0.010658 0.000000 0.000000 0.000000 0.009571 0.000000 0.000000 0.000000 0.019037 0.00000 0.00000 0.00000 Banerjee, S. Shanmugam, G. Stone, M.P. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.00 90.00 90.00 93.826 104.486 52.529 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 Ca 2 40.078 CALCIUM ION non-polymer 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 C10 H16 N5 O12 P3 491.182 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE 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 C14 H20 N5 O8 P 417.311 n 2'-DEOXY-N-[(1S)-1-METHYL-3-OXOPROPYL]GUANOSINE 5'-PHOSPHATE RNA 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 C5 H11 N O2 117.146 y VALINE L-peptide linking 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 S C N 60 N C N 61 N O N 62 N C N 63 N C N 64 N O N 65 N O 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 CA N 75 N N N 76 R C N 77 N C N 78 N O N 79 N C N 80 N S N 81 N O N 82 N H N 83 N H N 84 N H N 85 N H N 86 N H N 87 N H N 88 N H N 89 N O N 90 N P N 91 N O N 92 N O N 93 N O N 94 N C N 95 R C N 96 N O N 97 S C N 98 N O N 99 N C N 100 R C Y 101 N N Y 102 N C Y 103 N N Y 104 N C Y 105 N C N 106 N N Y 107 N N Y 108 N C Y 109 N N Y 110 N C 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 H N 124 N H N 125 N O N 126 N P N 127 N O N 128 N O N 129 N O N 130 N C N 131 R C N 132 N O N 133 S C N 134 N O N 135 N C N 136 R C N 137 N N N 138 N C N 139 N O N 140 N N N 141 N C N 142 N N N 143 N C N 144 N C N 145 N H N 146 N H N 147 N H N 148 N H 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 H N 157 N H N 158 N H N 159 N O N 160 N P N 161 N O N 162 N O N 163 N O N 164 N C N 165 R C N 166 N O N 167 S C N 168 N O N 169 N C N 170 R C Y 171 N N Y 172 N C Y 173 N N Y 174 N C N 175 N C N 176 N O N 177 N N N 178 N C N 179 N N N 180 N N Y 181 N C N 182 N H N 183 N H N 184 N H 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 O N 197 N P N 198 N O N 199 N O N 200 N O N 201 N C N 202 R C N 203 N O N 204 S C N 205 N O N 206 N C N 207 R C N 208 N N N 209 N C N 210 N O N 211 N N N 212 N C N 213 N O N 214 N C N 215 N C N 216 N C N 217 N H N 218 N H N 219 N H N 220 N H N 221 N H 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 P N 233 N O N 234 N O N 235 N O N 236 S P N 237 N O N 238 N O N 239 N O N 240 S P N 241 N O 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 Y 256 N C N 257 N N Y 258 N N Y 259 N C Y 260 N N Y 261 N C 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 H N 273 N H N 274 N H N 275 N H N 276 N H N 277 N H N 278 N N N 279 S C N 280 N C N 281 N O N 282 N C N 283 N C N 284 N C N 285 N O N 286 N N N 287 N O N 288 N H N 289 N H N 290 N H N 291 N H N 292 N H N 293 N H N 294 N H N 295 N H N 296 N H N 297 N H N 298 N N N 299 S C N 300 N C N 301 N O N 302 N C N 303 N C N 304 N C N 305 N O 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 H N 314 N H N 315 N H N 316 N H N 317 N N N 318 N C N 319 N C N 320 N O N 321 N O N 322 N H N 323 N H N 324 N H N 325 N H N 326 N H N 327 N N N 328 S C N 329 N C N 330 N O N 331 N C Y 332 N C Y 333 N N Y 334 N C Y 335 N C Y 336 N N N 337 N O N 338 N H N 339 N H N 340 N H N 341 N H 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 O N 349 N H N 350 N H N 351 N N N 352 S C N 353 N C N 354 N O N 355 S C N 356 N C N 357 N C N 358 N C N 359 N O N 360 N H N 361 N H N 362 N H N 363 N H N 364 N H N 365 N H 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 O N 374 N O N 375 N P N 376 N O N 377 N O N 378 N C N 379 R C N 380 N O N 381 S C N 382 N O N 383 N C N 384 R C Y 385 N N Y 386 N C N 387 N N Y 388 N C Y 389 N N Y 390 N C N 391 N C N 392 N O N 393 N N N 394 N C N 395 N N N 396 S C N 397 N C N 398 N C N 399 N C N 400 N O 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 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 H N 419 N H N 420 N H N 421 N N N 422 S C N 423 N C N 424 N O N 425 N C N 426 N C N 427 N C N 428 N C N 429 N O 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 H N 441 N H N 442 N H N 443 N N N 444 S C N 445 N C N 446 N O N 447 N C N 448 N C N 449 N C N 450 N C N 451 N N N 452 N O 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 H N 466 N H N 467 N H N 468 N N N 469 S C N 470 N C N 471 N O N 472 N C N 473 N C N 474 N S N 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 Y 493 N C Y 494 N C Y 495 N C Y 496 N C Y 497 N C Y 498 N C N 499 N O N 500 N H N 501 N H N 502 N H N 503 N H N 504 N H N 505 N H N 506 N H N 507 N H N 508 N H N 509 N H N 510 N H N 511 N N N 512 S C N 513 N C N 514 N O N 515 N C N 516 N C N 517 N C N 518 N O 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 N N 529 S C N 530 N C N 531 N O N 532 N C N 533 N O N 534 N O N 535 N H N 536 N H N 537 N H N 538 N H N 539 N H N 540 N H N 541 N H N 542 N N N 543 S C N 544 N C N 545 N O N 546 R C N 547 N O N 548 N C N 549 N O N 550 N H 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 N N 560 S C N 561 N C N 562 N O N 563 N C Y 564 N C Y 565 N C Y 566 N C Y 567 N C Y 568 N C Y 569 N C N 570 N O N 571 N O N 572 N H N 573 N H N 574 N H N 575 N H 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 N N 584 S C N 585 N C N 586 N O N 587 N C N 588 N C N 589 N C N 590 N O N 591 N H N 592 N H N 593 N H N 594 N H 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 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 doub 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 doub 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 doub N 86 N sing N 87 N sing N 88 N sing N 89 N sing 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 sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing Y 106 N sing Y 107 N sing Y 108 N doub N 109 N sing Y 110 N sing Y 111 N sing Y 112 N doub N 113 N sing Y 114 N doub N 115 N sing N 116 N sing Y 117 N sing Y 118 N doub N 119 N sing Y 120 N sing N 121 N sing N 122 N sing N 123 N doub 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 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 doub N 147 N sing N 148 N doub N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N doub N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N doub 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 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 Y 179 N sing Y 180 N sing Y 181 N doub N 182 N sing Y 183 N sing N 184 N sing Y 185 N doub N 186 N doub N 187 N sing N 188 N sing N 189 N sing N 190 N sing N 191 N doub N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N doub 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 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 doub N 221 N sing N 222 N sing N 223 N sing N 224 N doub N 225 N sing N 226 N sing N 227 N doub N 228 N sing N 229 N sing N 230 N sing N 231 N sing N 232 N doub N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N sing N 238 N doub 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 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 sing N 263 N sing N 264 N sing Y 265 N sing Y 266 N sing Y 267 N doub N 268 N sing Y 269 N sing Y 270 N sing Y 271 N doub N 272 N sing Y 273 N doub N 274 N sing N 275 N sing Y 276 N sing Y 277 N doub N 278 N sing Y 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 doub 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 doub 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 doub 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 doub 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 doub N 333 N sing N 334 N sing N 335 N sing N 336 N sing Y 337 N sing Y 338 N doub Y 339 N doub N 340 N sing Y 341 N sing N 342 N sing Y 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 doub 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 sing N 369 N sing N 370 N sing N 371 N sing N 372 N doub 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 sing Y 390 N sing Y 391 N sing N 392 N sing Y 393 N doub N 394 N doub Y 395 N doub N 396 N sing Y 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 doub 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 doub 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 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 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 doub 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 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 doub N 491 N sing N 492 N sing N 493 N sing N 494 N sing Y 495 N doub Y 496 N sing Y 497 N sing N 498 N sing Y 499 N doub N 500 N sing Y 501 N doub N 502 N sing Y 503 N sing N 504 N sing N 505 N sing 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 doub 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 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 doub N 531 N sing N 532 N sing N 533 N sing N 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 doub 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 sing N 554 N sing N 555 N sing N 556 N sing N 557 N sing N 558 N sing N 559 N doub N 560 N sing N 561 N sing N 562 N sing N 563 N sing Y 564 N doub Y 565 N sing Y 566 N sing N 567 N sing Y 568 N doub N 569 N sing Y 570 N doub N 571 N sing Y 572 N sing N 573 N sing N 574 N sing N 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 doub N 584 N sing N 585 N sing N 586 N sing 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 US Chem.Res.Toxicol. CRTOEC 2140 0893-228X 26 1348 1360 10.1021/tx400200b 23947567 Ring-Opening of the gamma-OH-PdG Adduct Promotes Error-Free Bypass by the Sulfolobus solfataricus DNA Polymerase Dpo4. 2013 10.2210/pdb4jv0/pdb pdb_00004jv0 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1 CCD 2009-10-15 MARMOSAIC 225 mm CCD SINGLE WAVELENGTH M x-ray 1 0.979 1.0 1.0 1.0 21-ID-F APS 0.979 1.0 SYNCHROTRON APS BEAMLINE 21-ID-F 39848.398 DNA polymerase IV 2.7.7.7 1 man polymer 4551.001 DNA (5'-D(P*TP*(KAG)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') 1 syn polymer 4385.852 DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*C)-3') 1 syn polymer 491.182 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE 1 syn non-polymer 40.078 CALCIUM ION 2 syn non-polymer 18.015 water 44 nat water Pol IV no no HHHHHHMIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYL PMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIA ADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYN EPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSE SVKLLQKILEEDERKIRRIGVRFSKFI HHHHHHMIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYL PMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIA ADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYN EPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSE SVKLLQKILEEDERKIRRIGVRFSKFI A polypeptide(L) no yes (DT)(KAG)(DG)(DA)(DA)(DT)(DC)(DC)(DT)(DT)(DC)(DC)(DC)(DC)(DC) TGGAATCCTTCCCCC B polydeoxyribonucleotide no no (DG)(DG)(DG)(DG)(DG)(DA)(DA)(DG)(DG)(DA)(DT)(DT)(DC)(DC) GGGGGAAGGATTCC 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 n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n ATCC 35092 / DSM 1617 / JCM 11322 / P2 sample dbh, dpo4, SSO2448 273057 Sulfolobus solfataricus 562 ESCHERICHIA COLI 1 2.640 53.390 VAPOR DIFFUSION, HANGING DROP 7.4 50 MM TRIS HCL, 15% PEG3350, 100MM CALCIUM DIACETATE, 2.5% GLYCEROL, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K 298 -3.333 1 19 B 5 C 32 2.169 B_KAG5:DC32_C 1 -10.122 0.861 -0.384 -0.092 -11.809 1 19 B 6 C 31 2.911 B_DG6:DC31_C 2 -9.733 -0.807 -0.486 -0.308 -6.994 1 20 B 7 C 30 1.403 B_DA7:DT30_C 3 -0.126 -0.278 -0.447 -0.187 0.191 1 20 B 8 C 29 4.941 B_DA8:DT29_C 4 -12.836 0.018 0.054 -0.111 9.757 1 20 B 9 C 28 2.907 B_DT9:DA28_C 5 -8.254 -0.231 -0.161 -0.230 4.514 1 19 B 10 C 27 0.185 B_DC10:DG27_C 6 -16.088 -0.171 -0.041 -0.347 -6.604 1 19 B 11 C 26 -6.542 B_DC11:DG26_C 7 -7.550 -0.579 0.383 -0.488 -3.972 1 20 B 12 C 25 -2.576 B_DT12:DA25_C 8 -7.409 -0.338 0.197 -0.206 -5.104 1 20 B 13 C 24 -5.279 B_DT13:DA24_C 9 -11.522 -0.428 0.214 -0.302 -3.842 1 19 B 14 C 23 4.480 B_DC14:DG23_C 10 -9.477 -0.129 0.380 -0.261 -16.427 1 19 B 15 C 22 -0.375 B_DC15:DG22_C 11 -10.344 -0.074 0.513 -0.170 -3.600 1 19 B 16 C 21 -8.790 B_DC16:DG21_C 12 -6.227 0.099 -0.103 -0.263 0.136 1 19 B 17 C 20 1.453 B_DC17:DG20_C 13 -7.570 0.175 -0.220 -0.369 3.279 1 19 B 18 C 19 -9.435 B_DC18:DG19_C 14 -7.642 -0.075 -0.255 -0.297 2.566 24.249 B B 5 6 30.387 C C 32 31 3.604 12.187 0.019 -1.112 BB_KAG5DG6:DC31DC32_CC 1 1.720 -4.289 20.934 -6.561 0.508 3.081 30.171 B B 6 7 14.680 C C 31 30 3.271 7.557 -0.074 -0.352 BB_DG6DA7:DT30DC31_CC 2 -2.215 4.303 29.148 -2.196 -0.303 3.278 37.039 B B 7 8 -0.168 C C 30 29 3.248 -0.106 -0.523 -0.337 BB_DA7DA8:DT29DT30_CC 3 -2.825 4.452 36.935 -0.517 0.444 2.918 26.994 B B 8 9 11.200 C C 29 28 3.104 5.197 0.022 -0.690 BB_DA8DT9:DA28DT29_CC 4 -0.024 0.052 26.498 -2.709 -0.054 3.406 37.883 B B 9 10 -4.723 C C 28 27 3.411 -3.061 0.115 -0.220 BB_DT9DC10:DG27DA28_CC 5 -2.185 3.370 37.703 0.071 -0.469 3.529 32.218 B B 10 11 9.661 C C 27 26 3.701 5.334 -0.430 -0.890 BB_DC10DC11:DG26DG27_CC 6 -2.048 3.709 31.721 -2.663 0.369 3.320 34.177 B B 11 12 -1.063 C C 26 25 3.311 -0.624 0.252 -0.202 BB_DC11DT12:DA25DG26_CC 7 1.000 -1.703 34.157 -0.243 -0.269 3.138 32.880 B B 12 13 8.931 C C 25 24 3.238 5.033 0.350 -0.531 BB_DT12DT13:DA24DA25_CC 8 2.045 -3.629 32.440 -1.782 -0.275 3.030 36.194 B B 13 14 11.478 C C 24 23 3.215 7.082 0.618 -0.390 BB_DT13DC14:DG23DA24_CC 9 -2.675 4.335 35.420 -1.590 -1.358 3.295 29.568 B B 14 15 10.429 C C 23 22 3.512 5.294 -0.276 -0.877 BB_DC14DC15:DG22DG23_CC 10 0.838 -1.652 29.088 -2.896 0.727 2.757 32.220 B B 15 16 10.198 C C 22 21 3.019 5.615 -0.833 -0.481 BB_DC15DC16:DG21DG22_CC 11 4.332 -7.867 31.450 -1.762 2.190 3.230 32.175 B B 16 17 17.567 C C 21 20 3.284 9.570 1.614 -0.299 BB_DC16DC17:DG20DG21_CC 12 4.106 -7.537 30.486 -2.291 -2.160 3.407 32.412 B B 17 18 5.949 C C 20 19 3.337 3.311 -1.210 -0.046 BB_DC17DC18:DG19DG20_CC 13 -2.854 5.128 32.124 -0.686 1.647 chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model pdbx_struct_conn_angle struct_conn struct_ref_seq_dif struct_site repository Initial release Database references Data collection Database references Derived calculations Refinement description 1 0 2013-08-28 1 1 2013-10-09 1 2 2023-09-20 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _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_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 2013-03-25 REL REL DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE CA CALCIUM ION HOH water 2BQU PDB experimental model DTP 1000 4 DTP DTP 1000 A CA 1001 5 CA CA 1001 A CA 1002 5 CA CA 1002 A HOH 342 6 HOH HOH 1101 A HOH 343 6 HOH HOH 1102 A HOH 344 6 HOH HOH 1103 A HOH 345 6 HOH HOH 1104 A HOH 346 6 HOH HOH 1105 A HOH 347 6 HOH HOH 1106 A HOH 348 6 HOH HOH 1107 A HOH 349 6 HOH HOH 1108 A HOH 350 6 HOH HOH 1109 A HOH 351 6 HOH HOH 1110 A HOH 352 6 HOH HOH 1111 A HOH 353 6 HOH HOH 1112 A HOH 354 6 HOH HOH 1113 A HOH 355 6 HOH HOH 1114 A HOH 356 6 HOH HOH 1115 A HOH 357 6 HOH HOH 1116 A HOH 358 6 HOH HOH 1117 A HOH 359 6 HOH HOH 1118 A HOH 360 6 HOH HOH 1119 A HOH 361 6 HOH HOH 1120 A HOH 362 6 HOH HOH 1121 A HOH 363 6 HOH HOH 1122 A HOH 364 6 HOH HOH 1123 A HOH 365 6 HOH HOH 1124 A HOH 366 6 HOH HOH 1125 A HOH 25 6 HOH HOH 101 B HOH 1 6 HOH HOH 102 B HOH 29 6 HOH HOH 103 B HOH 30 6 HOH HOH 104 B HOH 32 6 HOH HOH 105 B HOH 33 6 HOH HOH 106 B HOH 34 6 HOH HOH 107 B HOH 35 6 HOH HOH 108 B HOH 38 6 HOH HOH 109 B HOH 39 6 HOH HOH 110 B HOH 40 6 HOH HOH 111 B HOH 4 6 HOH HOH 101 C HOH 18 6 HOH HOH 102 C HOH 33 6 HOH HOH 103 C HOH 34 6 HOH HOH 104 C HOH 35 6 HOH HOH 105 C HOH 41 6 HOH HOH 106 C HOH 43 6 HOH HOH 107 C HOH 45 6 HOH HOH 108 C n 1 -5 A n 2 -4 A n 3 -3 A n 4 -2 A n 5 -1 A n 6 0 A MET 1 n 7 MET 1 A ILE 2 n 8 ILE 2 A VAL 3 n 9 VAL 3 A LEU 4 n 10 LEU 4 A PHE 5 n 11 PHE 5 A VAL 6 n 12 VAL 6 A ASP 7 n 13 ASP 7 A PHE 8 n 14 PHE 8 A ASP 9 n 15 ASP 9 A TYR 10 n 16 TYR 10 A PHE 11 n 17 PHE 11 A TYR 12 n 18 TYR 12 A ALA 13 n 19 ALA 13 A GLN 14 n 20 GLN 14 A VAL 15 n 21 VAL 15 A GLU 16 n 22 GLU 16 A GLU 17 n 23 GLU 17 A VAL 18 n 24 VAL 18 A LEU 19 n 25 LEU 19 A ASN 20 n 26 ASN 20 A PRO 21 n 27 PRO 21 A SER 22 n 28 SER 22 A LEU 23 n 29 LEU 23 A LYS 24 n 30 LYS 24 A GLY 25 n 31 GLY 25 A LYS 26 n 32 LYS 26 A PRO 27 n 33 PRO 27 A VAL 28 n 34 VAL 28 A VAL 29 n 35 VAL 29 A VAL 30 n 36 VAL 30 A CYS 31 n 37 CYS 31 A VAL 32 n 38 VAL 32 A PHE 33 n 39 PHE 33 A SER 34 n 40 SER 34 A GLY 35 n 41 GLY 35 A ARG 36 n 42 ARG 36 A PHE 37 n 43 PHE 37 A GLU 38 n 44 GLU 38 A ASP 39 n 45 ASP 39 A SER 40 n 46 SER 40 A GLY 41 n 47 GLY 41 A ALA 42 n 48 ALA 42 A VAL 43 n 49 VAL 43 A ALA 44 n 50 ALA 44 A THR 45 n 51 THR 45 A ALA 46 n 52 ALA 46 A ASN 47 n 53 ASN 47 A TYR 48 n 54 TYR 48 A GLU 49 n 55 GLU 49 A ALA 50 n 56 ALA 50 A ARG 51 n 57 ARG 51 A LYS 52 n 58 LYS 52 A PHE 53 n 59 PHE 53 A GLY 54 n 60 GLY 54 A VAL 55 n 61 VAL 55 A LYS 56 n 62 LYS 56 A ALA 57 n 63 ALA 57 A GLY 58 n 64 GLY 58 A ILE 59 n 65 ILE 59 A PRO 60 n 66 PRO 60 A ILE 61 n 67 ILE 61 A VAL 62 n 68 VAL 62 A GLU 63 n 69 GLU 63 A ALA 64 n 70 ALA 64 A LYS 65 n 71 LYS 65 A LYS 66 n 72 LYS 66 A ILE 67 n 73 ILE 67 A LEU 68 n 74 LEU 68 A PRO 69 n 75 PRO 69 A ASN 70 n 76 ASN 70 A ALA 71 n 77 ALA 71 A VAL 72 n 78 VAL 72 A TYR 73 n 79 TYR 73 A LEU 74 n 80 LEU 74 A PRO 75 n 81 PRO 75 A MET 76 n 82 MET 76 A ARG 77 n 83 ARG 77 A LYS 78 n 84 LYS 78 A GLU 79 n 85 GLU 79 A VAL 80 n 86 VAL 80 A TYR 81 n 87 TYR 81 A GLN 82 n 88 GLN 82 A GLN 83 n 89 GLN 83 A VAL 84 n 90 VAL 84 A SER 85 n 91 SER 85 A SER 86 n 92 SER 86 A ARG 87 n 93 ARG 87 A ILE 88 n 94 ILE 88 A MET 89 n 95 MET 89 A ASN 90 n 96 ASN 90 A LEU 91 n 97 LEU 91 A LEU 92 n 98 LEU 92 A ARG 93 n 99 ARG 93 A GLU 94 n 100 GLU 94 A TYR 95 n 101 TYR 95 A SER 96 n 102 SER 96 A GLU 97 n 103 GLU 97 A LYS 98 n 104 LYS 98 A ILE 99 n 105 ILE 99 A GLU 100 n 106 GLU 100 A ILE 101 n 107 ILE 101 A ALA 102 n 108 ALA 102 A SER 103 n 109 SER 103 A ILE 104 n 110 ILE 104 A ASP 105 n 111 ASP 105 A GLU 106 n 112 GLU 106 A ALA 107 n 113 ALA 107 A TYR 108 n 114 TYR 108 A LEU 109 n 115 LEU 109 A ASP 110 n 116 ASP 110 A ILE 111 n 117 ILE 111 A SER 112 n 118 SER 112 A ASP 113 n 119 ASP 113 A LYS 114 n 120 LYS 114 A VAL 115 n 121 VAL 115 A ARG 116 n 122 ARG 116 A ASP 117 n 123 ASP 117 A TYR 118 n 124 TYR 118 A ARG 119 n 125 ARG 119 A GLU 120 n 126 GLU 120 A ALA 121 n 127 ALA 121 A TYR 122 n 128 TYR 122 A ASN 123 n 129 ASN 123 A LEU 124 n 130 LEU 124 A GLY 125 n 131 GLY 125 A LEU 126 n 132 LEU 126 A GLU 127 n 133 GLU 127 A ILE 128 n 134 ILE 128 A LYS 129 n 135 LYS 129 A ASN 130 n 136 ASN 130 A LYS 131 n 137 LYS 131 A ILE 132 n 138 ILE 132 A LEU 133 n 139 LEU 133 A GLU 134 n 140 GLU 134 A LYS 135 n 141 LYS 135 A GLU 136 n 142 GLU 136 A LYS 137 n 143 LYS 137 A ILE 138 n 144 ILE 138 A THR 139 n 145 THR 139 A VAL 140 n 146 VAL 140 A THR 141 n 147 THR 141 A VAL 142 n 148 VAL 142 A GLY 143 n 149 GLY 143 A ILE 144 n 150 ILE 144 A SER 145 n 151 SER 145 A LYS 146 n 152 LYS 146 A ASN 147 n 153 ASN 147 A LYS 148 n 154 LYS 148 A VAL 149 n 155 VAL 149 A PHE 150 n 156 PHE 150 A ALA 151 n 157 ALA 151 A LYS 152 n 158 LYS 152 A ILE 153 n 159 ILE 153 A ALA 154 n 160 ALA 154 A ALA 155 n 161 ALA 155 A ASP 156 n 162 ASP 156 A MET 157 n 163 MET 157 A ALA 158 n 164 ALA 158 A LYS 159 n 165 LYS 159 A PRO 160 n 166 PRO 160 A ASN 161 n 167 ASN 161 A GLY 162 n 168 GLY 162 A ILE 163 n 169 ILE 163 A LYS 164 n 170 LYS 164 A VAL 165 n 171 VAL 165 A ILE 166 n 172 ILE 166 A ASP 167 n 173 ASP 167 A ASP 168 n 174 ASP 168 A GLU 169 n 175 GLU 169 A GLU 170 n 176 GLU 170 A VAL 171 n 177 VAL 171 A LYS 172 n 178 LYS 172 A ARG 173 n 179 ARG 173 A LEU 174 n 180 LEU 174 A ILE 175 n 181 ILE 175 A ARG 176 n 182 ARG 176 A GLU 177 n 183 GLU 177 A LEU 178 n 184 LEU 178 A ASP 179 n 185 ASP 179 A ILE 180 n 186 ILE 180 A ALA 181 n 187 ALA 181 A ASP 182 n 188 ASP 182 A VAL 183 n 189 VAL 183 A PRO 184 n 190 PRO 184 A GLY 185 n 191 GLY 185 A ILE 186 n 192 ILE 186 A GLY 187 n 193 GLY 187 A ASN 188 n 194 ASN 188 A ILE 189 n 195 ILE 189 A THR 190 n 196 THR 190 A ALA 191 n 197 ALA 191 A GLU 192 n 198 GLU 192 A LYS 193 n 199 LYS 193 A LEU 194 n 200 LEU 194 A LYS 195 n 201 LYS 195 A LYS 196 n 202 LYS 196 A LEU 197 n 203 LEU 197 A GLY 198 n 204 GLY 198 A ILE 199 n 205 ILE 199 A ASN 200 n 206 ASN 200 A LYS 201 n 207 LYS 201 A LEU 202 n 208 LEU 202 A VAL 203 n 209 VAL 203 A ASP 204 n 210 ASP 204 A THR 205 n 211 THR 205 A LEU 206 n 212 LEU 206 A SER 207 n 213 SER 207 A ILE 208 n 214 ILE 208 A GLU 209 n 215 GLU 209 A PHE 210 n 216 PHE 210 A ASP 211 n 217 ASP 211 A LYS 212 n 218 LYS 212 A LEU 213 n 219 LEU 213 A LYS 214 n 220 LYS 214 A GLY 215 n 221 GLY 215 A MET 216 n 222 MET 216 A ILE 217 n 223 ILE 217 A GLY 218 n 224 GLY 218 A GLU 219 n 225 GLU 219 A ALA 220 n 226 ALA 220 A LYS 221 n 227 LYS 221 A ALA 222 n 228 ALA 222 A LYS 223 n 229 LYS 223 A TYR 224 n 230 TYR 224 A LEU 225 n 231 LEU 225 A ILE 226 n 232 ILE 226 A SER 227 n 233 SER 227 A LEU 228 n 234 LEU 228 A ALA 229 n 235 ALA 229 A ARG 230 n 236 ARG 230 A ASP 231 n 237 ASP 231 A GLU 232 n 238 GLU 232 A TYR 233 n 239 TYR 233 A ASN 234 n 240 ASN 234 A GLU 235 n 241 GLU 235 A PRO 236 n 242 PRO 236 A ILE 237 n 243 ILE 237 A ARG 238 n 244 ARG 238 A THR 239 n 245 THR 239 A ARG 240 n 246 ARG 240 A VAL 241 n 247 VAL 241 A ARG 242 n 248 ARG 242 A LYS 243 n 249 LYS 243 A SER 244 n 250 SER 244 A ILE 245 n 251 ILE 245 A GLY 246 n 252 GLY 246 A ARG 247 n 253 ARG 247 A ILE 248 n 254 ILE 248 A VAL 249 n 255 VAL 249 A THR 250 n 256 THR 250 A MET 251 n 257 MET 251 A LYS 252 n 258 LYS 252 A ARG 253 n 259 ARG 253 A ASN 254 n 260 ASN 254 A SER 255 n 261 SER 255 A ARG 256 n 262 ARG 256 A ASN 257 n 263 ASN 257 A LEU 258 n 264 LEU 258 A GLU 259 n 265 GLU 259 A GLU 260 n 266 GLU 260 A ILE 261 n 267 ILE 261 A LYS 262 n 268 LYS 262 A PRO 263 n 269 PRO 263 A TYR 264 n 270 TYR 264 A LEU 265 n 271 LEU 265 A PHE 266 n 272 PHE 266 A ARG 267 n 273 ARG 267 A ALA 268 n 274 ALA 268 A ILE 269 n 275 ILE 269 A GLU 270 n 276 GLU 270 A GLU 271 n 277 GLU 271 A SER 272 n 278 SER 272 A TYR 273 n 279 TYR 273 A TYR 274 n 280 TYR 274 A LYS 275 n 281 LYS 275 A LEU 276 n 282 LEU 276 A ASP 277 n 283 ASP 277 A LYS 278 n 284 LYS 278 A ARG 279 n 285 ARG 279 A ILE 280 n 286 ILE 280 A PRO 281 n 287 PRO 281 A LYS 282 n 288 LYS 282 A ALA 283 n 289 ALA 283 A ILE 284 n 290 ILE 284 A HIS 285 n 291 HIS 285 A VAL 286 n 292 VAL 286 A VAL 287 n 293 VAL 287 A ALA 288 n 294 ALA 288 A VAL 289 n 295 VAL 289 A THR 290 n 296 THR 290 A GLU 291 n 297 GLU 291 A ASP 292 n 298 ASP 292 A LEU 293 n 299 LEU 293 A ASP 294 n 300 ASP 294 A ILE 295 n 301 ILE 295 A VAL 296 n 302 VAL 296 A SER 297 n 303 SER 297 A ARG 298 n 304 ARG 298 A GLY 299 n 305 GLY 299 A ARG 300 n 306 ARG 300 A THR 301 n 307 THR 301 A PHE 302 n 308 PHE 302 A PRO 303 n 309 PRO 303 A HIS 304 n 310 HIS 304 A GLY 305 n 311 GLY 305 A ILE 306 n 312 ILE 306 A SER 307 n 313 SER 307 A LYS 308 n 314 LYS 308 A GLU 309 n 315 GLU 309 A THR 310 n 316 THR 310 A ALA 311 n 317 ALA 311 A TYR 312 n 318 TYR 312 A SER 313 n 319 SER 313 A GLU 314 n 320 GLU 314 A SER 315 n 321 SER 315 A VAL 316 n 322 VAL 316 A LYS 317 n 323 LYS 317 A LEU 318 n 324 LEU 318 A LEU 319 n 325 LEU 319 A GLN 320 n 326 GLN 320 A LYS 321 n 327 LYS 321 A ILE 322 n 328 ILE 322 A LEU 323 n 329 LEU 323 A GLU 324 n 330 GLU 324 A GLU 325 n 331 GLU 325 A ASP 326 n 332 ASP 326 A GLU 327 n 333 GLU 327 A ARG 328 n 334 ARG 328 A LYS 329 n 335 LYS 329 A ILE 330 n 336 ILE 330 A ARG 331 n 337 ARG 331 A ARG 332 n 338 ARG 332 A ILE 333 n 339 ILE 333 A GLY 334 n 340 GLY 334 A VAL 335 n 341 VAL 335 A ARG 336 n 342 ARG 336 A PHE 337 n 343 PHE 337 A SER 338 n 344 SER 338 A LYS 339 n 345 LYS 339 A PHE 340 n 346 PHE 340 A ILE 341 n 347 ILE 341 A DT 4 n 1 DT 4 B KAG 5 n 2 KAG 5 B DG 6 n 3 DG 6 B DA 7 n 4 DA 7 B DA 8 n 5 DA 8 B DT 9 n 6 DT 9 B DC 10 n 7 DC 10 B DC 11 n 8 DC 11 B DT 12 n 9 DT 12 B DT 13 n 10 DT 13 B DC 14 n 11 DC 14 B DC 15 n 12 DC 15 B DC 16 n 13 DC 16 B DC 17 n 14 DC 17 B DC 18 n 15 DC 18 B DG 19 n 1 DG 19 C DG 20 n 2 DG 20 C DG 21 n 3 DG 21 C DG 22 n 4 DG 22 C DG 23 n 5 DG 23 C DA 24 n 6 DA 24 C DA 25 n 7 DA 25 C DG 26 n 8 DG 26 C DG 27 n 9 DG 27 C DA 28 n 10 DA 28 C DT 29 n 11 DT 29 C DT 30 n 12 DT 30 C DC 31 n 13 DC 31 C DC 32 n 14 DC 32 C author_and_software_defined_assembly PISA 3 trimeric 6070 -52 19890 A ASP 7 A OD1 ASP 13 1_555 A CA 1001 E CA CA 1_555 A PHE 8 A O PHE 14 1_555 102.6 A ASP 7 A OD1 ASP 13 1_555 A CA 1001 E CA CA 1_555 A ASP 105 A OD2 ASP 111 1_555 67.5 A PHE 8 A O PHE 14 1_555 A CA 1001 E CA CA 1_555 A ASP 105 A OD2 ASP 111 1_555 74.0 A ASP 7 A OD1 ASP 13 1_555 A CA 1001 E CA CA 1_555 A DTP 1000 D O1G DTP 1_555 118.7 A PHE 8 A O PHE 14 1_555 A CA 1001 E CA CA 1_555 A DTP 1000 D O1G DTP 1_555 137.6 A ASP 105 A OD2 ASP 111 1_555 A CA 1001 E CA CA 1_555 A DTP 1000 D O1G DTP 1_555 129.4 A ASP 7 A OD1 ASP 13 1_555 A CA 1001 E CA CA 1_555 A DTP 1000 D O1A DTP 1_555 81.1 A PHE 8 A O PHE 14 1_555 A CA 1001 E CA CA 1_555 A DTP 1000 D O1A DTP 1_555 125.9 A ASP 105 A OD2 ASP 111 1_555 A CA 1001 E CA CA 1_555 A DTP 1000 D O1A DTP 1_555 57.6 A DTP 1000 D O1G DTP 1_555 A CA 1001 E CA CA 1_555 A DTP 1000 D O1A DTP 1_555 73.3 A ASP 7 A OD1 ASP 13 1_555 A CA 1001 E CA CA 1_555 A DTP 1000 D O2B DTP 1_555 138.5 A PHE 8 A O PHE 14 1_555 A CA 1001 E CA CA 1_555 A DTP 1000 D O2B DTP 1_555 76.3 A ASP 105 A OD2 ASP 111 1_555 A CA 1001 E CA CA 1_555 A DTP 1000 D O2B DTP 1_555 72.6 A DTP 1000 D O1G DTP 1_555 A CA 1001 E CA CA 1_555 A DTP 1000 D O2B DTP 1_555 79.0 A DTP 1000 D O1A DTP 1_555 A CA 1001 E CA CA 1_555 A DTP 1000 D O2B DTP 1_555 68.0 A ALA 181 A O ALA 187 1_555 A CA 1002 F CA CA 1_555 A ILE 186 A O ILE 192 1_555 74.1 A ALA 181 A O ALA 187 1_555 A CA 1002 F CA CA 1_555 A HOH 1101 G O HOH 1_555 70.0 A ILE 186 A O ILE 192 1_555 A CA 1002 F CA CA 1_555 A HOH 1101 G O HOH 1_555 128.1 A ALA 181 A O ALA 187 1_555 A CA 1002 F CA CA 1_555 A HOH 1102 G O HOH 1_555 88.4 A ILE 186 A O ILE 192 1_555 A CA 1002 F CA CA 1_555 A HOH 1102 G O HOH 1_555 88.7 A HOH 1101 G O HOH 1_555 A CA 1002 F CA CA 1_555 A HOH 1102 G O HOH 1_555 125.5 A ALA 181 A O ALA 187 1_555 A CA 1002 F CA CA 1_555 C HOH 101 I O HOH 1_555 67.4 A ILE 186 A O ILE 192 1_555 A CA 1002 F CA CA 1_555 C HOH 101 I O HOH 1_555 65.7 A HOH 1101 G O HOH 1_555 A CA 1002 F CA CA 1_555 C HOH 101 I O HOH 1_555 66.5 A HOH 1102 G O HOH 1_555 A CA 1002 F CA CA 1_555 C HOH 101 I O HOH 1_555 148.3 B KAG 5 B KAG 2 G 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 GLU 100 A N GLU 106 A O TYR 108 A O TYR 114 A O LEU 109 A O LEU 115 A N LEU 4 A N LEU 10 A N VAL 3 A N VAL 9 A O SER 145 A O SER 151 A N ILE 144 A N ILE 150 A O LYS 164 A O LYS 170 A O THR 45 A O THR 51 A N VAL 30 A N VAL 36 A N CYS 31 A N CYS 37 A O LEU 74 A O LEU 80 A N ILE 245 A N ILE 251 A O PHE 337 A O PHE 343 A O ARG 331 A O ARG 337 A N VAL 289 A N VAL 295 A N VAL 286 A N VAL 292 A O ARG 298 A O ARG 304 1 B C1M KAG 5 B C1M KAG 2 1 Y 1 A HIS -5 A HIS 1 1 Y 1 A HIS -4 A HIS 2 1 Y 1 A HIS -3 A HIS 3 1 Y 1 A HIS -2 A HIS 4 1 Y 1 A HIS -1 A HIS 5 1 Y 1 A HIS 0 A HIS 6 1 Y 1 A B O O HOH HOH 1121 105 1.98 1 A A OE1 O GLU HOH 106 1122 2.00 1 A A O O ILE HOH 2 1123 2.05 1 A A NH2 OD1 ARG ASN 36 254 2.07 1 A B NH1 OP1 ARG DA 242 8 2.10 1 A A O1A O DTP HOH 1000 1122 2.12 1 B B O O HOH HOH 110 111 2.14 1 B B O O HOH HOH 105 106 2.15 1 A A O OG1 LEU THR 202 205 2.16 1 A A OD2 O ASP HOH 294 1116 2.18 1 A A NH2 O ARG HOH 267 1111 2.18 1 A A N O ILE HOH 111 1123 2.19 1 A B O O HOH HOH 1121 104 2.19 1 -16.88 2.20 105.20 88.32 B B B O3' P OP2 DT KAG KAG 4 5 5 Y 1 23.75 1.10 110.50 134.25 B B B O3' P OP1 DT KAG KAG 4 5 5 Y 1 -6.77 0.80 109.40 102.63 B B B O5' C5' C4' DG DG DG 6 6 6 N 1 -6.79 1.00 110.10 103.31 B B B C1' O4' C4' DA DA DA 7 7 7 N 1 -4.86 0.80 102.40 97.54 B B B C3' C2' C1' DA DA DA 7 7 7 N 1 -7.81 0.80 105.90 98.09 B B B O4' C1' C2' DA DA DA 7 7 7 N 1 5.73 0.30 108.30 114.03 B B B O4' C1' N9 DA DA DA 7 7 7 N 1 -5.44 0.70 108.00 102.56 B B B O4' C1' N9 DA DA DA 8 8 8 N 1 4.64 0.30 108.30 112.94 B B B O4' C1' N1 DC DC DC 11 11 11 N 1 3.90 0.60 119.90 123.80 B B B N3 C4 O4 DT DT DT 12 12 12 N 1 -2.81 0.40 104.50 101.69 B B B O4' C4' C3' DC DC DC 15 15 15 N 1 -7.35 1.00 110.10 102.75 B B B C1' O4' C4' DC DC DC 15 15 15 N 1 5.79 0.30 108.30 114.09 B B B O4' C1' N1 DC DC DC 17 17 17 N 1 -6.32 0.80 102.40 96.08 B B B C3' C2' C1' DC DC DC 18 18 18 N 1 3.23 0.30 108.30 111.53 C C C O4' C1' N9 DG DG DG 21 21 21 N 1 3.91 0.30 108.30 112.21 C C C O4' C1' N9 DG DG DG 22 22 22 N 1 -5.91 0.80 109.40 103.49 C C C O5' C5' C4' DA DA DA 24 24 24 N 1 6.04 0.30 108.30 114.34 C C C O4' C1' N1 DC DC DC 31 31 31 N 1 7.69 0.30 108.30 115.99 C C C O4' C1' N1 DC DC DC 32 32 32 N 1 B B O3' C3' DG DG 6 6 -0.037 0.006 1.419 1.382 N 1 A TYR 10 24.12 51.52 1 A ASN 20 -165.30 78.40 1 A ARG 36 -72.65 -80.43 1 A LEU 68 -118.71 63.12 1 A ARG 93 -56.09 -9.61 1 A ASP 105 -143.09 12.58 1 A ASP 113 -64.88 10.21 1 A ASP 117 -173.13 -173.54 1 A SER 145 -166.42 -161.96 1 A ASN 161 45.26 23.63 1 A ASP 231 30.96 53.60 1 A GLU 232 -141.89 12.47 1 A ASN 234 -158.73 45.24 1 A ASP 277 53.16 86.94 127.780 71.5388 45.960 14.4796 0.0000 0.0000 3.7151 -0.0000 -18.1947 0.2700 0.1920 0.2000 2.9500 34.9100 1118 11170 10.0100 98.1000 1.000 0.000 0.8100 1 1.360 MOLECULAR REPLACEMENT 29.0500 0.8600 1.1000 2BQU ML FLAT BULK SOLVENT MODEL 37.1600 0.3200 2.9500 34.9100 44 3415 32 595 2744 0.009 1.3 0.4542 0.3007 3.0844 125 1123 1248 8 90.0000 0.3177 0.2469 3.2469 133 1203 1336 8 96.0000 0.3197 0.2071 3.4502 139 1252 1391 8 100.0000 0.2916 0.1949 3.7163 141 1258 1399 8 100.0000 0.2716 0.1823 4.0898 141 1270 1411 8 100.0000 0.2230 0.1459 4.6804 142 1289 1431 8 100.0000 0.2150 0.1752 5.8922 144 1296 1440 8 100.0000 0.2709 0.2010 34.9077 153 1361 1514 8 100.0000 2.950 50.000 4JV0 11170 0.000 0.124 1 0.565 2.9 3.0 1 refinement Paul D. Adams PDAdams@lbl.gov C++ http://www.phenix-online.org/ PHENIX package 1.7.2_869 data extraction PDB deposit@deposit.rcsb.org April 22, 2011 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.11 data reduction HKL-2000 data scaling HKL-2000 phasing CNS Ring-Opening of the -OH-PdG Adduct in Ternary Complexes with the Sulfolobus solfataricus DNA polymerase Dpo4 1 N N 2 N N 3 N N 4 N N 5 N N 5 N N 6 N N 6 N N 6 N N A TYR 10 A TYR 16 HELX_P A LEU 19 A LEU 25 1 1 10 A ASN 20 A ASN 26 HELX_P A LYS 24 A LYS 30 5 2 5 A ASN 47 A ASN 53 HELX_P A LYS 52 A LYS 58 1 3 6 A PRO 60 A PRO 66 HELX_P A LEU 68 A LEU 74 1 4 9 A ARG 77 A ARG 83 HELX_P A ARG 93 A ARG 99 1 5 17 A ASP 117 A ASP 123 HELX_P A LYS 137 A LYS 143 1 6 21 A ASN 147 A ASN 153 HELX_P A LYS 159 A LYS 165 1 7 13 A ASP 167 A ASP 173 HELX_P A LEU 178 A LEU 184 1 8 12 A ASP 179 A ASP 185 HELX_P A VAL 183 A VAL 189 5 9 5 A GLY 187 A GLY 193 HELX_P A LYS 196 A LYS 202 1 10 10 A LYS 201 A LYS 207 HELX_P A LEU 206 A LEU 212 5 11 6 A GLU 209 A GLU 215 HELX_P A GLY 218 A GLY 224 1 12 10 A GLY 218 A GLY 224 HELX_P A ARG 230 A ARG 236 1 13 13 A ASN 257 A ASN 263 HELX_P A ASP 277 A ASP 283 1 14 21 A SER 307 A SER 313 HELX_P A ASP 326 A ASP 332 1 15 20 covale 1.615 both B DT 4 B O3' DT 1 1_555 B KAG 5 B P KAG 2 1_555 covale 1.600 both B KAG 5 B O3' KAG 2 1_555 B DG 6 B P DG 3 1_555 metalc 2.879 A ASP 7 A OD1 ASP 13 1_555 A CA 1001 E CA CA 1_555 metalc 2.670 A PHE 8 A O PHE 14 1_555 A CA 1001 E CA CA 1_555 metalc 2.690 A ASP 105 A OD2 ASP 111 1_555 A CA 1001 E CA CA 1_555 metalc 2.887 A ALA 181 A O ALA 187 1_555 A CA 1002 F CA CA 1_555 metalc 2.876 A ILE 186 A O ILE 192 1_555 A CA 1002 F CA CA 1_555 metalc 2.835 A DTP 1000 D O1G DTP 1_555 A CA 1001 E CA CA 1_555 metalc 2.843 A DTP 1000 D O1A DTP 1_555 A CA 1001 E CA CA 1_555 metalc 2.883 A DTP 1000 D O2B DTP 1_555 A CA 1001 E CA CA 1_555 metalc 2.975 A CA 1002 F CA CA 1_555 A HOH 1101 G O HOH 1_555 metalc 3.089 A CA 1002 F CA CA 1_555 A HOH 1102 G O HOH 1_555 metalc 2.950 A CA 1002 F CA CA 1_555 C HOH 101 I O HOH 1_555 hydrog WATSON-CRICK B KAG 5 B N1 KAG 2 1_555 C DC 32 C N3 DC 14 1_555 hydrog WATSON-CRICK B KAG 5 B N2 KAG 2 1_555 C DC 32 C O2 DC 14 1_555 hydrog WATSON-CRICK B KAG 5 B O6 KAG 2 1_555 C DC 32 C N4 DC 14 1_555 hydrog WATSON-CRICK B DG 6 B N1 DG 3 1_555 C DC 31 C N3 DC 13 1_555 hydrog WATSON-CRICK B DG 6 B N2 DG 3 1_555 C DC 31 C O2 DC 13 1_555 hydrog WATSON-CRICK B DG 6 B O6 DG 3 1_555 C DC 31 C N4 DC 13 1_555 hydrog WATSON-CRICK B DA 7 B N1 DA 4 1_555 C DT 30 C N3 DT 12 1_555 hydrog WATSON-CRICK B DA 7 B N6 DA 4 1_555 C DT 30 C O4 DT 12 1_555 hydrog WATSON-CRICK B DA 8 B N1 DA 5 1_555 C DT 29 C N3 DT 11 1_555 hydrog WATSON-CRICK B DA 8 B N6 DA 5 1_555 C DT 29 C O4 DT 11 1_555 hydrog WATSON-CRICK B DT 9 B N3 DT 6 1_555 C DA 28 C N1 DA 10 1_555 hydrog WATSON-CRICK B DT 9 B O4 DT 6 1_555 C DA 28 C N6 DA 10 1_555 hydrog WATSON-CRICK B DC 10 B N3 DC 7 1_555 C DG 27 C N1 DG 9 1_555 hydrog WATSON-CRICK B DC 10 B N4 DC 7 1_555 C DG 27 C O6 DG 9 1_555 hydrog WATSON-CRICK B DC 10 B O2 DC 7 1_555 C DG 27 C N2 DG 9 1_555 hydrog WATSON-CRICK B DC 11 B N3 DC 8 1_555 C DG 26 C N1 DG 8 1_555 hydrog WATSON-CRICK B DC 11 B N4 DC 8 1_555 C DG 26 C O6 DG 8 1_555 hydrog WATSON-CRICK B DC 11 B O2 DC 8 1_555 C DG 26 C N2 DG 8 1_555 hydrog WATSON-CRICK B DT 12 B N3 DT 9 1_555 C DA 25 C N1 DA 7 1_555 hydrog WATSON-CRICK B DT 12 B O4 DT 9 1_555 C DA 25 C N6 DA 7 1_555 hydrog WATSON-CRICK B DT 13 B N3 DT 10 1_555 C DA 24 C N1 DA 6 1_555 hydrog WATSON-CRICK B DT 13 B O4 DT 10 1_555 C DA 24 C N6 DA 6 1_555 hydrog WATSON-CRICK B DC 14 B N3 DC 11 1_555 C DG 23 C N1 DG 5 1_555 hydrog WATSON-CRICK B DC 14 B N4 DC 11 1_555 C DG 23 C O6 DG 5 1_555 hydrog WATSON-CRICK B DC 14 B O2 DC 11 1_555 C DG 23 C N2 DG 5 1_555 hydrog WATSON-CRICK B DC 15 B N3 DC 12 1_555 C DG 22 C N1 DG 4 1_555 hydrog WATSON-CRICK B DC 15 B N4 DC 12 1_555 C DG 22 C O6 DG 4 1_555 hydrog WATSON-CRICK B DC 15 B O2 DC 12 1_555 C DG 22 C N2 DG 4 1_555 hydrog WATSON-CRICK B DC 16 B N3 DC 13 1_555 C DG 21 C N1 DG 3 1_555 hydrog WATSON-CRICK B DC 16 B N4 DC 13 1_555 C DG 21 C O6 DG 3 1_555 hydrog WATSON-CRICK B DC 16 B O2 DC 13 1_555 C DG 21 C N2 DG 3 1_555 hydrog WATSON-CRICK B DC 17 B N3 DC 14 1_555 C DG 20 C N1 DG 2 1_555 hydrog WATSON-CRICK B DC 17 B N4 DC 14 1_555 C DG 20 C O6 DG 2 1_555 hydrog WATSON-CRICK B DC 17 B O2 DC 14 1_555 C DG 20 C N2 DG 2 1_555 hydrog WATSON-CRICK B DC 18 B N3 DC 15 1_555 C DG 19 C N1 DG 1 1_555 hydrog WATSON-CRICK B DC 18 B N4 DC 15 1_555 C DG 19 C O6 DG 1 1_555 hydrog WATSON-CRICK B DC 18 B O2 DC 15 1_555 C DG 19 C N2 DG 1 1_555 TRANSFERASE/DNA TERNARY COMPLEX OF DPO4-DNA-DATP, DNA POLYMERASE, DNA ADDUCT, TRANSFERASE-DNA COMPLEX A LYS 159 A LYS 165 1 A PRO 160 A PRO 166 1.81 DPO4_SULSO UNP 1 1 Q97W02 MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEV YQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKP NGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTR VRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQ KILEEDERKIRRIGVRFSKFI 4JV0 PDB 2 4JV0 4JV0 PDB 3 4JV0 1 341 4JV0 1 341 Q97W02 A 1 7 347 4 18 4JV0 4 18 4JV0 B 2 1 15 19 32 4JV0 19 32 4JV0 C 3 1 14 1 expression tag HIS -5 4JV0 A Q97W02 UNP 1 1 expression tag HIS -4 4JV0 A Q97W02 UNP 2 1 expression tag HIS -3 4JV0 A Q97W02 UNP 3 1 expression tag HIS -2 4JV0 A Q97W02 UNP 4 1 expression tag HIS -1 4JV0 A Q97W02 UNP 5 1 expression tag HIS 0 4JV0 A Q97W02 UNP 6 5 3 4 anti-parallel anti-parallel anti-parallel parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel A ILE 99 A ILE 105 A ILE 101 A ILE 107 A GLU 106 A GLU 112 A ASP 110 A ASP 116 A VAL 3 A VAL 9 A PHE 8 A PHE 14 A VAL 140 A VAL 146 A SER 145 A SER 151 A ILE 163 A ILE 169 A VAL 165 A VAL 171 A GLY 41 A GLY 47 A ALA 46 A ALA 52 A VAL 28 A VAL 34 A PHE 33 A PHE 39 A VAL 72 A VAL 78 A PRO 75 A PRO 81 A SER 244 A SER 250 A SER 255 A SER 261 A ILE 330 A ILE 336 A PHE 340 A PHE 346 A PRO 281 A PRO 287 A THR 290 A THR 296 A ILE 295 A ILE 301 A THR 301 A THR 307 BINDING SITE FOR RESIDUE DTP A 1000 A DTP 1000 Software 16 BINDING SITE FOR RESIDUE CA A 1001 A CA 1001 Software 4 BINDING SITE FOR RESIDUE CA A 1002 A CA 1002 Software 5 A PHE 8 A PHE 14 16 1_555 A ASP 9 A ASP 15 16 1_555 A TYR 10 A TYR 16 16 1_555 A PHE 11 A PHE 17 16 1_555 A TYR 12 A TYR 18 16 1_555 A ALA 44 A ALA 50 16 1_555 A THR 45 A THR 51 16 1_555 A TYR 48 A TYR 54 16 1_555 A ARG 51 A ARG 57 16 1_555 A ASP 105 A ASP 111 16 1_555 A LYS 159 A LYS 165 16 1_555 A CA 1001 E CA 16 1_555 A HOH 1122 G HOH 16 1_555 B DT 4 B DT 1 16 1_555 B KAG 5 B KAG 2 16 1_555 C DC 32 C DC 14 16 1_555 A ASP 7 A ASP 13 4 1_555 A PHE 8 A PHE 14 4 1_555 A ASP 105 A ASP 111 4 1_555 A DTP 1000 D DTP 4 1_555 A ALA 181 A ALA 187 5 1_555 A ILE 186 A ILE 192 5 1_555 A HOH 1101 G HOH 5 1_555 A HOH 1102 G HOH 5 1_555 C HOH 101 I HOH 5 1_555 18 P 21 21 2