0.014308 0.000000 0.002502 0.000000 0.025345 0.000000 0.000000 0.000000 0.018753 0.000000 0.000000 0.000000 Chao, X. Tempel, W. Bian, C. Bountra, C. Arrowsmith, C.H. Edwards, A.M. Min, J. Structural Genomics Consortium (SGC) http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.000 99.920 90.000 69.892 39.455 54.134 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 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 C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking UNKNOWN ATOM OR ION non-polymer C5 H11 N O2 117.146 y VALINE L-peptide linking Zn 2 65.409 ZINC ION non-polymer N 1 N N N 2 S C N 3 N C N 4 N O N 5 N C N 6 N O N 7 N H N 8 N H N 9 N H N 10 N H N 11 N H N 12 N H N 13 N H N 14 N N N 15 S C N 16 N C N 17 N O N 18 N C N 19 N C N 20 N C N 21 N N N 22 N C N 23 N N N 24 N N N 25 N O 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 H N 41 N N N 42 S C N 43 N C N 44 N O N 45 N C N 46 N C N 47 N O N 48 N N N 49 N O 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 N N 59 R C N 60 N C N 61 N O N 62 N C N 63 N S N 64 N O 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 O N 73 N P N 74 N O N 75 N O N 76 N O N 77 N C N 78 R C N 79 N O N 80 S C N 81 N O N 82 N C N 83 R C Y 84 N N Y 85 N C Y 86 N N Y 87 N C Y 88 N C N 89 N N Y 90 N N Y 91 N C Y 92 N N Y 93 N C N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N O N 109 N P N 110 N O N 111 N O N 112 N O N 113 N C N 114 R C N 115 N O N 116 S C N 117 N O N 118 N C N 119 R C N 120 N N N 121 N C N 122 N O N 123 N N N 124 N C N 125 N N N 126 N C N 127 N C N 128 N H N 129 N H N 130 N H N 131 N H 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 H N 141 N H N 142 N O N 143 N P N 144 N O N 145 N O N 146 N O N 147 N C N 148 R C N 149 N O N 150 S C N 151 N O N 152 N C N 153 R C Y 154 N N Y 155 N C Y 156 N N Y 157 N C N 158 N C N 159 N O N 160 N N N 161 N C N 162 N N N 163 N N Y 164 N C N 165 N H N 166 N H 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 O N 180 N P N 181 N O N 182 N O N 183 N O N 184 N C N 185 R C N 186 N O N 187 S C N 188 N O N 189 N C N 190 R C N 191 N N N 192 N C N 193 N O N 194 N N N 195 N C N 196 N O N 197 N C N 198 N C N 199 N C 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 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 N N 216 S C N 217 N C N 218 N O N 219 N C N 220 N C N 221 N C N 222 N O N 223 N N N 224 N O 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 N N 236 S C N 237 N C N 238 N O N 239 N C N 240 N C N 241 N C N 242 N O N 243 N O N 244 N O 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 N N 255 N C N 256 N C N 257 N O N 258 N O 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 Y 269 N C Y 270 N N Y 271 N C Y 272 N C Y 273 N N N 274 N O 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 H N 285 N O N 286 N H N 287 N H N 288 N N N 289 S C N 290 N C N 291 N O N 292 S C N 293 N C N 294 N C N 295 N C N 296 N O 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 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 N N 311 S C N 312 N C N 313 N O N 314 N C N 315 N C N 316 N C N 317 N C N 318 N O N 319 N H N 320 N H N 321 N H N 322 N H N 323 N H 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 N N 333 S C N 334 N C N 335 N O N 336 N C N 337 N C N 338 N C N 339 N C N 340 N N N 341 N O N 342 N H N 343 N H N 344 N H N 345 N H 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 N N 358 S C N 359 N C N 360 N O N 361 N C N 362 N C N 363 N S N 364 N C N 365 N O N 366 N H N 367 N H 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 N N 378 S C N 379 N C N 380 N O N 381 N C Y 382 N C Y 383 N C Y 384 N C Y 385 N C Y 386 N C Y 387 N C N 388 N O N 389 N H N 390 N H 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 N N 401 S C N 402 N C N 403 N O N 404 N C N 405 N C N 406 N C N 407 N O 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 N N 418 S C N 419 N C N 420 N O N 421 N C N 422 N O N 423 N O 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 N N 432 S C N 433 N C N 434 N O N 435 R C N 436 N O N 437 N C N 438 N O 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 N N 449 S C N 450 N C N 451 N O N 452 N C Y 453 N C Y 454 N C Y 455 N C Y 456 N C Y 457 N C Y 458 N C N 459 N O N 460 N O N 461 N H N 462 N H 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 C N 478 N C N 479 N O 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 H N 489 N H N 490 N H N 491 N ZN N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub 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 doub 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 doub 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 doub 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 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 doub 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 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 sing N 88 N sing N 89 N sing N 90 N sing Y 91 N sing Y 92 N sing Y 93 N doub N 94 N sing Y 95 N sing Y 96 N sing Y 97 N doub N 98 N sing Y 99 N doub N 100 N sing N 101 N sing Y 102 N sing Y 103 N doub N 104 N sing Y 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 N 129 N sing N 130 N sing N 131 N doub 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 doub N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N doub N 144 N sing N 145 N sing N 146 N sing 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 Y 164 N sing Y 165 N sing Y 166 N doub N 167 N sing Y 168 N sing N 169 N sing Y 170 N doub 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 sing N 182 N doub 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 N 202 N sing N 203 N sing N 204 N sing N 205 N doub N 206 N sing N 207 N sing N 208 N sing N 209 N doub N 210 N sing N 211 N sing N 212 N doub 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 doub 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 doub 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 doub 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 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 doub 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 doub N 270 N sing N 271 N sing N 272 N sing N 273 N sing Y 274 N sing Y 275 N doub Y 276 N doub N 277 N sing Y 278 N sing N 279 N sing Y 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 sing N 290 N sing N 291 N sing N 292 N doub 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 sing N 304 N sing N 305 N sing N 306 N sing N 307 N sing N 308 N sing N 309 N sing N 310 N sing N 311 N sing N 312 N sing N 313 N doub 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 sing N 331 N sing N 332 N sing N 333 N sing N 334 N doub N 335 N sing N 336 N sing N 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 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 doub 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 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 doub N 378 N sing N 379 N sing N 380 N sing N 381 N sing Y 382 N doub Y 383 N sing Y 384 N sing N 385 N sing Y 386 N doub N 387 N sing Y 388 N doub N 389 N sing Y 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 doub 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 doub 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 doub 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 sing N 442 N sing N 443 N sing N 444 N sing N 445 N sing N 446 N doub N 447 N sing N 448 N sing N 449 N sing N 450 N sing Y 451 N doub Y 452 N sing Y 453 N sing N 454 N sing Y 455 N doub N 456 N sing Y 457 N doub N 458 N sing Y 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 doub 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 sing N 478 N sing N 479 N sing N 480 N sing N 481 N sing US Cell(Cambridge,Mass.) CELLB5 0998 0092-8674 151 1200 1213 10.1016/j.cell.2012.11.014 23217707 Tet3 CXXC Domain and Dioxygenase Activity Cooperatively Regulate Key Genes for Xenopus Eye and Neural Development. 2012 10.2210/pdb4hp3/pdb pdb_00004hp3 100 1 CCD 2012-01-25 MARMOSAIC 300 mm CCD SINGLE WAVELENGTH M x-ray 1 0.97949 1.0 08ID-1 CLSI 0.97949 SYNCHROTRON CLSI BEAMLINE 08ID-1 3663.392 DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3') 2 syn polymer 8430.049 LOC100036628 protein 1 man polymer UNKNOWN ATOM OR ION 3 syn non-polymer 65.409 ZINC ION 2 syn non-polymer 18.015 water 23 nat water no no (DG)(DC)(DC)(DA)(DA)(DC)(DG)(DT)(DT)(DG)(DG)(DC) GCCAACGTTGGC A,B polydeoxyribonucleotide no no MHHHHHHSSGRENLYFQGSNKKRKRCGVCVPCLRKEPCGACYNCVNRSTSHQICKMRKCEQLKKKRVVPMKG MHHHHHHSSGRENLYFQGSNKKRKRCGVCVPCLRKEPCGACYNCVNRSTSHQICKMRKCEQLKKKRVVPMKG C 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 WESTERN CLAWED FROG sample 8364 XENOPUS (SILURANA) TROPICALIS 511693 Escherichia coli BL21-V2R-pRARE2 plasmid pET28-MHL 1 2.33 47.28 VAPOR DIFFUSION, SITTING DROP 7.5 30% PEG-1500, 0.2M sodium chloride, 0.1M HEPES, pH 7.5, vapor diffusion, sitting drop, temperature 291K 291 -2.267 1 19 A 1 B 12 1.401 A_DG1:DC12_B 1 -2.526 -0.376 -0.116 -0.105 -10.705 1 19 A 2 B 11 -2.341 A_DC2:DG11_B 2 -8.203 -0.028 0.478 -0.095 -5.009 1 19 A 3 B 10 0.628 A_DC3:DG10_B 3 -10.236 0.421 0.241 -0.050 -7.322 1 20 A 4 B 9 0.376 A_DA4:DT9_B 4 -1.787 0.155 -0.107 -0.134 3.637 1 20 A 5 B 8 4.712 A_DA5:DT8_B 5 -2.250 -0.079 0.092 -0.178 -2.055 1 19 A 6 B 7 -6.026 A_DC6:DG7_B 6 -10.065 0.003 -0.032 -0.216 -3.898 1 19 A 7 B 6 0.090 A_DG7:DC6_B 7 -6.176 -0.262 0.132 -0.206 1.366 1 20 A 8 B 5 -0.882 A_DT8:DA5_B 8 -5.639 0.090 -0.036 -0.106 3.361 1 20 A 9 B 4 0.991 A_DT9:DA4_B 9 -8.779 0.062 -0.238 -0.061 1.652 1 19 A 10 B 3 0.983 A_DG10:DC3_B 10 -3.210 -0.234 -0.115 -0.122 3.841 1 19 A 11 B 2 -2.603 A_DG11:DC2_B 11 -6.479 -0.147 0.054 -0.215 -3.175 1 19 A 12 B 1 1.342 A_DC12:DG1_B 12 -4.018 0.403 -0.015 -0.139 3.589 36.883 A A 1 2 -5.128 B B 12 11 3.452 -3.228 -1.009 -0.432 AA_DG1DC2:DG11DC12_BB 1 -5.750 9.135 36.308 -0.208 0.750 3.136 33.824 A A 2 3 8.144 B B 11 10 3.156 4.718 -0.002 0.152 AA_DC2DC3:DG10DG11_BB 2 2.993 -5.167 33.372 -0.476 0.471 3.389 43.555 A A 3 4 0.690 B B 10 9 3.366 0.512 0.241 1.582 AA_DC3DA4:DT9DG10_BB 3 1.332 -1.795 43.533 2.081 -0.192 2.870 25.736 A A 4 5 17.639 B B 9 8 3.168 7.714 0.754 -0.074 AA_DA4DA5:DT8DT9_BB 4 -3.587 8.203 24.312 -2.222 -2.648 3.455 40.601 A A 5 6 -7.233 B B 8 7 3.412 -5.006 -1.759 -0.154 AA_DA5DC6:DG7DT8_BB 5 -1.201 1.735 40.287 0.365 2.395 3.356 35.973 A A 6 7 6.776 B B 7 6 3.384 4.173 0.044 0.036 AA_DC6DG7:DC6DG7_BB 6 -2.551 4.142 35.649 -0.557 -0.447 3.247 32.276 A A 7 8 0.585 B B 6 5 3.246 0.325 0.148 -0.053 AA_DG7DT8:DA5DC6_BB 7 0.356 -0.641 32.273 -0.153 -0.203 3.294 36.509 A A 8 9 2.628 B B 5 4 3.262 1.642 0.471 0.065 AA_DT8DT9:DA4DA5_BB 8 4.548 -7.279 36.198 -0.125 -0.119 3.536 33.822 A A 9 10 5.496 B B 4 3 3.416 3.191 0.926 0.975 AA_DT9DG10:DC3DA4_BB 9 1.879 -3.235 33.625 1.127 -1.268 3.312 36.336 A A 10 11 8.885 B B 3 2 3.227 5.514 -0.883 0.388 AA_DG10DG11:DC2DC3_BB 10 -3.206 5.166 35.791 -0.152 0.966 3.508 37.266 A A 11 12 -0.939 B B 2 1 3.482 -0.600 0.713 -0.467 AA_DG11DC12:DG1DC2_BB 11 1.109 -1.736 37.246 -0.645 -0.959 chem_comp_atom chem_comp_bond database_2 pdbx_struct_conn_angle struct_conn struct_ref_seq_dif struct_site pdbx_initial_refinement_model repository Initial release Database references Data collection Database references Derived calculations Refinement description 1 0 2012-12-05 1 1 2012-12-19 1 2 2024-02-28 1 3 2024-04-03 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _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 2012-10-23 REL REL UNX UNKNOWN ATOM OR ION ZN ZINC ION HOH water unpublished model of complex between same protein construct and a methylated DNA fragment. That structure was solved by a combination of zinc-SAD (SHELXD/E) and molecular replacement in ""density"" mode (MOLREP), using ideal DNA (COOT) and human MLL2 (currently unpublished) as search models. Other experimental model UNX 2 3 UNX UNX 101 A UNX 3 3 UNX UNX 102 A ZN 1 4 ZN ZN 201 C ZN 2 4 ZN ZN 202 C UNX 1 3 UNX UNX 203 C HOH 5 5 HOH HOH 201 A HOH 6 5 HOH HOH 202 A HOH 10 5 HOH HOH 203 A HOH 11 5 HOH HOH 204 A HOH 16 5 HOH HOH 205 A HOH 17 5 HOH HOH 101 B HOH 21 5 HOH HOH 102 B HOH 1 5 HOH HOH 301 C HOH 2 5 HOH HOH 302 C HOH 3 5 HOH HOH 303 C HOH 4 5 HOH HOH 304 C HOH 7 5 HOH HOH 305 C HOH 8 5 HOH HOH 306 C HOH 9 5 HOH HOH 307 C HOH 12 5 HOH HOH 308 C HOH 13 5 HOH HOH 309 C HOH 14 5 HOH HOH 310 C HOH 15 5 HOH HOH 311 C HOH 19 5 HOH HOH 312 C HOH 20 5 HOH HOH 313 C HOH 22 5 HOH HOH 314 C HOH 23 5 HOH HOH 315 C HOH 24 5 HOH HOH 316 C DG 1 n 1 DG 1 A DC 2 n 2 DC 2 A DC 3 n 3 DC 3 A DA 4 n 4 DA 4 A DA 5 n 5 DA 5 A DC 6 n 6 DC 6 A DG 7 n 7 DG 7 A DT 8 n 8 DT 8 A DT 9 n 9 DT 9 A DG 10 n 10 DG 10 A DG 11 n 11 DG 11 A DC 12 n 12 DC 12 A DG 1 n 1 DG 1 B DC 2 n 2 DC 2 B DC 3 n 3 DC 3 B DA 4 n 4 DA 4 B DA 5 n 5 DA 5 B DC 6 n 6 DC 6 B DG 7 n 7 DG 7 B DT 8 n 8 DT 8 B DT 9 n 9 DT 9 B DG 10 n 10 DG 10 B DG 11 n 11 DG 11 B DC 12 n 12 DC 12 B n 1 40 C n 2 41 C n 3 42 C n 4 43 C n 5 44 C n 6 45 C n 7 46 C n 8 47 C n 9 48 C n 10 49 C n 11 50 C n 12 51 C n 13 52 C n 14 53 C n 15 54 C n 16 55 C n 17 56 C n 18 57 C n 19 58 C ASN 59 n 20 ASN 59 C LYS 60 n 21 LYS 60 C LYS 61 n 22 LYS 61 C ARG 62 n 23 ARG 62 C LYS 63 n 24 LYS 63 C ARG 64 n 25 ARG 64 C CYS 65 n 26 CYS 65 C GLY 66 n 27 GLY 66 C VAL 67 n 28 VAL 67 C CYS 68 n 29 CYS 68 C VAL 69 n 30 VAL 69 C PRO 70 n 31 PRO 70 C CYS 71 n 32 CYS 71 C LEU 72 n 33 LEU 72 C ARG 73 n 34 ARG 73 C LYS 74 n 35 LYS 74 C GLU 75 n 36 GLU 75 C PRO 76 n 37 PRO 76 C CYS 77 n 38 CYS 77 C GLY 78 n 39 GLY 78 C ALA 79 n 40 ALA 79 C CYS 80 n 41 CYS 80 C TYR 81 n 42 TYR 81 C ASN 82 n 43 ASN 82 C CYS 83 n 44 CYS 83 C VAL 84 n 45 VAL 84 C ASN 85 n 46 ASN 85 C ARG 86 n 47 ARG 86 C SER 87 n 48 SER 87 C THR 88 n 49 THR 88 C SER 89 n 50 SER 89 C HIS 90 n 51 HIS 90 C GLN 91 n 52 GLN 91 C ILE 92 n 53 ILE 92 C CYS 93 n 54 CYS 93 C LYS 94 n 55 LYS 94 C MET 95 n 56 MET 95 C ARG 96 n 57 ARG 96 C LYS 97 n 58 LYS 97 C CYS 98 n 59 CYS 98 C GLU 99 n 60 GLU 99 C GLN 100 n 61 GLN 100 C LEU 101 n 62 LEU 101 C LYS 102 n 63 LYS 102 C LYS 103 n 64 LYS 103 C LYS 104 n 65 LYS 104 C ARG 105 n 66 ARG 105 C VAL 106 n 67 VAL 106 C VAL 107 n 68 VAL 107 C PRO 108 n 69 PRO 108 C MET 109 n 70 MET 109 C n 71 110 C n 72 111 C 4.0949 5.2510 -0.6890 9.4711 0.4565 4.6317 -0.6484 0.9541 -0.2178 -0.5534 0.5198 0.1219 -0.0817 0.0359 0.1286 0.2734 -0.2114 0.0867 0.5299 -0.1094 0.1427 refined -18.4712 -18.9190 8.1644 X-RAY DIFFRACTION 9.5126 6.4532 0.5532 7.8003 0.9141 5.0148 -0.1653 0.3001 0.0626 -0.4054 0.1393 0.2939 0.1253 -0.2641 0.0260 0.2464 -0.0713 -0.0169 0.3459 0.0136 0.1683 refined -18.7733 -18.0552 9.3508 X-RAY DIFFRACTION 3.8636 0.4324 -2.1731 10.3005 0.3064 5.4021 -0.0772 0.3738 0.0030 -0.5485 0.1085 -0.0284 -0.1633 -0.1043 -0.0313 0.2750 -0.0699 0.0221 0.1512 -0.0065 0.0413 refined -19.7853 -17.3567 19.5889 X-RAY DIFFRACTION A 1 A 12 X-RAY DIFFRACTION 1 B 1 B 12 X-RAY DIFFRACTION 2 C 59 C 109 X-RAY DIFFRACTION 3 software_defined_assembly PISA 3 trimeric 2940 -18 7060 C CYS 65 C SG CYS 26 1_555 C ZN 201 F ZN ZN 1_555 C CYS 68 C SG CYS 29 1_555 108.8 C CYS 65 C SG CYS 26 1_555 C ZN 201 F ZN ZN 1_555 C CYS 71 C SG CYS 32 1_555 116.4 C CYS 68 C SG CYS 29 1_555 C ZN 201 F ZN ZN 1_555 C CYS 71 C SG CYS 32 1_555 101.2 C CYS 65 C SG CYS 26 1_555 C ZN 201 F ZN ZN 1_555 C CYS 98 C SG CYS 59 1_555 105.9 C CYS 68 C SG CYS 29 1_555 C ZN 201 F ZN ZN 1_555 C CYS 98 C SG CYS 59 1_555 124.5 C CYS 71 C SG CYS 32 1_555 C ZN 201 F ZN ZN 1_555 C CYS 98 C SG CYS 59 1_555 100.5 C CYS 77 C SG CYS 38 1_555 C ZN 202 G ZN ZN 1_555 C CYS 80 C SG CYS 41 1_555 112.1 C CYS 77 C SG CYS 38 1_555 C ZN 202 G ZN ZN 1_555 C CYS 83 C SG CYS 44 1_555 119.2 C CYS 80 C SG CYS 41 1_555 C ZN 202 G ZN ZN 1_555 C CYS 83 C SG CYS 44 1_555 102.7 C CYS 77 C SG CYS 38 1_555 C ZN 202 G ZN ZN 1_555 C CYS 93 C SG CYS 54 1_555 102.4 C CYS 80 C SG CYS 41 1_555 C ZN 202 G ZN ZN 1_555 C CYS 93 C SG CYS 54 1_555 116.2 C CYS 83 C SG CYS 44 1_555 C ZN 202 G ZN ZN 1_555 C CYS 93 C SG CYS 54 1_555 104.7 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 C CG LYS 60 C CG LYS 21 1 Y 1 C CD LYS 60 C CD LYS 21 1 Y 1 C CE LYS 60 C CE LYS 21 1 Y 1 C NZ LYS 60 C NZ LYS 21 1 Y 1 C CG LYS 74 C CG LYS 35 1 Y 1 C CD LYS 74 C CD LYS 35 1 Y 1 C CE LYS 74 C CE LYS 35 1 Y 1 C NZ LYS 74 C NZ LYS 35 1 Y 1 C CD GLU 75 C CD GLU 36 1 Y 1 C OE1 GLU 75 C OE1 GLU 36 1 Y 1 C OE2 GLU 75 C OE2 GLU 36 1 Y 1 C OG1 THR 88 C OG1 THR 49 1 Y 1 C CG2 THR 88 C CG2 THR 49 1 Y 1 C CG LYS 104 C CG LYS 65 1 Y 1 C CD LYS 104 C CD LYS 65 1 Y 1 C CE LYS 104 C CE LYS 65 1 Y 1 C NZ LYS 104 C NZ LYS 65 1 Y 1 C CG1 VAL 106 C CG1 VAL 67 1 Y 1 C CG2 VAL 106 C CG2 VAL 67 1 Y 1 C CG1 VAL 107 C CG1 VAL 68 1 Y 1 C CG2 VAL 107 C CG2 VAL 68 1 Y 1 C MET 40 C MET 1 1 Y 1 C HIS 41 C HIS 2 1 Y 1 C HIS 42 C HIS 3 1 Y 1 C HIS 43 C HIS 4 1 Y 1 C HIS 44 C HIS 5 1 Y 1 C HIS 45 C HIS 6 1 Y 1 C HIS 46 C HIS 7 1 Y 1 C SER 47 C SER 8 1 Y 1 C SER 48 C SER 9 1 Y 1 C GLY 49 C GLY 10 1 Y 1 C ARG 50 C ARG 11 1 Y 1 C GLU 51 C GLU 12 1 Y 1 C ASN 52 C ASN 13 1 Y 1 C LEU 53 C LEU 14 1 Y 1 C TYR 54 C TYR 15 1 Y 1 C PHE 55 C PHE 16 1 Y 1 C GLN 56 C GLN 17 1 Y 1 C GLY 57 C GLY 18 1 Y 1 C SER 58 C SER 19 1 Y 1 C LYS 110 C LYS 71 1 Y 1 C GLY 111 C GLY 72 1 Y 1 8.29 1.20 119.70 127.99 A A A C3' O3' P DA DA DC 5 5 6 Y 1 C LYS 60 -109.25 -168.48 1 C ASN 85 -111.16 51.47 122.830 52.7690 27.080 -1.0000 0.0000 0.3950 -0.7390 0.0000 1.8750 0.9600 0.9480 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. COOT and the MOLPROBITY server were also used during refinement. 0.2434 0.2155 0.2170 2.0500 30.0000 452 9281 4.8700 99.6780 0.2560 0.2200 1.000 0.500 8.2140 0.1390 RANDOM 1 THROUGHOUT 0.000 MOLECULAR REPLACEMENT 0.1860 0.1620 0.8000 0.8000 1.2000 unpublished model of complex between same protein construct and a methylated DNA fragment. That structure was solved by a combination of zinc-SAD (SHELXD/E) and molecular replacement in "density" mode (MOLREP), using ideal DNA (COOT) and human MLL2 (currently unpublished) as search models. MAXIMUM LIKELIHOOD MASK BULK SOLVENT 2.0500 30.0000 23 898 5 486 384 0.013 0.014 940 0.003 0.020 662 1.359 1.602 1359 1.160 3.010 1530 6.013 5.000 50 40.342 20.000 14 14.940 15.000 79 20.480 15.000 6 0.064 0.200 127 0.008 0.021 719 0.001 0.020 213 0.415 0.321 2.103 32 651 685 20 99.708 0.345 0.278 2.160 30 631 661 20 100.000 0.288 0.268 2.223 35 628 663 20 100.000 0.297 0.267 2.291 27 568 596 20 99.832 0.187 0.243 2.365 24 601 626 20 99.840 0.292 0.232 2.448 32 542 576 20 99.653 0.312 0.238 2.540 25 531 558 20 99.642 0.365 0.257 2.642 28 527 555 20 100.000 0.264 0.288 2.759 19 490 512 20 99.414 0.278 0.287 2.892 22 499 521 20 100.000 0.312 0.240 3.047 33 436 469 20 100.000 0.289 0.250 3.230 28 424 453 20 99.779 0.244 0.178 3.450 25 399 426 20 99.531 0.178 0.200 3.723 14 382 397 20 99.748 0.201 0.189 4.072 24 353 379 20 99.472 0.135 0.166 4.542 17 317 335 20 99.701 0.225 0.191 5.224 14 282 297 20 99.663 0.223 0.183 6.351 8 249 257 20 100.000 0.192 0.188 8.786 7 196 205 20 99.024 0.266 0.193 30.000 8 120 130 20 98.462 2.05 34.42 4HP3 9281 0.053 1 12.5727 3.71 99.79 0.67 2.05 2.16 4996 1345 1 3.71 99.85 0.39 2.16 2.29 4711 1267 1 3.72 99.92 0.24 2.29 2.45 4523 1206 1 3.75 99.79 0.14 2.45 2.65 4169 1111 1 3.75 99.81 0.10 2.65 2.90 3840 1029 1 3.73 99.75 0.06 2.90 3.24 3456 926 1 3.73 99.89 0.04 3.24 3.74 3078 825 1 3.73 99.68 0.04 3.74 4.58 2619 708 1 3.70 99.70 0.04 4.58 6.48 1976 550 1 3.59 99.90 0.04 6.48 34.42 1052 314 1 3.35 99.03 data scaling Phil R. Evans pre@mrc-lmb.cam.ac.uk 2011/05/18 Fortran_77 http://www.ccp4.ac.uk/dist/html/scala.html SCALA other CCP4_3.3.20 phasing Randy J. Read cimr-phaser@lists.cam.ac.uk http://www-structmed.cimr.cam.ac.uk/phaser/ PHASER program refinement Garib N. Murshudov garib@ysbl.york.ac.uk Fortran_77 http://www.ccp4.ac.uk/dist/html/refmac5.html REFMAC program 5.7.0027 data extraction PDB deposit@deposit.rcsb.org August 3, 2011 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.11 data reduction XDS Crystal structure of Tet3 in complex with a CpG dsDNA 1 N N 1 N N 2 N N 3 N N 3 N N 4 N N 4 N N 3 N N 5 N N 5 N N 5 N N AUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN. C CYS 68 C CYS 29 HELX_P C ARG 73 C ARG 34 1 1 6 C CYS 80 C CYS 41 HELX_P C ASN 85 C ASN 46 1 2 6 C ASN 85 C ASN 46 HELX_P C HIS 90 C HIS 51 1 3 6 metalc 2.336 C CYS 65 C SG CYS 26 1_555 C ZN 201 F ZN ZN 1_555 metalc 2.309 C CYS 68 C SG CYS 29 1_555 C ZN 201 F ZN ZN 1_555 metalc 2.284 C CYS 71 C SG CYS 32 1_555 C ZN 201 F ZN ZN 1_555 metalc 2.332 C CYS 77 C SG CYS 38 1_555 C ZN 202 G ZN ZN 1_555 metalc 2.282 C CYS 80 C SG CYS 41 1_555 C ZN 202 G ZN ZN 1_555 metalc 2.335 C CYS 83 C SG CYS 44 1_555 C ZN 202 G ZN ZN 1_555 metalc 2.379 C CYS 93 C SG CYS 54 1_555 C ZN 202 G ZN ZN 1_555 metalc 2.303 C CYS 98 C SG CYS 59 1_555 C ZN 201 F ZN ZN 1_555 hydrog WATSON-CRICK A DG 1 A N1 DG 1 1_555 B DC 12 B N3 DC 12 1_555 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 B DC 12 B O2 DC 12 1_555 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 B DC 12 B N4 DC 12 1_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 B DG 11 B N1 DG 11 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 B DG 11 B O6 DG 11 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 B DG 11 B N2 DG 11 1_555 hydrog WATSON-CRICK A DC 3 A N3 DC 3 1_555 B DG 10 B N1 DG 10 1_555 hydrog WATSON-CRICK A DC 3 A N4 DC 3 1_555 B DG 10 B O6 DG 10 1_555 hydrog WATSON-CRICK A DC 3 A O2 DC 3 1_555 B DG 10 B N2 DG 10 1_555 hydrog WATSON-CRICK A DA 4 A N1 DA 4 1_555 B DT 9 B N3 DT 9 1_555 hydrog WATSON-CRICK A DA 4 A N6 DA 4 1_555 B DT 9 B O4 DT 9 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B DT 8 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B DT 8 B O4 DT 8 1_555 hydrog WATSON-CRICK A DC 6 A N3 DC 6 1_555 B DG 7 B N1 DG 7 1_555 hydrog WATSON-CRICK A DC 6 A N4 DC 6 1_555 B DG 7 B O6 DG 7 1_555 hydrog WATSON-CRICK A DC 6 A O2 DC 6 1_555 B DG 7 B N2 DG 7 1_555 hydrog WATSON-CRICK A DG 7 A N1 DG 7 1_555 B DC 6 B N3 DC 6 1_555 hydrog WATSON-CRICK A DG 7 A N2 DG 7 1_555 B DC 6 B O2 DC 6 1_555 hydrog WATSON-CRICK A DG 7 A O6 DG 7 1_555 B DC 6 B N4 DC 6 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 B DA 5 B N1 DA 5 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 B DA 5 B N6 DA 5 1_555 hydrog WATSON-CRICK A DT 9 A N3 DT 9 1_555 B DA 4 B N1 DA 4 1_555 hydrog WATSON-CRICK A DT 9 A O4 DT 9 1_555 B DA 4 B N6 DA 4 1_555 hydrog WATSON-CRICK A DG 10 A N1 DG 10 1_555 B DC 3 B N3 DC 3 1_555 hydrog WATSON-CRICK A DG 10 A N2 DG 10 1_555 B DC 3 B O2 DC 3 1_555 hydrog WATSON-CRICK A DG 10 A O6 DG 10 1_555 B DC 3 B N4 DC 3 1_555 hydrog WATSON-CRICK A DG 11 A N1 DG 11 1_555 B DC 2 B N3 DC 2 1_555 hydrog WATSON-CRICK A DG 11 A N2 DG 11 1_555 B DC 2 B O2 DC 2 1_555 hydrog WATSON-CRICK A DG 11 A O6 DG 11 1_555 B DC 2 B N4 DC 2 1_555 hydrog WATSON-CRICK A DC 12 A N3 DC 12 1_555 B DG 1 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 12 A N4 DC 12 1_555 B DG 1 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 12 A O2 DC 12 1_555 B DG 1 B N2 DG 1 1_555 DNA BINDING PROTEIN/DNA CXXC, DNA methylation, DNA BINDING PROTEIN-DNA complex A0JP82_XENTR UNP 2 58 A0JP82 SNKKRKRCGVCVPCLRKEPCGACYNCVNRSTSHQICKMRKCEQLKKKRVVPMKG 4HP3 PDB 1 4HP3 58 111 4HP3 58 111 A0JP82 C 1 19 72 1 12 4HP3 1 12 4HP3 A 2 1 12 1 12 4HP3 1 12 4HP3 B 2 1 12 1 expression tag MET 40 4HP3 C A0JP82 UNP 1 1 expression tag HIS 41 4HP3 C A0JP82 UNP 2 1 expression tag HIS 42 4HP3 C A0JP82 UNP 3 1 expression tag HIS 43 4HP3 C A0JP82 UNP 4 1 expression tag HIS 44 4HP3 C A0JP82 UNP 5 1 expression tag HIS 45 4HP3 C A0JP82 UNP 6 1 expression tag HIS 46 4HP3 C A0JP82 UNP 7 1 expression tag SER 47 4HP3 C A0JP82 UNP 8 1 expression tag SER 48 4HP3 C A0JP82 UNP 9 1 expression tag GLY 49 4HP3 C A0JP82 UNP 10 1 expression tag ARG 50 4HP3 C A0JP82 UNP 11 1 expression tag GLU 51 4HP3 C A0JP82 UNP 12 1 expression tag ASN 52 4HP3 C A0JP82 UNP 13 1 expression tag LEU 53 4HP3 C A0JP82 UNP 14 1 expression tag TYR 54 4HP3 C A0JP82 UNP 15 1 expression tag PHE 55 4HP3 C A0JP82 UNP 16 1 expression tag GLN 56 4HP3 C A0JP82 UNP 17 1 expression tag GLY 57 4HP3 C A0JP82 UNP 18 BINDING SITE FOR RESIDUE ZN C 201 C ZN 201 Software 4 BINDING SITE FOR RESIDUE ZN C 202 C ZN 202 Software 4 C CYS 65 C CYS 26 4 1_555 C CYS 68 C CYS 29 4 1_555 C CYS 71 C CYS 32 4 1_555 C CYS 98 C CYS 59 4 1_555 C CYS 77 C CYS 38 4 1_555 C CYS 80 C CYS 41 4 1_555 C CYS 83 C CYS 44 4 1_555 C CYS 93 C CYS 54 4 1_555 5 C 1 2 1