0.024349 0.000000 0.000000 0.000000 0.017908 0.000000 0.000000 0.000000 0.010347 0.00000 0.00000 0.00000 Morera, S. Vigouroux, A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 90.00 90.00 41.070 55.840 96.650 C5 H11 O6 P 198.111 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE ABASIC DIDEOXYRIBOSE DNA linking 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 C2 H6 O2 62.068 1,2-ETHANEDIOL ETHYLENE GLYCOL non-polymer 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 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 O N 2 N P N 3 N O N 4 N O N 5 N O N 6 N C N 7 N C N 8 R C N 9 N O N 10 N C N 11 S C N 12 N O N 13 N H N 14 N H N 15 N H N 16 N H N 17 N H N 18 N H N 19 N H N 20 N H N 21 N H N 22 N H N 23 N H N 24 N N N 25 S C N 26 N C N 27 N O N 28 N C N 29 N O 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 N N 38 S C N 39 N C N 40 N O N 41 N C N 42 N C N 43 N C N 44 N N N 45 N C N 46 N N N 47 N N N 48 N O 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 H N 56 N H N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N N N 65 S C N 66 N C N 67 N O N 68 N C N 69 N C N 70 N O N 71 N N N 72 N O 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 N N 82 S C N 83 N C N 84 N O N 85 N C N 86 N C N 87 N O N 88 N O N 89 N O N 90 N H 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 N N 98 R C N 99 N C N 100 N O N 101 N C N 102 N S N 103 N O N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N O N 112 N P N 113 N O N 114 N O N 115 N O N 116 N C N 117 R C N 118 N O N 119 S C N 120 N O N 121 N C N 122 R C Y 123 N N Y 124 N C Y 125 N N Y 126 N C Y 127 N C N 128 N N Y 129 N N Y 130 N C Y 131 N N Y 132 N C N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N H N 145 N H N 146 N H N 147 N O N 148 N P N 149 N O N 150 N O N 151 N O N 152 N C N 153 R C N 154 N O N 155 S C N 156 N O N 157 N C N 158 R C N 159 N N N 160 N C N 161 N O N 162 N N N 163 N C N 164 N N N 165 N C N 166 N C N 167 N H N 168 N H N 169 N H N 170 N H N 171 N H N 172 N H N 173 N H N 174 N H N 175 N H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N O N 182 N P N 183 N O N 184 N O N 185 N O N 186 N C N 187 R C N 188 N O N 189 S C N 190 N O N 191 N C N 192 R C Y 193 N N Y 194 N C Y 195 N N Y 196 N C N 197 N C N 198 N O N 199 N N N 200 N C N 201 N N N 202 N N Y 203 N C N 204 N H N 205 N H N 206 N H N 207 N H N 208 N H N 209 N H N 210 N H N 211 N H N 212 N H N 213 N H N 214 N H N 215 N H N 216 N H N 217 N H N 218 N O N 219 N P N 220 N O N 221 N O N 222 N O N 223 N C N 224 R C N 225 N O N 226 S C N 227 N O N 228 N C N 229 R C N 230 N N N 231 N C N 232 N O N 233 N N N 234 N C N 235 N O N 236 N C N 237 N C N 238 N C N 239 N H N 240 N H N 241 N H N 242 N H N 243 N H N 244 N H N 245 N H N 246 N H N 247 N H N 248 N H N 249 N H N 250 N H N 251 N H N 252 N H N 253 N H N 254 N C N 255 N O N 256 N C N 257 N O 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 N N 265 S C N 266 N C N 267 N O N 268 N C N 269 N C N 270 N C N 271 N O N 272 N N N 273 N O N 274 N H N 275 N H N 276 N H N 277 N H N 278 N H N 279 N H N 280 N H N 281 N H N 282 N H N 283 N H N 284 N N N 285 S C N 286 N C N 287 N O N 288 N C N 289 N C N 290 N C N 291 N O N 292 N O N 293 N O N 294 N H N 295 N H N 296 N H N 297 N H N 298 N H N 299 N H N 300 N H N 301 N H N 302 N H N 303 N N N 304 N C N 305 N C N 306 N O N 307 N O N 308 N H N 309 N H N 310 N H N 311 N H N 312 N H N 313 N N N 314 S C N 315 N C N 316 N O N 317 N C Y 318 N C Y 319 N N Y 320 N C Y 321 N C Y 322 N N N 323 N O N 324 N H N 325 N H N 326 N H N 327 N H N 328 N H N 329 N H N 330 N H N 331 N H N 332 N H N 333 N H N 334 N O N 335 N H N 336 N H N 337 N N N 338 S C N 339 N C N 340 N O N 341 S C N 342 N C N 343 N C N 344 N C N 345 N O N 346 N H N 347 N H N 348 N H N 349 N H N 350 N H 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 N N 360 S C N 361 N C N 362 N O N 363 N C N 364 N C N 365 N C N 366 N C N 367 N O N 368 N H N 369 N H N 370 N H N 371 N H N 372 N H 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 N N 382 S C N 383 N C N 384 N O N 385 N C N 386 N C N 387 N C N 388 N C N 389 N N N 390 N O N 391 N H N 392 N H N 393 N H N 394 N H N 395 N H 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 N N 407 S C N 408 N C N 409 N O N 410 N C N 411 N C N 412 N S N 413 N C N 414 N O N 415 N H N 416 N H N 417 N H N 418 N H N 419 N H 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 N N 427 S C N 428 N C N 429 N O N 430 N C Y 431 N C Y 432 N C Y 433 N C Y 434 N C Y 435 N C Y 436 N C N 437 N O N 438 N H N 439 N H N 440 N H N 441 N H N 442 N H N 443 N H N 444 N H N 445 N H N 446 N H N 447 N H N 448 N H N 449 N N N 450 S C N 451 N C N 452 N O N 453 N C N 454 N C N 455 N C N 456 N O N 457 N H N 458 N H N 459 N H N 460 N H N 461 N H N 462 N H N 463 N H N 464 N H N 465 N H N 466 N N N 467 S C N 468 N C N 469 N O N 470 N C N 471 N O N 472 N O N 473 N H N 474 N H N 475 N H N 476 N H N 477 N H N 478 N H N 479 N H N 480 N N N 481 S C N 482 N C N 483 N O N 484 R C N 485 N O N 486 N C N 487 N O N 488 N H N 489 N H N 490 N H N 491 N H N 492 N H N 493 N H N 494 N H N 495 N H N 496 N H N 497 N N N 498 S C N 499 N C N 500 N O N 501 N C Y 502 N C Y 503 N C Y 504 N C Y 505 N N Y 506 N C Y 507 N C Y 508 N C Y 509 N C Y 510 N C N 511 N O N 512 N H N 513 N H N 514 N H N 515 N H N 516 N H N 517 N H 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 N N 525 S C N 526 N C N 527 N O N 528 N C Y 529 N C Y 530 N C Y 531 N C Y 532 N C Y 533 N C Y 534 N C N 535 N O N 536 N O N 537 N H N 538 N H N 539 N H N 540 N H N 541 N H N 542 N H N 543 N H N 544 N H N 545 N H N 546 N H N 547 N H N 548 N N N 549 S C N 550 N C N 551 N O N 552 N C N 553 N C N 554 N C N 555 N O N 556 N H N 557 N H N 558 N H N 559 N H N 560 N H N 561 N H N 562 N H N 563 N H N 564 N H N 565 N H N 566 N H N 1 N sing N 2 N sing N 3 N doub N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing 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 sing 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 doub 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 doub 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 sing 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 doub N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing 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 doub N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N doub N 74 N sing N 75 N sing 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 doub N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N doub N 90 N sing N 91 N sing N 92 N sing 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 doub N 100 N sing N 101 N sing N 102 N sing N 103 N sing 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 sing 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 sing N 128 N sing Y 129 N sing Y 130 N sing Y 131 N doub N 132 N sing Y 133 N sing Y 134 N sing Y 135 N doub N 136 N sing Y 137 N doub N 138 N sing N 139 N sing Y 140 N sing Y 141 N doub N 142 N sing Y 143 N sing N 144 N sing N 145 N sing N 146 N doub N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N doub N 170 N sing N 171 N doub N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N doub N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N doub 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 sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N sing Y 202 N sing Y 203 N sing Y 204 N doub N 205 N sing Y 206 N sing N 207 N sing Y 208 N doub N 209 N doub N 210 N sing N 211 N sing N 212 N sing N 213 N sing N 214 N doub N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N sing N 220 N doub N 221 N sing N 222 N sing N 223 N sing N 224 N sing N 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N sing N 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N sing N 238 N sing N 239 N sing N 240 N sing N 241 N sing N 242 N sing N 243 N doub N 244 N sing N 245 N sing N 246 N sing N 247 N doub N 248 N sing N 249 N sing N 250 N doub 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 sing N 263 N sing N 264 N sing N 265 N sing N 266 N sing N 267 N sing N 268 N sing N 269 N sing N 270 N doub 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 doub N 279 N sing N 280 N sing 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 sing N 289 N doub 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 doub N 298 N sing N 299 N sing 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 doub N 317 N sing N 318 N sing N 319 N sing N 320 N sing Y 321 N sing Y 322 N doub Y 323 N doub N 324 N sing Y 325 N sing N 326 N sing Y 327 N sing N 328 N sing N 329 N sing N 330 N sing N 331 N sing N 332 N sing N 333 N sing N 334 N sing N 335 N sing N 336 N sing N 337 N sing N 338 N sing N 339 N doub 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 sing 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 doub 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 sing 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 doub 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 sing 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 doub 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 sing 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 doub N 425 N sing N 426 N sing N 427 N sing N 428 N sing Y 429 N doub Y 430 N sing Y 431 N sing N 432 N sing Y 433 N doub N 434 N sing Y 435 N doub N 436 N sing Y 437 N sing N 438 N sing N 439 N sing N 440 N sing N 441 N sing N 442 N sing N 443 N sing N 444 N sing N 445 N sing N 446 N sing N 447 N doub 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 sing 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 doub 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 sing N 473 N sing N 474 N sing N 475 N sing N 476 N sing N 477 N doub 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 sing 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 doub N 494 N sing N 495 N sing N 496 N sing N 497 N sing Y 498 N doub Y 499 N sing Y 500 N sing N 501 N sing Y 502 N doub Y 503 N sing Y 504 N sing N 505 N sing Y 506 N sing Y 507 N doub N 508 N sing Y 509 N doub N 510 N sing Y 511 N sing N 512 N sing N 513 N sing N 514 N sing N 515 N sing N 516 N sing N 517 N sing N 518 N sing N 519 N sing N 520 N sing N 521 N doub N 522 N sing N 523 N sing N 524 N sing N 525 N sing Y 526 N doub Y 527 N sing Y 528 N sing N 529 N sing Y 530 N doub N 531 N sing Y 532 N doub N 533 N sing Y 534 N sing N 535 N sing N 536 N sing N 537 N sing N 538 N sing N 539 N sing N 540 N sing N 541 N sing N 542 N sing N 543 N sing N 544 N sing N 545 N doub 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 sing N 554 N sing N 555 N sing N 556 N sing UK Nucleic Acids Res. NARHAD 0389 0305-1048 40 9917 9926 10.1093/nar/gks714 22848106 Biochemical and structural characterization of the glycosylase domain of MBD4 bound to thymine and 5-hydroxymethyuracil-containing DNA. 2012 10.2210/pdb4e9f/pdb pdb_00004e9f 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 PIXEL 2011-08-29 PSI PILATUS 6M Si 111 CHANNEL SINGLE WAVELENGTH M x-ray 1 0.9 1.0 ID29 ESRF 0.9 SYNCHROTRON ESRF BEAMLINE ID29 19416.393 Methyl-CpG-binding domain protein 4 3.2.2.- glycosylase domain of MBD4 (residues 426-580) 1 man polymer DNA fragment with 3DR site 3524.284 DNA (5'-D(*CP*CP*AP*GP*CP*GP*(3DR)P*GP*CP*AP*GP*C)-3') 1 syn polymer DNA fragment 3695.390 DNA (5'-D(*GP*CP*TP*GP*CP*GP*CP*GP*CP*TP*GP*G)-3') 1 syn polymer 62.068 1,2-ETHANEDIOL 1 syn non-polymer 18.015 water 86 nat water Methyl-CpG-binding endonuclease 1, Methyl-CpG-binding protein MBD4, Mismatch-specific DNA N-glycosylase no no MLSPPRRKAFKKWTPPRSPFNLVQETLFHDPWKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELLKP LGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSYRIFCVNEWKQVHPEDHKLNKYHDWLWENHEKLSLSHHHHH H MLSPPRRKAFKKWTPPRSPFNLVQETLFHDPWKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELLKP LGLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSYRIFCVNEWKQVHPEDHKLNKYHDWLWENHEKLSLSHHHHH H A polypeptide(L) no yes (DC)(DC)(DA)(DG)(DC)(DG)(3DR)(DG)(DC)(DA)(DG)(DC) CCAGCGNGCAGC C polydeoxyribonucleotide no no (DG)(DC)(DT)(DG)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DG) GCTGCGCGCTGG D 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 human sample MBD4, MED1 9606 Homo sapiens 562 Escherichia coli 1 2.08 40.88 VAPOR DIFFUSION, HANGING DROP 8 25% ethylene glycol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K 298 -32.907 1 C 1 D 12 -14.628 C_DC1:DG12_D 1 -9.443 -0.388 0.529 0.519 -10.099 1 C 2 D 11 11.581 C_DC2:DG11_D 2 -0.971 1.907 0.162 -0.254 9.398 1 20 C 3 D 10 -0.959 C_DA3:DT10_D 3 -10.200 0.510 0.199 -0.354 4.109 1 19 C 4 D 9 -2.211 C_DG4:DC9_D 4 -9.659 -0.825 0.188 -0.511 -4.700 1 19 C 5 D 8 1.491 C_DC5:DG8_D 5 -5.342 0.219 0.010 -0.273 8.392 1 19 C 6 D 7 3.491 C_DG6:DC7_D 6 -10.224 -0.577 0.331 -0.226 -16.731 1 19 C 8 D 5 -1.775 C_DG8:DC5_D 7 -7.115 -0.231 -0.508 -0.164 3.438 1 19 C 9 D 4 -1.493 C_DC9:DG4_D 8 -4.113 0.318 -0.001 -0.196 8.086 1 20 C 10 D 3 2.008 C_DA10:DT3_D 9 -11.753 -0.029 0.004 -0.222 7.552 1 19 C 11 D 2 -1.805 C_DG11:DC2_D 10 -14.333 -0.149 0.157 -0.273 10.260 1 19 C 12 D 1 -1.484 C_DC12:DG1_D 11 -9.444 0.073 -0.343 -0.266 2.869 44.440 C C 1 2 5.870 D D 12 11 2.899 4.427 0.257 -0.302 CC_DC1DC2:DG11DG12_DD 1 4.331 -5.743 44.028 -0.761 0.014 3.115 30.088 C C 2 3 9.901 D D 11 10 2.992 5.114 -0.749 1.251 CC_DC2DA3:DT10DG11_DD 2 1.602 -3.102 29.618 1.425 1.751 3.382 30.063 C C 3 4 2.425 D D 10 9 3.357 1.256 -0.579 -0.162 CC_DA3DG4:DC9DT10_DD 3 -2.329 4.496 29.949 -0.577 0.623 3.644 38.838 C C 4 5 -2.621 D D 9 8 3.580 -1.741 0.697 -0.521 CC_DG4DC5:DG8DC9_DD 4 3.272 -4.927 38.668 -0.548 -0.608 3.289 33.483 C C 5 6 5.994 D D 8 7 3.170 3.443 -0.589 0.959 CC_DC5DG6:DC7DG8_DD 5 -3.054 5.318 33.174 1.102 0.523 2.843 25.760 C C 8 9 2.806 D D 5 4 2.839 1.238 -0.365 0.047 CC_DG8DC9:DG4DC5_DD 6 -6.251 14.164 24.972 -0.202 -0.727 3.304 36.900 C C 9 10 9.178 D D 4 3 3.233 5.778 0.440 0.540 CC_DC9DA10:DT3DG4_DD 7 3.494 -5.550 36.298 0.065 -0.219 3.408 33.082 C C 10 11 8.620 D D 3 2 3.406 4.890 -0.164 0.230 CC_DA10DG11:DC2DT3_DD 8 -1.556 2.743 32.692 -0.462 0.013 3.321 34.871 C C 11 12 -8.066 D D 2 1 3.280 -4.792 0.751 0.081 CC_DG11DC12:DG1DC2_DD 9 6.528 -10.987 33.946 0.880 -0.239 chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model struct_conn struct_ref_seq_dif struct_site repository Initial release Database references Structure summary Data collection Database references Derived calculations Refinement description 1 0 2012-08-08 1 1 2012-11-07 1 2 2016-12-28 1 3 2023-09-13 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2012-03-21 REL REL EDO 1,2-ETHANEDIOL HOH water Synthetic DNA sample Synthetic DNA sample 4ENE PDB ENTRY 4ENE PDB experimental model EGL 1003 4 EDO EDO 101 C HOH 1 5 HOH HOH 601 A HOH 2 5 HOH HOH 602 A HOH 3 5 HOH HOH 603 A HOH 4 5 HOH HOH 604 A HOH 5 5 HOH HOH 605 A HOH 6 5 HOH HOH 606 A HOH 7 5 HOH HOH 607 A HOH 8 5 HOH HOH 608 A HOH 10 5 HOH HOH 609 A HOH 11 5 HOH HOH 610 A HOH 12 5 HOH HOH 611 A HOH 13 5 HOH HOH 612 A HOH 15 5 HOH HOH 613 A HOH 16 5 HOH HOH 614 A HOH 17 5 HOH HOH 615 A HOH 18 5 HOH HOH 616 A HOH 19 5 HOH HOH 617 A HOH 20 5 HOH HOH 618 A HOH 21 5 HOH HOH 619 A HOH 22 5 HOH HOH 620 A HOH 23 5 HOH HOH 621 A HOH 24 5 HOH HOH 622 A HOH 25 5 HOH HOH 623 A HOH 26 5 HOH HOH 624 A HOH 27 5 HOH HOH 625 A HOH 28 5 HOH HOH 626 A HOH 29 5 HOH HOH 627 A HOH 30 5 HOH HOH 628 A HOH 31 5 HOH HOH 629 A HOH 32 5 HOH HOH 630 A HOH 35 5 HOH HOH 631 A HOH 36 5 HOH HOH 632 A HOH 37 5 HOH HOH 633 A HOH 39 5 HOH HOH 634 A HOH 40 5 HOH HOH 635 A HOH 41 5 HOH HOH 636 A HOH 42 5 HOH HOH 637 A HOH 43 5 HOH HOH 638 A HOH 44 5 HOH HOH 639 A HOH 45 5 HOH HOH 640 A HOH 46 5 HOH HOH 641 A HOH 53 5 HOH HOH 642 A HOH 54 5 HOH HOH 643 A HOH 56 5 HOH HOH 644 A HOH 57 5 HOH HOH 645 A HOH 58 5 HOH HOH 646 A HOH 59 5 HOH HOH 647 A HOH 62 5 HOH HOH 648 A HOH 64 5 HOH HOH 649 A HOH 65 5 HOH HOH 650 A HOH 66 5 HOH HOH 651 A HOH 71 5 HOH HOH 652 A HOH 80 5 HOH HOH 653 A HOH 81 5 HOH HOH 654 A HOH 82 5 HOH HOH 655 A HOH 85 5 HOH HOH 656 A HOH 87 5 HOH HOH 657 A HOH 89 5 HOH HOH 658 A HOH 90 5 HOH HOH 659 A HOH 93 5 HOH HOH 660 A HOH 97 5 HOH HOH 661 A HOH 98 5 HOH HOH 662 A HOH 103 5 HOH HOH 663 A HOH 105 5 HOH HOH 664 A HOH 9 5 HOH HOH 201 C HOH 38 5 HOH HOH 202 C HOH 47 5 HOH HOH 203 C HOH 48 5 HOH HOH 204 C HOH 67 5 HOH HOH 205 C HOH 88 5 HOH HOH 206 C HOH 91 5 HOH HOH 207 C HOH 92 5 HOH HOH 208 C HOH 107 5 HOH HOH 209 C HOH 14 5 HOH HOH 101 D HOH 68 5 HOH HOH 102 D HOH 69 5 HOH HOH 103 D HOH 72 5 HOH HOH 104 D HOH 77 5 HOH HOH 105 D HOH 78 5 HOH HOH 106 D HOH 79 5 HOH HOH 107 D HOH 86 5 HOH HOH 108 D HOH 95 5 HOH HOH 109 D HOH 99 5 HOH HOH 110 D HOH 104 5 HOH HOH 111 D HOH 106 5 HOH HOH 112 D HOH 108 5 HOH HOH 113 D n 1 426 A n 2 427 A n 3 428 A n 4 429 A n 5 430 A n 6 431 A n 7 432 A n 8 433 A n 9 434 A n 10 435 A n 11 436 A LYS 437 n 12 LYS 437 A TRP 438 n 13 TRP 438 A THR 439 n 14 THR 439 A PRO 440 n 15 PRO 440 A PRO 441 n 16 PRO 441 A ARG 442 n 17 ARG 442 A SER 443 n 18 SER 443 A PRO 444 n 19 PRO 444 A PHE 445 n 20 PHE 445 A ASN 446 n 21 ASN 446 A LEU 447 n 22 LEU 447 A VAL 448 n 23 VAL 448 A GLN 449 n 24 GLN 449 A GLU 450 n 25 GLU 450 A THR 451 n 26 THR 451 A LEU 452 n 27 LEU 452 A PHE 453 n 28 PHE 453 A HIS 454 n 29 HIS 454 A ASP 455 n 30 ASP 455 A PRO 456 n 31 PRO 456 A TRP 457 n 32 TRP 457 A LYS 458 n 33 LYS 458 A LEU 459 n 34 LEU 459 A LEU 460 n 35 LEU 460 A ILE 461 n 36 ILE 461 A ALA 462 n 37 ALA 462 A THR 463 n 38 THR 463 A ILE 464 n 39 ILE 464 A PHE 465 n 40 PHE 465 A LEU 466 n 41 LEU 466 A ASN 467 n 42 ASN 467 A ARG 468 n 43 ARG 468 A THR 469 n 44 THR 469 A SER 470 n 45 SER 470 A GLY 471 n 46 GLY 471 A LYS 472 n 47 LYS 472 A MET 473 n 48 MET 473 A ALA 474 n 49 ALA 474 A ILE 475 n 50 ILE 475 A PRO 476 n 51 PRO 476 A VAL 477 n 52 VAL 477 A LEU 478 n 53 LEU 478 A TRP 479 n 54 TRP 479 A LYS 480 n 55 LYS 480 A PHE 481 n 56 PHE 481 A LEU 482 n 57 LEU 482 A GLU 483 n 58 GLU 483 A LYS 484 n 59 LYS 484 A TYR 485 n 60 TYR 485 A PRO 486 n 61 PRO 486 A SER 487 n 62 SER 487 A ALA 488 n 63 ALA 488 A GLU 489 n 64 GLU 489 A VAL 490 n 65 VAL 490 A ALA 491 n 66 ALA 491 A ARG 492 n 67 ARG 492 A THR 493 n 68 THR 493 A ALA 494 n 69 ALA 494 A ASP 495 n 70 ASP 495 A TRP 496 n 71 TRP 496 A ARG 497 n 72 ARG 497 A ASP 498 n 73 ASP 498 A VAL 499 n 74 VAL 499 A SER 500 n 75 SER 500 A GLU 501 n 76 GLU 501 A LEU 502 n 77 LEU 502 A LEU 503 n 78 LEU 503 A LYS 504 n 79 LYS 504 A PRO 505 n 80 PRO 505 A LEU 506 n 81 LEU 506 A GLY 507 n 82 GLY 507 A LEU 508 n 83 LEU 508 A TYR 509 n 84 TYR 509 A ASP 510 n 85 ASP 510 A LEU 511 n 86 LEU 511 A ARG 512 n 87 ARG 512 A ALA 513 n 88 ALA 513 A LYS 514 n 89 LYS 514 A THR 515 n 90 THR 515 A ILE 516 n 91 ILE 516 A VAL 517 n 92 VAL 517 A LYS 518 n 93 LYS 518 A PHE 519 n 94 PHE 519 A SER 520 n 95 SER 520 A ASP 521 n 96 ASP 521 A GLU 522 n 97 GLU 522 A TYR 523 n 98 TYR 523 A LEU 524 n 99 LEU 524 A THR 525 n 100 THR 525 A LYS 526 n 101 LYS 526 A GLN 527 n 102 GLN 527 A TRP 528 n 103 TRP 528 A LYS 529 n 104 LYS 529 A TYR 530 n 105 TYR 530 A PRO 531 n 106 PRO 531 A ILE 532 n 107 ILE 532 A GLU 533 n 108 GLU 533 A LEU 534 n 109 LEU 534 A HIS 535 n 110 HIS 535 A GLY 536 n 111 GLY 536 A ILE 537 n 112 ILE 537 A GLY 538 n 113 GLY 538 A LYS 539 n 114 LYS 539 A TYR 540 n 115 TYR 540 A GLY 541 n 116 GLY 541 A ASN 542 n 117 ASN 542 A ASP 543 n 118 ASP 543 A SER 544 n 119 SER 544 A TYR 545 n 120 TYR 545 A ARG 546 n 121 ARG 546 A ILE 547 n 122 ILE 547 A PHE 548 n 123 PHE 548 A CYS 549 n 124 CYS 549 A VAL 550 n 125 VAL 550 A ASN 551 n 126 ASN 551 A GLU 552 n 127 GLU 552 A TRP 553 n 128 TRP 553 A LYS 554 n 129 LYS 554 A GLN 555 n 130 GLN 555 A VAL 556 n 131 VAL 556 A HIS 557 n 132 HIS 557 A PRO 558 n 133 PRO 558 A GLU 559 n 134 GLU 559 A ASP 560 n 135 ASP 560 A HIS 561 n 136 HIS 561 A LYS 562 n 137 LYS 562 A LEU 563 n 138 LEU 563 A ASN 564 n 139 ASN 564 A LYS 565 n 140 LYS 565 A TYR 566 n 141 TYR 566 A HIS 567 n 142 HIS 567 A ASP 568 n 143 ASP 568 A TRP 569 n 144 TRP 569 A LEU 570 n 145 LEU 570 A TRP 571 n 146 TRP 571 A GLU 572 n 147 GLU 572 A ASN 573 n 148 ASN 573 A HIS 574 n 149 HIS 574 A n 150 575 A n 151 576 A n 152 577 A n 153 578 A n 154 579 A n 155 580 A n 156 581 A n 157 582 A n 158 583 A n 159 584 A n 160 585 A n 161 586 A C 1 n 1 DC 1 C C 2 n 2 DC 2 C A 3 n 3 DA 3 C G 4 n 4 DG 4 C C 5 n 5 DC 5 C G 6 n 6 DG 6 C 3DR 7 n 7 3DR 7 C G 8 n 8 DG 8 C C 9 n 9 DC 9 C A 10 n 10 DA 10 C G 11 n 11 DG 11 C C 12 n 12 DC 12 C G 1 n 1 DG 1 D C 2 n 2 DC 2 D T 3 n 3 DT 3 D G 4 n 4 DG 4 D C 5 n 5 DC 5 D G 6 n 6 DG 6 D C 7 n 7 DC 7 D G 8 n 8 DG 8 D C 9 n 9 DC 9 D T 10 n 10 DT 10 D G 11 n 11 DG 11 D G 12 n 12 DG 12 D author_and_software_defined_assembly PISA 3 trimeric 3820 -11 10240 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 1 A MET 426 A MET 1 1 Y 1 A LEU 427 A LEU 2 1 Y 1 A SER 428 A SER 3 1 Y 1 A PRO 429 A PRO 4 1 Y 1 A PRO 430 A PRO 5 1 Y 1 A ARG 431 A ARG 6 1 Y 1 A ARG 432 A ARG 7 1 Y 1 A LYS 433 A LYS 8 1 Y 1 A ALA 434 A ALA 9 1 Y 1 A PHE 435 A PHE 10 1 Y 1 A LYS 436 A LYS 11 1 Y 1 A GLU 575 A GLU 150 1 Y 1 A LYS 576 A LYS 151 1 Y 1 A LEU 577 A LEU 152 1 Y 1 A SER 578 A SER 153 1 Y 1 A LEU 579 A LEU 154 1 Y 1 A SER 580 A SER 155 1 Y 1 A HIS 581 A HIS 156 1 Y 1 A HIS 582 A HIS 157 1 Y 1 A HIS 583 A HIS 158 1 Y 1 A HIS 584 A HIS 159 1 Y 1 A HIS 585 A HIS 160 1 Y 1 A HIS 586 A HIS 161 1 Y 1 4.64 0.30 108.30 112.94 C C C O4' C1' N1 DC DC DC 1 1 1 N 1 4.88 0.60 118.90 123.78 C C C N1 C2 O2 DC DC DC 1 1 1 N 1 -4.38 0.70 121.90 117.52 C C C N3 C2 O2 DC DC DC 1 1 1 N 1 7.52 1.10 118.80 126.32 C C C C2 N1 C1' DC DC DC 1 1 1 N 1 7.75 1.20 119.70 127.45 C C C C3' O3' P DG DG DC 4 4 5 Y 1 2.67 0.30 108.30 110.97 C C C O4' C1' N1 DC DC DC 5 5 5 N 1 7.20 1.20 119.70 126.90 C C C C3' O3' P DG DG 3DR 6 6 7 Y 1 2.53 0.30 108.30 110.83 C C C O4' C1' N9 DG DG DG 11 11 11 N 1 9.35 1.20 119.70 129.05 C C C C3' O3' P DG DG DC 11 11 12 Y 1 2.02 0.30 108.30 110.32 C C C O4' C1' N1 DC DC DC 12 12 12 N 1 11.55 1.20 119.70 131.25 D D D C3' O3' P DG DG DC 1 1 2 Y 1 9.86 1.20 119.70 129.56 D D D C3' O3' P DC DC DT 2 2 3 Y 1 3.55 0.30 108.30 111.85 D D D O4' C1' N1 DC DC DC 5 5 5 N 1 2.42 0.30 108.30 110.72 D D D O4' C1' N1 DT DT DT 10 10 10 N 1 8.06 1.20 119.70 127.76 D D D C3' O3' P DG DG DG 11 11 12 Y 1 2.99 0.30 108.30 111.29 D D D O4' C1' N9 DG DG DG 12 12 12 N 0.9431 0.9289 0.2485 0.2141 0.2158 1.79 37.80 1101 21600 21487 5.12 99.27 0.132 RANDOM 1 THROUGHOUT 0.0 MOLECULAR REPLACEMENT PDB ENTRY 4ENE Engh & Huber 0.238 1.79 37.80 86 1747 4 478 1179 0.010 1760 HARMONIC 2.00 1.07 2479 HARMONIC 2.00 678 SINUSOIDAL 2.00 26 HARMONIC 2.00 193 HARMONIC 5.00 1760 HARMONIC 20.00 3.21 18.29 216 SEMIHARMONIC 5.00 1915 SEMIHARMONIC 4.00 0.1973 0.2340 0.2319 1.88 140 2564 2704 11 5.18 99.27 1.79 38 4E9F 21600 21525 2 2 0.063 1 13.3 99.6 1.79 1.9 1 98.5 data collection DNA phasing PHASER refinement BUSTER 2.10.0 data reduction XDS data scaling XDS Structure of the glycosylase domain of MBD4 bound to AP site containing DNA 1 N N 2 N N 3 N N 4 N N 5 N N 5 N N 5 N N A VAL 448 A VAL 23 HELX_P A PHE 453 A PHE 28 1 1 6 A ASP 455 A ASP 30 HELX_P A LEU 466 A LEU 41 1 2 12 A SER 470 A SER 45 HELX_P A TYR 485 A TYR 60 1 3 16 A SER 487 A SER 62 HELX_P A ARG 492 A ARG 67 1 4 6 A ASP 495 A ASP 70 HELX_P A LYS 504 A LYS 79 1 5 10 A PRO 505 A PRO 80 HELX_P A GLY 507 A GLY 82 5 6 3 A LEU 508 A LEU 83 HELX_P A LYS 526 A LYS 101 1 7 19 A TYR 530 A TYR 105 HELX_P A LEU 534 A LEU 109 5 8 5 A GLY 538 A GLY 113 HELX_P A CYS 549 A CYS 124 1 9 12 A GLU 552 A GLU 127 HELX_P A VAL 556 A VAL 131 5 10 5 A ASP 560 A ASP 135 HELX_P A ASN 573 A ASN 148 1 11 14 covale 1.656 both C DG 6 B O3' DG 6 1_555 C 3DR 7 B P 3DR 7 1_555 covale 1.605 both C 3DR 7 B O3' 3DR 7 1_555 C DG 8 B P DG 8 1_555 hydrog DC-DG PAIR C DC 1 B N4 DC 1 1_555 D DG 12 C O6 DG 12 1_555 hydrog DC-DG PAIR C DC 2 B O2 DC 2 1_555 D DG 11 C N1 DG 11 1_555 hydrog WATSON-CRICK C DA 3 B N1 DA 3 1_555 D DT 10 C N3 DT 10 1_555 hydrog WATSON-CRICK C DA 3 B N6 DA 3 1_555 D DT 10 C O4 DT 10 1_555 hydrog WATSON-CRICK C DG 4 B N1 DG 4 1_555 D DC 9 C N3 DC 9 1_555 hydrog WATSON-CRICK C DG 4 B N2 DG 4 1_555 D DC 9 C O2 DC 9 1_555 hydrog WATSON-CRICK C DG 4 B O6 DG 4 1_555 D DC 9 C N4 DC 9 1_555 hydrog WATSON-CRICK C DC 5 B N3 DC 5 1_555 D DG 8 C N1 DG 8 1_555 hydrog WATSON-CRICK C DC 5 B N4 DC 5 1_555 D DG 8 C O6 DG 8 1_555 hydrog WATSON-CRICK C DC 5 B O2 DC 5 1_555 D DG 8 C N2 DG 8 1_555 hydrog WATSON-CRICK C DG 6 B N1 DG 6 1_555 D DC 7 C N3 DC 7 1_555 hydrog WATSON-CRICK C DG 6 B N2 DG 6 1_555 D DC 7 C O2 DC 7 1_555 hydrog WATSON-CRICK C DG 6 B O6 DG 6 1_555 D DC 7 C N4 DC 7 1_555 hydrog WATSON-CRICK C DG 8 B N1 DG 8 1_555 D DC 5 C N3 DC 5 1_555 hydrog WATSON-CRICK C DG 8 B N2 DG 8 1_555 D DC 5 C O2 DC 5 1_555 hydrog WATSON-CRICK C DG 8 B O6 DG 8 1_555 D DC 5 C N4 DC 5 1_555 hydrog WATSON-CRICK C DC 9 B N3 DC 9 1_555 D DG 4 C N1 DG 4 1_555 hydrog WATSON-CRICK C DC 9 B N4 DC 9 1_555 D DG 4 C O6 DG 4 1_555 hydrog WATSON-CRICK C DC 9 B O2 DC 9 1_555 D DG 4 C N2 DG 4 1_555 hydrog WATSON-CRICK C DA 10 B N1 DA 10 1_555 D DT 3 C N3 DT 3 1_555 hydrog WATSON-CRICK C DA 10 B N6 DA 10 1_555 D DT 3 C O4 DT 3 1_555 hydrog WATSON-CRICK C DG 11 B N1 DG 11 1_555 D DC 2 C N3 DC 2 1_555 hydrog WATSON-CRICK C DG 11 B N2 DG 11 1_555 D DC 2 C O2 DC 2 1_555 hydrog WATSON-CRICK C DG 11 B O6 DG 11 1_555 D DC 2 C N4 DC 2 1_555 hydrog WATSON-CRICK C DC 12 B N3 DC 12 1_555 D DG 1 C N1 DG 1 1_555 hydrog WATSON-CRICK C DC 12 B N4 DC 12 1_555 D DG 1 C O6 DG 1 1_555 hydrog WATSON-CRICK C DC 12 B O2 DC 12 1_555 D DG 1 C N2 DG 1 1_555 HYDROLASE/DNA HhH DNA glycosylase family, HYDROLASE-DNA complex A LYS 437 A LYS 12 1 A TRP 438 A TRP 13 -6.56 MBD4_HUMAN UNP 1 427 O95243 LSPPRRKAFKKWTPPRSPFNLVQETLFHDPWKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELLKPL GLYDLRAKTIVKFSDEYLTKQWKYPIELHGIGKYGNDSYRIFCVNEWKQVHPEDHKLNKYHDWLWENHEKLSLS 4E9F PDB 2 1 4E9F CCAGCGNGCAGC 4E9F PDB 3 1 4E9F GCTGCGCGCTGG 427 580 4E9F 427 580 O95243 A 1 2 155 1 12 4E9F 1 12 4E9F C 2 1 12 1 12 4E9F 1 12 4E9F D 3 1 12 1 expression tag MET 426 4E9F A O95243 UNP 1 1 expression tag HIS 581 4E9F A O95243 UNP 156 1 expression tag HIS 582 4E9F A O95243 UNP 157 1 expression tag HIS 583 4E9F A O95243 UNP 158 1 expression tag HIS 584 4E9F A O95243 UNP 159 1 expression tag HIS 585 4E9F A O95243 UNP 160 1 expression tag HIS 586 4E9F A O95243 UNP 161 BINDING SITE FOR RESIDUE EDO C 101 C EDO 101 Software 4 A ARG 468 A ARG 43 4 1_555 C DC 5 B DC 5 4 1_555 C DG 6 B DG 6 4 1_555 D DG 6 C DG 6 4 1_555 19 P 21 21 21