0.011275 0.000000 0.000000 0.000000 0.010229 0.000000 0.000000 0.000000 0.017945 0.00000 0.00000 0.00000 Otani, J. Arita, K. Kato, T. Kinoshita, M. Ariyoshi, M. Shirakawa, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 88.693 97.758 55.725 C10 H16 N3 O7 P 321.224 n 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H16 N3 O8 P 337.223 n 2'-deoxy-5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate) DNA linking C2 H3 O2 -1 59.044 ACETATE ION 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 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 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 N N 2 N C N 3 N N N 4 N C N 5 N C N 6 N C N 7 N C N 8 N O N 9 N N N 10 R C N 11 N C N 12 S C N 13 R C N 14 N O N 15 N O N 16 N C N 17 N O N 18 N P N 19 N O N 20 N O N 21 N O N 22 N H 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 P N 39 N O N 40 N O N 41 N O N 42 N C N 43 R C N 44 N O N 45 S C N 46 N O N 47 N C N 48 R C N 49 N N N 50 N C N 51 N O N 52 N N N 53 N C N 54 N N N 55 N C N 56 N C N 57 N O N 58 N C N 59 N O N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H 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 C N 77 N O N 78 N O N 79 N C N 80 N H N 81 N H N 82 N H N 83 N N N 84 S C N 85 N C N 86 N O N 87 N C N 88 N O N 89 N H 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 N N 97 S C N 98 N C N 99 N O N 100 N C N 101 N C N 102 N C N 103 N N N 104 N C N 105 N N N 106 N N 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 H N 116 N H N 117 N H N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N N N 124 S C N 125 N C N 126 N O N 127 N C N 128 N C N 129 N O N 130 N N N 131 N O N 132 N H 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 N N 141 S C N 142 N C N 143 N O N 144 N C N 145 N C N 146 N O N 147 N O N 148 N O N 149 N H N 150 N H N 151 N H N 152 N H N 153 N H N 154 N H N 155 N H N 156 N N N 157 R C N 158 N C N 159 N O N 160 N C N 161 N S N 162 N O N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N H N 169 N H N 170 N O N 171 N P N 172 N O N 173 N O N 174 N O N 175 N C N 176 R C N 177 N O N 178 S C N 179 N O N 180 N C N 181 R C Y 182 N N Y 183 N C Y 184 N N Y 185 N C Y 186 N C N 187 N N Y 188 N N Y 189 N C Y 190 N N Y 191 N C 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 H N 200 N H N 201 N H N 202 N H N 203 N H N 204 N H N 205 N H N 206 N O N 207 N P N 208 N O N 209 N O N 210 N O N 211 N C N 212 R C N 213 N O N 214 S C N 215 N O N 216 N C N 217 R C N 218 N N N 219 N C N 220 N O N 221 N N N 222 N C N 223 N N N 224 N C N 225 N C 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 H N 237 N H N 238 N H N 239 N H N 240 N O N 241 N P N 242 N O N 243 N O N 244 N O N 245 N C N 246 R C N 247 N O N 248 S C N 249 N O N 250 N C N 251 R C Y 252 N N Y 253 N C Y 254 N N Y 255 N C N 256 N C N 257 N O N 258 N N N 259 N C N 260 N N N 261 N N Y 262 N C 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 H N 273 N H N 274 N H N 275 N H N 276 N H N 277 N O N 278 N P N 279 N O N 280 N O N 281 N O N 282 N C N 283 R C N 284 N O N 285 S C N 286 N O N 287 N C N 288 R C N 289 N N N 290 N C N 291 N O N 292 N N N 293 N C N 294 N O N 295 N C N 296 N C N 297 N C N 298 N H N 299 N H N 300 N H N 301 N H 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 H N 312 N H N 313 N C N 314 N O N 315 N C N 316 N O N 317 N H N 318 N H N 319 N H N 320 N H N 321 N H N 322 N H N 323 N N N 324 S C N 325 N C N 326 N O N 327 N C N 328 N C N 329 N C N 330 N O N 331 N N N 332 N O 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 H N 343 N N N 344 S C N 345 N C N 346 N O N 347 N C N 348 N C N 349 N C N 350 N O N 351 N O N 352 N O 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 N N 363 N C N 364 N C N 365 N O N 366 N O N 367 N H N 368 N H N 369 N H N 370 N H N 371 N H N 372 N N N 373 S C N 374 N C N 375 N O N 376 N C Y 377 N C Y 378 N N Y 379 N C Y 380 N C Y 381 N N N 382 N O N 383 N H N 384 N H N 385 N H N 386 N H N 387 N H N 388 N H N 389 N H N 390 N H N 391 N H N 392 N H N 393 N O N 394 N H N 395 N H N 396 N N N 397 S C N 398 N C N 399 N O N 400 S C N 401 N C N 402 N C N 403 N C N 404 N O 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 H N 412 N H N 413 N H N 414 N H N 415 N H N 416 N H N 417 N H N 418 N N N 419 S C N 420 N C N 421 N O N 422 N C N 423 N C N 424 N C N 425 N C N 426 N O N 427 N H N 428 N H N 429 N H N 430 N H N 431 N H N 432 N H N 433 N H N 434 N H N 435 N H N 436 N H N 437 N H N 438 N H N 439 N H N 440 N N N 441 S C N 442 N C N 443 N O N 444 N C N 445 N C N 446 N C N 447 N C N 448 N N N 449 N O N 450 N H N 451 N H N 452 N H N 453 N H N 454 N H N 455 N H N 456 N H 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 N N 466 S C N 467 N C N 468 N O N 469 N C Y 470 N C Y 471 N C Y 472 N C Y 473 N C Y 474 N C Y 475 N C N 476 N O N 477 N H N 478 N H 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 H N 487 N H N 488 N N N 489 S C N 490 N C N 491 N O N 492 N C N 493 N C N 494 N C N 495 N O 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 H N 504 N H N 505 N N N 506 S C N 507 N C N 508 N O N 509 N C N 510 N O 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 N N 520 S C N 521 N C N 522 N O N 523 R C N 524 N O N 525 N C N 526 N O N 527 N H N 528 N H N 529 N H N 530 N H N 531 N H N 532 N H N 533 N H N 534 N H N 535 N H N 536 N N N 537 S C N 538 N C N 539 N O N 540 N C Y 541 N C Y 542 N C Y 543 N C Y 544 N N Y 545 N C Y 546 N C Y 547 N C Y 548 N C Y 549 N C N 550 N O N 551 N H N 552 N H N 553 N H N 554 N H N 555 N H 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 N N 564 S C N 565 N C N 566 N O N 567 N C Y 568 N C Y 569 N C Y 570 N C Y 571 N C Y 572 N C Y 573 N C N 574 N O N 575 N O N 576 N H N 577 N H N 578 N H N 579 N H N 580 N H N 581 N H N 582 N H N 583 N H N 584 N H N 585 N H N 586 N H N 587 N N N 588 S C N 589 N C N 590 N O N 591 N C N 592 N C N 593 N C N 594 N O N 595 N H N 596 N H N 597 N H N 598 N H N 599 N H N 600 N H N 601 N H N 602 N H N 603 N H N 604 N H N 605 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 doub N 7 N sing N 8 N sing N 9 N sing N 10 N doub 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 sing N 31 N sing N 32 N sing N 33 N sing N 34 N doub 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 doub 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 doub N 51 N sing N 52 N sing N 53 N doub N 54 N sing N 55 N doub N 56 N sing 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 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 sing N 76 N sing N 77 N sing N 78 N doub 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 sing N 88 N sing N 89 N sing N 90 N doub 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 sing N 100 N sing N 101 N sing N 102 N doub N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing 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 doub 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 doub N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N doub 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 doub N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N doub 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 doub 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 doub 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 sing Y 189 N sing Y 190 N sing Y 191 N doub N 192 N sing Y 193 N sing Y 194 N sing Y 195 N doub N 196 N sing Y 197 N doub N 198 N sing N 199 N sing Y 200 N sing Y 201 N doub N 202 N sing Y 203 N sing N 204 N sing N 205 N sing N 206 N doub 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 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 doub N 230 N sing N 231 N doub N 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N doub N 237 N sing N 238 N sing N 239 N sing N 240 N sing N 241 N doub 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 Y 262 N sing Y 263 N sing Y 264 N doub N 265 N sing Y 266 N sing N 267 N sing Y 268 N doub N 269 N doub N 270 N sing N 271 N sing N 272 N sing N 273 N sing N 274 N doub 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 sing 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 sing N 300 N sing N 301 N sing N 302 N sing N 303 N doub 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 doub 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 sing 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 sing N 327 N sing N 328 N sing N 329 N sing N 330 N doub 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 doub 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 sing N 348 N sing N 349 N doub 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 doub 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 doub 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 doub N 377 N sing N 378 N sing N 379 N sing N 380 N sing Y 381 N sing Y 382 N doub Y 383 N doub N 384 N sing Y 385 N sing N 386 N sing Y 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 doub 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 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 doub 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 sing N 433 N sing N 434 N sing N 435 N sing N 436 N sing N 437 N sing N 438 N sing N 439 N sing N 440 N sing N 441 N doub N 442 N sing N 443 N sing N 444 N sing N 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 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 sing N 465 N doub N 466 N sing N 467 N sing N 468 N sing N 469 N sing Y 470 N doub Y 471 N sing Y 472 N sing N 473 N sing Y 474 N doub N 475 N sing Y 476 N doub N 477 N sing Y 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 doub 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 sing N 502 N sing N 503 N sing N 504 N sing N 505 N doub N 506 N sing N 507 N sing N 508 N sing N 509 N sing N 510 N sing N 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 doub N 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 sing N 530 N sing N 531 N sing N 532 N sing N 533 N sing N 534 N doub N 535 N sing N 536 N sing N 537 N sing N 538 N sing Y 539 N doub Y 540 N sing Y 541 N sing N 542 N sing Y 543 N doub Y 544 N sing Y 545 N sing N 546 N sing Y 547 N sing Y 548 N doub N 549 N sing Y 550 N doub N 551 N sing Y 552 N sing N 553 N sing 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 doub N 563 N sing N 564 N sing N 565 N sing N 566 N sing Y 567 N doub Y 568 N sing Y 569 N sing N 570 N sing Y 571 N doub N 572 N sing Y 573 N doub N 574 N sing Y 575 N sing N 576 N sing N 577 N sing N 578 N sing N 579 N sing N 580 N sing N 581 N sing N 582 N sing N 583 N sing N 584 N sing N 585 N sing N 586 N doub N 587 N sing N 588 N sing N 589 N sing N 590 N sing N 591 N sing N 592 N sing N 593 N sing N 594 N sing N 595 N sing N 596 N sing N 597 N sing US J.Biol.Chem. JBCHA3 0071 0021-9258 288 6351 6362 10.1074/jbc.M112.431098 23316048 Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4 2013 10.2210/pdb3vyb/pdb pdb_00003vyb 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 95 1 CCD 2010-10-08 ADSC QUANTUM 315r SINGLE WAVELENGTH M x-ray 1 1.0 1.0 BL-17A Photon Factory 1.0 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 7829.089 Methyl-CpG-binding domain protein 4 3.2.2.- methyl CpG binding domain, UNP residues 69-136 1 man polymer 4263.809 DNA (5'-D(*GP*TP*CP*AP*CP*TP*AP*CP*(5CM)P*GP*GP*AP*CP*A)-3') 1 syn polymer 4341.827 DNA (5'-D(*GP*TP*CP*(5HC)P*GP*GP*TP*AP*GP*TP*GP*AP*CP*T)-3') 1 syn polymer 59.044 ACETATE ION 1 syn non-polymer 62.068 1,2-ETHANEDIOL 1 syn non-polymer 18.015 water 71 nat water Methyl-CpG-binding protein MBD4, Mismatch-specific DNA N-glycosylase no no SGHKPVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFNFTVLPKG SGHKPVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFNFTVLPKG A polypeptide(L) no yes (DG)(DT)(DC)(DA)(DC)(DT)(DA)(DC)(5CM)(DG)(DG)(DA)(DC)(DA) GTCACTACCGGACA B polydeoxyribonucleotide no yes (DG)(DT)(DC)(5HC)(DG)(DG)(DT)(DA)(DG)(DT)(DG)(DA)(DC)(DT) GTCXGGTAGTGACT 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 mouse sample Mbd4 10090 Mus musculus 562 Escherichia coli BL21(DE3) plasmid 1 3.67 66.53 VAPOR DIFFUSION, HANGING DROP 4 8% PEG 1500, 0.1M sodium acetate, 0.1M sodium cacodylate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 293K 293 -26.739 1 19 B 1 C 13 0.231 B_DG1:DC13_C 1 -17.226 -0.319 -0.144 0.038 -10.893 1 20 B 2 C 12 -4.546 B_DT2:DA12_C 2 -10.534 -0.503 -0.011 0.073 -2.889 1 19 B 3 C 11 1.502 B_DC3:DG11_C 3 -3.934 -0.013 -0.177 -0.037 0.282 1 20 B 4 C 10 5.729 B_DA4:DT10_C 4 -12.127 0.589 -0.064 0.115 5.967 1 19 B 5 C 9 5.404 B_DC5:DG9_C 5 -17.236 0.564 0.052 -0.092 -0.578 1 20 B 6 C 8 0.891 B_DT6:DA8_C 6 -13.758 -0.282 -0.043 -0.037 -5.904 1 20 B 7 C 7 1.699 B_DA7:DT7_C 7 -13.062 0.266 -0.043 0.014 -5.070 1 19 B 8 C 6 0.695 B_DC8:DG6_C 8 -5.702 0.441 0.318 0.060 7.480 1 19 B 9 C 5 -1.535 B_5CM9:DG5_C 9 -6.857 0.380 -0.169 -0.059 28.458 1 19 B 11 C 3 0.983 B_DG11:DC3_C 10 4.535 -0.221 0.286 -0.034 20.432 1 20 B 12 C 2 -0.320 B_DA12:DT2_C 11 -17.314 -0.041 0.442 -0.119 14.465 1 19 B 13 C 1 4.603 B_DC13:DG1_C 12 -14.451 0.273 -0.071 -0.005 2.833 30.733 B B 1 2 4.160 C C 13 12 2.883 2.203 -1.046 -0.787 BB_DG1DT2:DA12DC13_CC 1 -0.374 0.706 30.654 -1.862 1.910 3.121 40.721 B B 2 3 5.655 C C 12 11 3.078 3.926 0.784 0.070 BB_DT2DC3:DG11DA12_CC 2 3.127 -4.505 40.423 -0.312 -0.798 3.221 32.536 B B 3 4 19.197 C C 11 10 3.263 10.570 0.010 0.397 BB_DC3DA4:DT10DG11_CC 3 0.525 -0.953 30.811 -1.174 0.075 3.111 29.442 B B 4 5 3.887 C C 10 9 3.171 1.974 0.519 -0.574 BB_DA4DC5:DG9DT10_CC 4 -0.794 1.564 29.367 -1.535 -1.185 3.203 31.087 B B 5 6 13.680 C C 9 8 3.435 7.246 -0.191 -0.382 BB_DC5DT6:DA8DG9_CC 5 4.160 -7.855 29.970 -2.149 1.180 3.452 37.340 B B 6 7 9.125 C C 8 7 3.480 5.817 0.290 0.008 BB_DT6DA7:DT7DA8_CC 6 2.196 -3.445 36.837 -0.808 -0.143 3.275 34.283 B B 7 8 8.087 C C 7 6 3.346 4.750 -0.266 -0.370 BB_DA7DC8:DG6DT7_CC 7 -2.082 3.545 33.900 -1.387 0.118 3.139 30.152 B B 8 9 0.267 C C 6 5 3.074 0.138 0.661 0.166 BB_DC85CM9:DG5DG6_CC 8 4.744 -9.155 29.785 0.292 -0.347 6.471 66.436 B B 9 11 -3.336 C C 5 3 6.650 -3.637 0.487 -0.080 BB_5CM9DG11:DC3DG5_CC 9 -12.511 11.477 65.290 0.220 -1.455 3.521 36.182 B B 11 12 6.670 C C 3 2 3.451 4.098 -1.268 -0.970 BB_DG11DA12:DT2DC3_CC 10 -8.451 13.755 34.981 -2.187 0.751 3.344 33.986 B B 12 13 5.261 C C 2 1 3.455 3.070 0.434 -1.287 BB_DA12DC13:DG1DT2_CC 11 1.479 -2.535 33.819 -2.713 -0.497 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 Data collection Database references Derived calculations Refinement description 1 0 2013-01-16 1 1 2013-08-14 1 2 2023-11-08 _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 PDBJ Y PDBJ 2012-09-22 REL REL ACT ACETATE ION EDO 1,2-ETHANEDIOL HOH water 3VXV PDB ENTRY 3VXV PDB experimental model ACT 1 4 ACT ACT 201 A EDO 10 5 EDO EDO 202 A HOH 2 6 HOH HOH 301 A HOH 5 6 HOH HOH 302 A HOH 8 6 HOH HOH 303 A HOH 11 6 HOH HOH 304 A HOH 14 6 HOH HOH 305 A HOH 16 6 HOH HOH 306 A HOH 19 6 HOH HOH 307 A HOH 21 6 HOH HOH 308 A HOH 22 6 HOH HOH 309 A HOH 25 6 HOH HOH 310 A HOH 26 6 HOH HOH 311 A HOH 30 6 HOH HOH 312 A HOH 31 6 HOH HOH 313 A HOH 32 6 HOH HOH 314 A HOH 36 6 HOH HOH 315 A HOH 40 6 HOH HOH 316 A HOH 42 6 HOH HOH 317 A HOH 43 6 HOH HOH 318 A HOH 45 6 HOH HOH 319 A HOH 46 6 HOH HOH 320 A HOH 47 6 HOH HOH 321 A HOH 48 6 HOH HOH 322 A HOH 51 6 HOH HOH 323 A HOH 52 6 HOH HOH 324 A HOH 55 6 HOH HOH 325 A HOH 58 6 HOH HOH 326 A HOH 66 6 HOH HOH 327 A HOH 67 6 HOH HOH 328 A HOH 68 6 HOH HOH 329 A HOH 69 6 HOH HOH 330 A HOH 71 6 HOH HOH 331 A HOH 13 6 HOH HOH 332 A HOH 9 6 HOH HOH 101 B HOH 10 6 HOH HOH 102 B HOH 12 6 HOH HOH 103 B HOH 17 6 HOH HOH 104 B HOH 23 6 HOH HOH 105 B HOH 24 6 HOH HOH 106 B HOH 27 6 HOH HOH 107 B HOH 28 6 HOH HOH 108 B HOH 29 6 HOH HOH 109 B HOH 35 6 HOH HOH 110 B HOH 41 6 HOH HOH 111 B HOH 50 6 HOH HOH 112 B HOH 56 6 HOH HOH 113 B HOH 59 6 HOH HOH 114 B HOH 60 6 HOH HOH 115 B HOH 61 6 HOH HOH 116 B HOH 62 6 HOH HOH 117 B HOH 63 6 HOH HOH 118 B HOH 64 6 HOH HOH 119 B HOH 39 6 HOH HOH 101 C HOH 1 6 HOH HOH 102 C HOH 3 6 HOH HOH 103 C HOH 4 6 HOH HOH 104 C HOH 6 6 HOH HOH 105 C HOH 7 6 HOH HOH 106 C HOH 15 6 HOH HOH 107 C HOH 18 6 HOH HOH 108 C HOH 20 6 HOH HOH 109 C HOH 33 6 HOH HOH 110 C HOH 34 6 HOH HOH 111 C HOH 37 6 HOH HOH 112 C HOH 38 6 HOH HOH 113 C HOH 44 6 HOH HOH 114 C HOH 49 6 HOH HOH 115 C HOH 53 6 HOH HOH 116 C HOH 54 6 HOH HOH 117 C HOH 57 6 HOH HOH 118 C HOH 65 6 HOH HOH 119 C HOH 70 6 HOH HOH 120 C n 1 68 A n 2 69 A n 3 70 A n 4 71 A PRO 72 n 5 PRO 72 A VAL 73 n 6 VAL 73 A PRO 74 n 7 PRO 74 A CYS 75 n 8 CYS 75 A GLY 76 n 9 GLY 76 A TRP 77 n 10 TRP 77 A GLU 78 n 11 GLU 78 A ARG 79 n 12 ARG 79 A VAL 80 n 13 VAL 80 A VAL 81 n 14 VAL 81 A LYS 82 n 15 LYS 82 A GLN 83 n 16 GLN 83 A ARG 84 n 17 ARG 84 A LEU 85 n 18 LEU 85 A SER 86 n 19 SER 86 A GLY 87 n 20 GLY 87 A LYS 88 n 21 LYS 88 A THR 89 n 22 THR 89 A ALA 90 n 23 ALA 90 A GLY 91 n 24 GLY 91 A LYS 92 n 25 LYS 92 A PHE 93 n 26 PHE 93 A ASP 94 n 27 ASP 94 A VAL 95 n 28 VAL 95 A TYR 96 n 29 TYR 96 A PHE 97 n 30 PHE 97 A ILE 98 n 31 ILE 98 A SER 99 n 32 SER 99 A PRO 100 n 33 PRO 100 A GLN 101 n 34 GLN 101 A GLY 102 n 35 GLY 102 A LEU 103 n 36 LEU 103 A LYS 104 n 37 LYS 104 A PHE 105 n 38 PHE 105 A ARG 106 n 39 ARG 106 A SER 107 n 40 SER 107 A LYS 108 n 41 LYS 108 A ARG 109 n 42 ARG 109 A SER 110 n 43 SER 110 A LEU 111 n 44 LEU 111 A ALA 112 n 45 ALA 112 A ASN 113 n 46 ASN 113 A TYR 114 n 47 TYR 114 A LEU 115 n 48 LEU 115 A LEU 116 n 49 LEU 116 A LYS 117 n 50 LYS 117 A ASN 118 n 51 ASN 118 A GLY 119 n 52 GLY 119 A GLU 120 n 53 GLU 120 A THR 121 n 54 THR 121 A PHE 122 n 55 PHE 122 A LEU 123 n 56 LEU 123 A LYS 124 n 57 LYS 124 A PRO 125 n 58 PRO 125 A GLU 126 n 59 GLU 126 A ASP 127 n 60 ASP 127 A PHE 128 n 61 PHE 128 A ASN 129 n 62 ASN 129 A PHE 130 n 63 PHE 130 A THR 131 n 64 THR 131 A VAL 132 n 65 VAL 132 A LEU 133 n 66 LEU 133 A PRO 134 n 67 PRO 134 A n 68 135 A n 69 136 A DG 1 n 1 DG 1 B DT 2 n 2 DT 2 B DC 3 n 3 DC 3 B DA 4 n 4 DA 4 B DC 5 n 5 DC 5 B DT 6 n 6 DT 6 B DA 7 n 7 DA 7 B DC 8 n 8 DC 8 B 5CM 9 n 9 5CM 9 B DG 10 n 10 DG 10 B DG 11 n 11 DG 11 B DA 12 n 12 DA 12 B DC 13 n 13 DC 13 B DA 14 n 14 DA 14 B DG 1 n 1 DG 1 C DT 2 n 2 DT 2 C DC 3 n 3 DC 3 C 5HM 4 n 4 5HC 4 C DG 5 n 5 DG 5 C DG 6 n 6 DG 6 C DT 7 n 7 DT 7 C DA 8 n 8 DA 8 C DG 9 n 9 DG 9 C DT 10 n 10 DT 10 C DG 11 n 11 DG 11 C DA 12 n 12 DA 12 C DC 13 n 13 DC 13 C DT 14 n 14 DT 14 C 0.5204 -0.0042 0.5374 0.7592 0.1364 0.8684 -0.0335 0.0180 0.1899 -0.1543 0.1438 0.0997 0.0208 0.0187 -0.1022 0.1781 -0.0150 0.0346 0.2414 0.0650 0.2715 refined 3.7555 12.0077 4.2199 X-RAY DIFFRACTION 2.3511 1.1076 0.2227 0.6930 0.0412 0.6149 -0.0025 -0.4850 -0.5973 -0.2576 -0.0716 -0.4990 -0.1390 -0.1881 0.0227 0.3464 -0.1182 0.0550 0.3574 0.1039 0.5079 refined 18.9074 12.4405 -14.1120 X-RAY DIFFRACTION 1.9438 -0.9158 0.2530 0.4368 -0.2555 0.0450 -0.3740 -0.2072 0.4443 -0.2628 0.2009 -0.3107 0.0173 0.1768 0.1312 0.2686 -0.0809 0.0508 0.5933 -0.0093 0.3734 refined 22.4674 13.8384 -11.5003 X-RAY DIFFRACTION A 72 A 134 X-RAY DIFFRACTION 1 chain A B 1 B 14 X-RAY DIFFRACTION 2 chain B C 1 C 14 X-RAY DIFFRACTION 3 chain C author_and_software_defined_assembly PISA 3 trimeric 3250 -8 10580 B 5CM 9 B 5CM 9 DC C 5HC 4 C 5HC 4 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 N VAL 80 A N VAL 13 A O TYR 96 A O TYR 29 A N PHE 97 A N PHE 30 A O PHE 105 A O PHE 38 1 B HOH 101 G HOH 1 A SER 68 A SER 1 1 Y 1 A GLY 69 A GLY 2 1 Y 1 A HIS 70 A HIS 3 1 Y 1 A LYS 71 A LYS 4 1 Y 1 A LYS 135 A LYS 68 1 Y 1 A GLY 136 A GLY 69 1 Y 1 4.66 0.30 108.30 112.96 B B B O4' C1' N9 DG DG DG 11 11 11 N 100.750 47.8984 22.030 -11.0243 0.0000 0.0000 8.1093 0.0000 2.9149 0.2199 0.1906 0.1924 2.400 34.700 456 9351 4.88 95.52 1.000 0.500 0.43 RANDOM 1 0.00 MOLECULAR REPLACEMENT 24.3500 0.72 1.00 PDB ENTRY 3VXV ML FLAT BULK SOLVENT MODEL 39.965 0.329 2.400 34.700 71 1161 8 571 511 0.004 1171 1.008 1694 26.872 475 0.056 182 0.003 118 0.3224 0.2838 2.7472 133 2712 3 89.00 0.2278 0.1948 3.4607 170 3013 3 99.00 0.1968 0.1716 34.7032 153 3170 3 99.00 48.250 2.19 50 3VYB 11517 1.0 1.0 0.052 1 14.7 6.5 89.6 0.317 2.19 2.27 701 1 4.1 54.7 data collection HKL-2000 phasing MOLREP refinement PHENIX (phenix.refine: 1.6.4_486) data reduction HKL-2000 data scaling HKL-2000 Crystal structure of methyl CpG binding domain of MBD4 in complex with the 5mCG/hmCG sequence 1 N N 2 N N 3 N N 4 N N 5 N N 6 N N 6 N N 6 N N A SER 107 A SER 40 HELX_P A GLY 119 A GLY 52 1 1 13 A LYS 124 A LYS 57 HELX_P A PHE 128 A PHE 61 5 2 5 disulf 2.029 A CYS 75 A SG CYS 8 1_555 A CYS 75 A SG CYS 8 3_555 covale 1.604 both B DC 8 B O3' DC 8 1_555 B 5CM 9 B P 5CM 9 1_555 covale 1.603 both B 5CM 9 B O3' 5CM 9 1_555 B DG 10 B P DG 10 1_555 covale 1.607 both C DC 3 C O3' DC 3 1_555 C 5HC 4 C P 5HC 4 1_555 covale 1.610 both C 5HC 4 C O3' 5HC 4 1_555 C DG 5 C P DG 5 1_555 hydrog WATSON-CRICK B DG 1 B N1 DG 1 1_555 C DC 13 C N3 DC 13 1_555 hydrog WATSON-CRICK B DG 1 B N2 DG 1 1_555 C DC 13 C O2 DC 13 1_555 hydrog WATSON-CRICK B DG 1 B O6 DG 1 1_555 C DC 13 C N4 DC 13 1_555 hydrog WATSON-CRICK B DT 2 B N3 DT 2 1_555 C DA 12 C N1 DA 12 1_555 hydrog WATSON-CRICK B DT 2 B O4 DT 2 1_555 C DA 12 C N6 DA 12 1_555 hydrog WATSON-CRICK B DC 3 B N3 DC 3 1_555 C DG 11 C N1 DG 11 1_555 hydrog WATSON-CRICK B DC 3 B N4 DC 3 1_555 C DG 11 C O6 DG 11 1_555 hydrog WATSON-CRICK B DC 3 B O2 DC 3 1_555 C DG 11 C N2 DG 11 1_555 hydrog WATSON-CRICK B DA 4 B N1 DA 4 1_555 C DT 10 C N3 DT 10 1_555 hydrog WATSON-CRICK B DA 4 B N6 DA 4 1_555 C DT 10 C O4 DT 10 1_555 hydrog WATSON-CRICK B DC 5 B N3 DC 5 1_555 C DG 9 C N1 DG 9 1_555 hydrog WATSON-CRICK B DC 5 B N4 DC 5 1_555 C DG 9 C O6 DG 9 1_555 hydrog WATSON-CRICK B DC 5 B O2 DC 5 1_555 C DG 9 C N2 DG 9 1_555 hydrog WATSON-CRICK B DT 6 B N3 DT 6 1_555 C DA 8 C N1 DA 8 1_555 hydrog WATSON-CRICK B DT 6 B O4 DT 6 1_555 C DA 8 C N6 DA 8 1_555 hydrog WATSON-CRICK B DA 7 B N1 DA 7 1_555 C DT 7 C N3 DT 7 1_555 hydrog WATSON-CRICK B DA 7 B N6 DA 7 1_555 C DT 7 C O4 DT 7 1_555 hydrog WATSON-CRICK B DC 8 B N3 DC 8 1_555 C DG 6 C N1 DG 6 1_555 hydrog WATSON-CRICK B DC 8 B N4 DC 8 1_555 C DG 6 C O6 DG 6 1_555 hydrog WATSON-CRICK B DC 8 B O2 DC 8 1_555 C DG 6 C N2 DG 6 1_555 hydrog WATSON-CRICK B 5CM 9 B N3 5CM 9 1_555 C DG 5 C N1 DG 5 1_555 hydrog WATSON-CRICK B 5CM 9 B N4 5CM 9 1_555 C DG 5 C O6 DG 5 1_555 hydrog WATSON-CRICK B 5CM 9 B O2 5CM 9 1_555 C DG 5 C N2 DG 5 1_555 hydrog WATSON-CRICK B DG 11 B N1 DG 11 1_555 C DC 3 C N3 DC 3 1_555 hydrog WATSON-CRICK B DG 11 B N2 DG 11 1_555 C DC 3 C O2 DC 3 1_555 hydrog WATSON-CRICK B DG 11 B O6 DG 11 1_555 C DC 3 C N4 DC 3 1_555 hydrog WATSON-CRICK B DA 12 B N1 DA 12 1_555 C DT 2 C N3 DT 2 1_555 hydrog WATSON-CRICK B DA 12 B N6 DA 12 1_555 C DT 2 C O4 DT 2 1_555 hydrog WATSON-CRICK B DC 13 B N3 DC 13 1_555 C DG 1 C N1 DG 1 1_555 hydrog WATSON-CRICK B DC 13 B N4 DC 13 1_555 C DG 1 C O6 DG 1 1_555 hydrog WATSON-CRICK B DC 13 B O2 DC 13 1_555 C DG 1 C N2 DG 1 1_555 HYDROLASE/DNA methyl CpG binding domain, protein-DNA complex, versatile base recognition, HYDROLASE-DNA complex MBD4_MOUSE UNP 1 69 Q9Z2D7 GHKPVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFNFTVLPKG 3VYB PDB 2 3VYB 3VYB PDB 3 3VYB 69 136 3VYB 69 136 Q9Z2D7 A 1 2 69 1 14 3VYB 1 14 3VYB B 2 1 14 1 14 3VYB 1 14 3VYB C 3 1 14 1 expression tag SER 68 3VYB A Q9Z2D7 UNP 1 3 anti-parallel anti-parallel A GLU 78 A GLU 11 A GLN 83 A GLN 16 A PHE 93 A PHE 26 A ILE 98 A ILE 31 A LYS 104 A LYS 37 A PHE 105 A PHE 38 BINDING SITE FOR RESIDUE ACT A 201 A ACT 201 Software 4 BINDING SITE FOR RESIDUE EDO A 202 A EDO 202 Software 6 A GLU 120 A GLU 53 4 1_555 A GLU 120 A GLU 53 4 3_555 C DT 14 C DT 14 4 6_555 C DT 14 C DT 14 4 8_455 A GLN 83 A GLN 16 6 1_555 A ARG 84 A ARG 17 6 1_555 A HOH 323 F HOH 6 1_555 C DC 3 C DC 3 6 1_555 C 5HC 4 C 5HC 4 6 1_555 C HOH 106 H HOH 6 1_555 20 C 2 2 21