 12 1_555 C DT 30 C N3 DT 3 1_555 hydrog WATSON-CRICK B DA 21 B N6 DA 12 1_555 C DT 30 C O4 DT 3 1_555 hydrog WATSON-CRICK B DC 22 B N3 DC 13 1_555 C DG 29 C N1 DG 2 1_555 hydrog WATSON-CRICK B DC 22 B N4 DC 13 1_555 C DG 29 C O6 DG 2 1_555 hydrog WATSON-CRICK B DC 22 B O2 DC 13 1_555 C DG 29 C N2 DG 2 1_555 hydrog WATSON-CRICK B DA 23 B N1 DA 14 1_555 C DT 28 C N3 DT 1 1_555 hydrog WATSON-CRICK B DA 23 B N6 DA 14 1_555 C DT 28 C O4 DT 1 1_555 OXIDOREDUCTASE/DNA protein-DNA complex, OXIDOREDUCTASE-DNA complex A HIS 228 A HIS 174 1 A PRO 229 A PRO 175 -3.22 ALKB2_HUMAN UNP 1 56 Q6NS38 SWRHIRAEGLDCSYTVLFGKAEADEIFQELEKEVEYFTGALARVQVFGKWHSVPRKQATYGDAGLTYTFSGLTLSPKPWI PVLERIRDHVSGVTGQTFNFVLINRYKDGCDHIGEHRDDERELAPGSPIASVSFGACRDFVFRHKDSRGKSPSRRVAVVR LPLAHGSLLMMNHPTNTHWYHSLPVRKKVLAPRVNLTFRKILL 4MGT PDB 2 4MGT 4MGT PDB 3 4MGT 56 258 4MGT 56 258 Q6NS38 A 1 2 204 10 23 4MGT 10 23 4MGT B 2 1 14 28 40 4MGT 28 40 4MGT C 3 1 13 1 initiating methionine MET 55 4MGT A Q6NS38 UNP 1 1 CYS conflict SER 67 4MGT A Q6NS38 UNP 67 13 1 ARG engineered mutation ALA 110 4MGT A Q6NS38 UNP 110 56 1 CYS conflict SER 165 4MGT A Q6NS38 UNP 165 111 1 GLY conflict CYS 169 4MGT A Q6NS38 UNP 169 115 1 CYS conflict SER 192 4MGT A Q6NS38 UNP 192 138 1 expression tag GLY 259 4MGT A Q6NS38 UNP 205 8 2 2 4 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A ARG 58 A ARG 4 A ALA 62 A ALA 8 A LEU 65 A LEU 11 A VAL 71 A VAL 17 A SER 222 A SER 168 A ASN 227 A ASN 173 A ILE 184 A ILE 130 A GLY 190 A GLY 136 A ARG 248 A ARG 194 A ARG 254 A ARG 200 A PHE 155 A PHE 101 A TYR 161 A TYR 107 A GLN 112 A GLN 58 A GLY 116 A GLY 62 A LYS 132 A LYS 78 A PRO 133 A PRO 79 A ARG 98 A ARG 44 A VAL 101 A VAL 47 A LYS 104 A LYS 50 A SER 107 A SER 53 A TYR 122 A TYR 68 A PHE 124 A PHE 70 A LEU 127 A LEU 73 A LEU 129 A LEU 75 A ILE 168 A ILE 114 A HIS 171 A HIS 117 A TRP 234 A TRP 180 A LEU 238 A LEU 184 A ARG 193 A ARG 139 A HIS 199 A HIS 145 A VAL 213 A VAL 159 A LEU 218 A LEU 164 BINDING SITE FOR RESIDUE MG A 301 A MG 301 Software 3 A HIS 171 A HIS 117 3 1_555 A ASP 173 A ASP 119 3 1_555 A HIS 236 A HIS 182 3 1_555 182 P 63 2 2