0.009727 0.005616 0.000000 0.000000 0.011232 0.000000 0.000000 0.000000 0.015554 0.00000 0.00000 0.00000 Bunting, K.A. Roe, S.M. Headley, A. Brown, T. Savva, R. Pearl, L.H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.00 90.00 120.00 102.805 102.805 64.290 C10 H16 N3 O7 P 321.224 n 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE DNA linking C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O7 P 347.221 y 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking 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 Zn 2 65.409 ZINC ION non-polymer 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 N N 39 S C N 40 N C N 41 N O N 42 N C N 43 N O N 44 N H N 45 N H N 46 N H N 47 N H N 48 N H N 49 N H N 50 N H N 51 N N N 52 S C N 53 N C N 54 N O N 55 N C N 56 N C N 57 N C N 58 N N N 59 N C N 60 N N N 61 N N N 62 N O 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 H N 77 N H N 78 N N N 79 S C N 80 N C N 81 N O N 82 N C N 83 N C N 84 N O N 85 N N N 86 N O N 87 N H N 88 N H 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 N N 96 S C N 97 N C N 98 N O N 99 N C N 100 N C N 101 N O N 102 N O N 103 N O N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N N N 112 R C N 113 N C N 114 N O N 115 N C N 116 N S N 117 N O 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 Y 137 N N Y 138 N C Y 139 N N Y 140 N C Y 141 N C N 142 N N Y 143 N N Y 144 N C Y 145 N N Y 146 N C 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 H N 160 N H N 161 N O N 162 N P N 163 N O N 164 N O N 165 N O N 166 N C N 167 R C N 168 N O N 169 S C N 170 N O N 171 N C N 172 R C N 173 N N N 174 N C N 175 N O N 176 N N N 177 N C N 178 N N N 179 N C N 180 N C N 181 N H 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 O N 196 N P N 197 N O N 198 N O N 199 N O N 200 N C N 201 R C N 202 N O N 203 S C N 204 N O N 205 N C N 206 R C Y 207 N N Y 208 N C Y 209 N N Y 210 N C N 211 N C N 212 N O N 213 N N N 214 N C N 215 N N N 216 N N Y 217 N C 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 O N 233 N P N 234 N O N 235 N O N 236 N O N 237 N C N 238 R C N 239 N O N 240 S C N 241 N O N 242 N C N 243 R C N 244 N N N 245 N C N 246 N O N 247 N N N 248 N C N 249 N O N 250 N C N 251 N C N 252 N C N 253 N H N 254 N H N 255 N H N 256 N H N 257 N H N 258 N H N 259 N H N 260 N H N 261 N H N 262 N H N 263 N H N 264 N H N 265 N H N 266 N H N 267 N H N 268 N N N 269 S C N 270 N C N 271 N O N 272 N C N 273 N C N 274 N C N 275 N O N 276 N N N 277 N O 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 H 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 N C N 293 N C N 294 N C N 295 N O N 296 N O N 297 N O 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 N N 308 N C N 309 N C N 310 N O N 311 N O 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 S C N 319 N C N 320 N O N 321 N C Y 322 N C Y 323 N N Y 324 N C Y 325 N C Y 326 N N N 327 N O N 328 N H N 329 N H N 330 N H N 331 N H N 332 N H N 333 N H N 334 N H N 335 N H N 336 N H N 337 N H N 338 N O N 339 N H N 340 N H N 341 N N N 342 S C N 343 N C N 344 N O N 345 S C N 346 N C N 347 N C N 348 N C N 349 N O N 350 N H N 351 N H N 352 N H N 353 N H N 354 N H N 355 N H N 356 N H N 357 N H N 358 N H N 359 N H N 360 N H N 361 N H N 362 N H N 363 N N N 364 S C N 365 N C N 366 N O N 367 N C N 368 N C N 369 N C N 370 N C N 371 N O N 372 N H N 373 N H N 374 N H N 375 N H N 376 N H N 377 N H N 378 N H N 379 N H N 380 N H N 381 N H N 382 N H N 383 N H N 384 N H N 385 N N N 386 S C N 387 N C N 388 N O N 389 N C N 390 N C N 391 N C N 392 N C N 393 N N N 394 N O N 395 N H N 396 N H N 397 N H N 398 N H N 399 N H N 400 N H N 401 N H N 402 N H N 403 N H N 404 N H N 405 N H N 406 N H N 407 N H N 408 N H N 409 N H N 410 N N N 411 S C N 412 N C N 413 N O N 414 N C Y 415 N C Y 416 N C Y 417 N C Y 418 N C Y 419 N C Y 420 N C N 421 N O N 422 N H N 423 N H N 424 N H N 425 N H N 426 N H N 427 N H N 428 N H N 429 N H N 430 N H N 431 N H N 432 N H N 433 N N N 434 S C N 435 N C N 436 N O N 437 N C N 438 N C N 439 N C N 440 N O N 441 N H N 442 N H N 443 N H N 444 N H N 445 N H N 446 N H N 447 N H N 448 N H N 449 N H N 450 N N N 451 S C N 452 N C N 453 N O N 454 N C N 455 N O N 456 N O N 457 N H N 458 N H N 459 N H N 460 N H N 461 N H N 462 N H N 463 N H N 464 N N N 465 S C N 466 N C N 467 N O N 468 R C N 469 N O N 470 N C N 471 N O N 472 N H N 473 N H N 474 N H N 475 N H N 476 N H N 477 N H N 478 N H N 479 N H N 480 N H N 481 N N N 482 S C N 483 N C N 484 N O N 485 N C Y 486 N C Y 487 N C Y 488 N C Y 489 N N Y 490 N C Y 491 N C Y 492 N C Y 493 N C Y 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 H N 506 N H N 507 N H N 508 N N N 509 S C N 510 N C N 511 N O N 512 N C Y 513 N C Y 514 N C Y 515 N C Y 516 N C Y 517 N C Y 518 N C N 519 N O N 520 N O N 521 N H N 522 N H N 523 N H N 524 N H N 525 N H N 526 N H N 527 N H N 528 N H N 529 N H N 530 N H N 531 N H N 532 N N N 533 S C N 534 N C N 535 N O N 536 N C N 537 N C N 538 N C N 539 N O N 540 N H N 541 N H N 542 N H N 543 N H N 544 N H N 545 N H N 546 N H N 547 N H N 548 N H N 549 N H N 550 N H N 551 N ZN 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 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 sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N doub 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 doub 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 doub N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N doub 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 doub N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N doub 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 doub 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 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 Y 144 N sing Y 145 N sing Y 146 N doub N 147 N sing Y 148 N sing Y 149 N sing Y 150 N doub N 151 N sing Y 152 N doub N 153 N sing N 154 N sing Y 155 N sing Y 156 N doub N 157 N sing Y 158 N sing N 159 N sing N 160 N sing N 161 N doub 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 N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N doub N 185 N sing 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 doub 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 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 Y 217 N sing Y 218 N sing Y 219 N doub N 220 N sing Y 221 N sing N 222 N sing Y 223 N doub N 224 N doub 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 sing N 232 N sing N 233 N sing N 234 N sing N 235 N doub N 236 N sing N 237 N sing N 238 N sing N 239 N sing N 240 N sing N 241 N sing N 242 N sing N 243 N 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 doub N 259 N sing N 260 N sing N 261 N sing N 262 N doub N 263 N sing N 264 N sing N 265 N doub N 266 N sing N 267 N sing N 268 N sing N 269 N sing N 270 N sing N 271 N sing N 272 N sing N 273 N sing N 274 N sing N 275 N sing N 276 N doub N 277 N sing N 278 N sing N 279 N sing N 280 N sing N 281 N sing N 282 N sing N 283 N sing N 284 N doub 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 doub 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 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 doub N 323 N sing N 324 N sing N 325 N sing N 326 N sing Y 327 N sing Y 328 N doub Y 329 N doub N 330 N sing Y 331 N sing N 332 N sing Y 333 N sing N 334 N sing N 335 N sing N 336 N sing N 337 N sing N 338 N sing N 339 N sing N 340 N sing N 341 N sing N 342 N sing N 343 N sing N 344 N sing N 345 N doub N 346 N sing N 347 N sing N 348 N sing N 349 N sing N 350 N sing N 351 N sing N 352 N sing N 353 N sing N 354 N sing N 355 N sing N 356 N sing N 357 N sing N 358 N sing N 359 N sing N 360 N sing N 361 N sing N 362 N sing N 363 N sing N 364 N sing N 365 N sing N 366 N doub N 367 N sing N 368 N sing N 369 N sing N 370 N sing N 371 N sing N 372 N sing N 373 N sing N 374 N sing N 375 N sing N 376 N sing N 377 N sing N 378 N sing N 379 N sing N 380 N sing N 381 N sing N 382 N sing N 383 N sing N 384 N sing N 385 N sing N 386 N sing N 387 N doub N 388 N sing N 389 N sing N 390 N sing N 391 N sing N 392 N sing N 393 N sing N 394 N sing N 395 N sing N 396 N sing N 397 N sing N 398 N sing N 399 N sing N 400 N sing N 401 N sing N 402 N sing N 403 N sing N 404 N sing N 405 N sing N 406 N sing N 407 N sing N 408 N sing N 409 N sing N 410 N sing N 411 N doub N 412 N sing N 413 N sing N 414 N sing N 415 N sing Y 416 N doub Y 417 N sing Y 418 N sing N 419 N sing Y 420 N doub N 421 N sing Y 422 N doub N 423 N sing Y 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 doub 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 sing N 448 N sing N 449 N sing N 450 N sing N 451 N doub N 452 N sing N 453 N sing N 454 N sing N 455 N sing N 456 N sing N 457 N sing N 458 N sing N 459 N sing N 460 N sing N 461 N sing N 462 N sing N 463 N sing N 464 N doub N 465 N sing N 466 N sing N 467 N sing N 468 N sing N 469 N sing N 470 N sing N 471 N sing N 472 N sing N 473 N sing N 474 N sing N 475 N sing N 476 N sing N 477 N sing N 478 N sing N 479 N sing N 480 N doub N 481 N sing N 482 N sing N 483 N sing N 484 N sing Y 485 N doub Y 486 N sing Y 487 N sing N 488 N sing Y 489 N doub Y 490 N sing Y 491 N sing N 492 N sing Y 493 N sing Y 494 N doub N 495 N sing Y 496 N doub N 497 N sing Y 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 sing N 506 N sing N 507 N sing N 508 N doub N 509 N sing N 510 N sing N 511 N sing N 512 N sing Y 513 N doub Y 514 N sing Y 515 N sing N 516 N sing Y 517 N doub N 518 N sing Y 519 N doub N 520 N sing Y 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 doub 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 sing UK Nucleic Acids Res. NARHAD 0389 0305-1048 31 1633 10.1093/NAR/GKG273 12626704 Crystal Structure of the Escherichia Coli Dcm Very-Short-Patch DNA Repair Endonuclease Bound to its Reaction Product-Site in a DNA Superhelix 2003 10.2210/pdb1odg/pdb pdb_00001odg 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100.0 1 CCD 2000-02-15 ADSC CCD SINGLE WAVELENGTH M x-ray 1 0.933 1.0 ID14-2 ESRF 0.933 SYNCHROTRON ESRF BEAMLINE ID14-2 15568.826 DNA MISMATCH ENDONUCLEASE 1 man polymer 3692.430 5'-D(*TP*AP*GP*GP*CP*5CM*TP*GP*GP*AP*TP*CP)-3' 2 nat polymer 65.409 ZINC ION 1 syn non-polymer 18.015 water 81 nat water VERY SHORT PATCH REPAIR PROTEIN, VSR MISMATCH ENDONUCLEASE, V.ECOKDCM, VSR, B1960 no no AIEKRLASLLTGQGLAFRVQDASLPGRPDFVVDEYRCVIFTHGCFWHHHHCYLFKVPATRTEFWLEKIGKNVERDRRDIS RLQELGWRVLIVWECALRGREKLTDEALTERLEEWICGEGASAQIDTQGIHLLA AIEKRLASLLTGQGLAFRVQDASLPGRPDFVVDEYRCVIFTHGCFWHHHHCYLFKVPATRTEFWLEKIGKNVERDRRDIS RLQELGWRVLIVWECALRGREKLTDEALTERLEEWICGEGASAQIDTQGIHLLA A polypeptide(L) no yes (DT)(DA)(DG)(DG)(DC)(5CM)(DT)(DG)(DG)(DA)(DT)(DC) TAGGCCTGGATC F,W 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 sample 562 ESCHERICHIA COLI 562 ESCHERICHIA COLI B834 (DE3) PET28 sample 562 ESCHERICHIA COLI 1 4.20 70.70 6.50 25 MM HEPES PH7.0, 75 MM NACL, 15% PEG 8000, 50 MM SODIUM CACODYLATE PH 6.5, 75 MM AMMONIUM SULPHATE AND 10% GLYCEROL PROTEIN 2.5 MG/ML -7.450 1 28 F 1 W 8 9.952 F_DT1:DG8_W 1 -10.118 1.554 0.386 -0.193 6.422 3 23 F 2 W 7 80.840 F_DA2:DT7_W 2 0.246 -0.104 -0.292 -2.331 -0.965 1 19 F 3 W 6 -2.869 F_DG3:5CM6_W 3 -3.328 0.188 -0.313 -0.257 -11.245 1 19 F 4 W 5 -3.955 F_DG4:DC5_W 4 0.221 -0.066 -0.636 -0.222 -11.620 1 19 F 5 W 4 -4.376 F_DC5:DG4_W 5 -3.061 -0.041 -0.188 -0.292 -12.545 1 19 F 6 W 3 0.756 F_5CM6:DG3_W 6 -3.145 0.186 0.250 -0.261 -1.498 3 23 F 7 W 2 -73.645 F_DT7:DA2_W 7 -9.764 0.172 0.095 2.699 0.444 1 28 F 8 W 1 -3.554 F_DG8:DT1_W 8 -5.310 -2.060 0.344 -0.598 0.766 -177.794 F F 1 2 11.573 W W 8 7 0.515 -23.105 -0.603 3.053 FF_DT1DA2:DT7DG8_WW 1 170.215 85.257 -148.858 -1.515 -0.215 -0.639 -179.256 F F 2 3 -54.145 W W 7 6 -0.371 108.251 0.842 3.711 FF_DA2DG3:5CM6DT7_WW 2 -138.241 -69.145 -160.600 -1.829 0.455 2.955 35.239 F F 3 4 23.978 W W 6 5 3.557 14.125 -0.636 -0.891 FF_DG3DG4:DC55CM6_WW 3 -1.874 3.181 32.314 -3.659 0.761 3.051 31.818 F F 4 5 12.608 W W 5 4 3.412 6.857 -0.116 -1.359 FF_DG4DC5:DG4DC5_WW 4 -1.796 3.302 31.039 -3.733 -0.117 3.246 34.891 F F 5 6 14.432 W W 4 3 3.454 8.569 0.802 -0.528 FF_DC55CM6:DG3DG4_WW 5 0.825 -1.390 33.844 -2.233 -1.208 3.089 76.666 F F 6 7 1.821 W W 3 2 2.995 2.258 2.348 -1.266 FF_5CM6DT7:DA2DG3_WW 6 5.040 -4.065 76.497 -1.082 -1.756 3.934 -58.333 F F 7 8 56.024 W W 2 1 7.355 -46.408 0.067 -0.073 FF_DT7DG8:DT1DA2_WW 7 -19.492 -23.530 -30.495 5.914 -2.383 chem_comp_atom chem_comp_bond database_2 pdbx_database_status pdbx_initial_refinement_model pdbx_struct_conn_angle struct_conn struct_conn_type struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Other Refinement description 1 0 2003-03-13 1 1 2011-05-08 1 2 2011-07-13 1 3 2023-12-13 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.status_code_sf _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_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.conn_type_id _struct_conn.id _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn_type.id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id CRYSTAL STRUCTURE ANALYSIS OF VERY SHORT PATCH REPAIR (VSR) ENDONUCLEASE IN COMPLEX WITH A DUPLEX DEOXYRIBONUCLEIC ACID VERY SHORT PATCH REPAIR (VSR) ENDONUCLEASE FROM ESCHERICHIA COLI PDBE Y PDBE 2003-02-19 REL REL ZN ZINC ION HOH water FUNCTIONS IN THE DEAMINATION OF 5-METHYLCYTOSINE IN DNA CAUSING MISMATCHES IN T/G WHICH CAN LEAD TO C-TO-T TRANSITION MUTATIONS IF UNREPAIRED. 1CW0 PDB ENTRY 1CW0 PDB experimental model ZN 200 3 ZN ZN 200 A HOH 2001 4 HOH HOH 2001 A HOH 2002 4 HOH HOH 2002 A HOH 2003 4 HOH HOH 2003 A HOH 2004 4 HOH HOH 2004 A HOH 2005 4 HOH HOH 2005 A HOH 2006 4 HOH HOH 2006 A HOH 2007 4 HOH HOH 2007 A HOH 2008 4 HOH HOH 2008 A HOH 2009 4 HOH HOH 2009 A HOH 2010 4 HOH HOH 2010 A HOH 2011 4 HOH HOH 2011 A HOH 2012 4 HOH HOH 2012 A HOH 2013 4 HOH HOH 2013 A HOH 2014 4 HOH HOH 2014 A HOH 2015 4 HOH HOH 2015 A HOH 2016 4 HOH HOH 2016 A HOH 2017 4 HOH HOH 2017 A HOH 2018 4 HOH HOH 2018 A HOH 2019 4 HOH HOH 2019 A HOH 2020 4 HOH HOH 2020 A HOH 2021 4 HOH HOH 2021 A HOH 2022 4 HOH HOH 2022 A HOH 2023 4 HOH HOH 2023 A HOH 2024 4 HOH HOH 2024 A HOH 2025 4 HOH HOH 2025 A HOH 2026 4 HOH HOH 2026 A HOH 2027 4 HOH HOH 2027 A HOH 2028 4 HOH HOH 2028 A HOH 2029 4 HOH HOH 2029 A HOH 2030 4 HOH HOH 2030 A HOH 2031 4 HOH HOH 2031 A HOH 2032 4 HOH HOH 2032 A HOH 2033 4 HOH HOH 2033 A HOH 2034 4 HOH HOH 2034 A HOH 2001 4 HOH HOH 2001 F HOH 2002 4 HOH HOH 2002 F HOH 2003 4 HOH HOH 2003 F HOH 2004 4 HOH HOH 2004 F HOH 2005 4 HOH HOH 2005 F HOH 2006 4 HOH HOH 2006 F HOH 2007 4 HOH HOH 2007 F HOH 2008 4 HOH HOH 2008 F HOH 2009 4 HOH HOH 2009 F HOH 2010 4 HOH HOH 2010 F HOH 2011 4 HOH HOH 2011 F HOH 2012 4 HOH HOH 2012 F HOH 2013 4 HOH HOH 2013 F HOH 2014 4 HOH HOH 2014 F HOH 2015 4 HOH HOH 2015 F HOH 2016 4 HOH HOH 2016 F HOH 2017 4 HOH HOH 2017 F HOH 2018 4 HOH HOH 2018 F HOH 2019 4 HOH HOH 2019 F HOH 2020 4 HOH HOH 2020 F HOH 2021 4 HOH HOH 2021 F HOH 2022 4 HOH HOH 2022 F HOH 2023 4 HOH HOH 2023 F HOH 2024 4 HOH HOH 2024 F HOH 2025 4 HOH HOH 2025 F HOH 2026 4 HOH HOH 2026 F HOH 2027 4 HOH HOH 2027 F HOH 2001 4 HOH HOH 2001 W HOH 2002 4 HOH HOH 2002 W HOH 2003 4 HOH HOH 2003 W HOH 2004 4 HOH HOH 2004 W HOH 2005 4 HOH HOH 2005 W HOH 2006 4 HOH HOH 2006 W HOH 2007 4 HOH HOH 2007 W HOH 2008 4 HOH HOH 2008 W HOH 2009 4 HOH HOH 2009 W HOH 2010 4 HOH HOH 2010 W HOH 2011 4 HOH HOH 2011 W HOH 2012 4 HOH HOH 2012 W HOH 2013 4 HOH HOH 2013 W HOH 2014 4 HOH HOH 2014 W HOH 2015 4 HOH HOH 2015 W HOH 2016 4 HOH HOH 2016 W HOH 2017 4 HOH HOH 2017 W HOH 2018 4 HOH HOH 2018 W HOH 2019 4 HOH HOH 2019 W HOH 2020 4 HOH HOH 2020 W ALA 23 n 1 ALA 23 A ILE 24 n 2 ILE 24 A GLU 25 n 3 GLU 25 A LYS 26 n 4 LYS 26 A ARG 27 n 5 ARG 27 A LEU 28 n 6 LEU 28 A ALA 29 n 7 ALA 29 A SER 30 n 8 SER 30 A LEU 31 n 9 LEU 31 A LEU 32 n 10 LEU 32 A THR 33 n 11 THR 33 A GLY 34 n 12 GLY 34 A GLN 35 n 13 GLN 35 A GLY 36 n 14 GLY 36 A LEU 37 n 15 LEU 37 A ALA 38 n 16 ALA 38 A PHE 39 n 17 PHE 39 A ARG 40 n 18 ARG 40 A VAL 41 n 19 VAL 41 A GLN 42 n 20 GLN 42 A ASP 43 n 21 ASP 43 A ALA 44 n 22 ALA 44 A SER 45 n 23 SER 45 A LEU 46 n 24 LEU 46 A PRO 47 n 25 PRO 47 A GLY 48 n 26 GLY 48 A ARG 49 n 27 ARG 49 A PRO 50 n 28 PRO 50 A ASP 51 n 29 ASP 51 A PHE 52 n 30 PHE 52 A VAL 53 n 31 VAL 53 A VAL 54 n 32 VAL 54 A ASP 55 n 33 ASP 55 A GLU 56 n 34 GLU 56 A TYR 57 n 35 TYR 57 A ARG 58 n 36 ARG 58 A CYS 59 n 37 CYS 59 A VAL 60 n 38 VAL 60 A ILE 61 n 39 ILE 61 A PHE 62 n 40 PHE 62 A THR 63 n 41 THR 63 A HIS 64 n 42 HIS 64 A GLY 65 n 43 GLY 65 A CYS 66 n 44 CYS 66 A PHE 67 n 45 PHE 67 A TRP 68 n 46 TRP 68 A HIS 69 n 47 HIS 69 A HIS 70 n 48 HIS 70 A HIS 71 n 49 HIS 71 A HIS 72 n 50 HIS 72 A CYS 73 n 51 CYS 73 A TYR 74 n 52 TYR 74 A LEU 75 n 53 LEU 75 A PHE 76 n 54 PHE 76 A LYS 77 n 55 LYS 77 A VAL 78 n 56 VAL 78 A PRO 79 n 57 PRO 79 A ALA 80 n 58 ALA 80 A THR 81 n 59 THR 81 A ARG 82 n 60 ARG 82 A THR 83 n 61 THR 83 A GLU 84 n 62 GLU 84 A PHE 85 n 63 PHE 85 A TRP 86 n 64 TRP 86 A LEU 87 n 65 LEU 87 A GLU 88 n 66 GLU 88 A LYS 89 n 67 LYS 89 A ILE 90 n 68 ILE 90 A GLY 91 n 69 GLY 91 A LYS 92 n 70 LYS 92 A ASN 93 n 71 ASN 93 A VAL 94 n 72 VAL 94 A GLU 95 n 73 GLU 95 A ARG 96 n 74 ARG 96 A ASP 97 n 75 ASP 97 A ARG 98 n 76 ARG 98 A ARG 99 n 77 ARG 99 A ASP 100 n 78 ASP 100 A ILE 101 n 79 ILE 101 A SER 102 n 80 SER 102 A ARG 103 n 81 ARG 103 A LEU 104 n 82 LEU 104 A GLN 105 n 83 GLN 105 A GLU 106 n 84 GLU 106 A LEU 107 n 85 LEU 107 A GLY 108 n 86 GLY 108 A TRP 109 n 87 TRP 109 A ARG 110 n 88 ARG 110 A VAL 111 n 89 VAL 111 A LEU 112 n 90 LEU 112 A ILE 113 n 91 ILE 113 A VAL 114 n 92 VAL 114 A TRP 115 n 93 TRP 115 A GLU 116 n 94 GLU 116 A CYS 117 n 95 CYS 117 A ALA 118 n 96 ALA 118 A LEU 119 n 97 LEU 119 A ARG 120 n 98 ARG 120 A GLY 121 n 99 GLY 121 A ARG 122 n 100 ARG 122 A GLU 123 n 101 GLU 123 A LYS 124 n 102 LYS 124 A LEU 125 n 103 LEU 125 A THR 126 n 104 THR 126 A ASP 127 n 105 ASP 127 A GLU 128 n 106 GLU 128 A ALA 129 n 107 ALA 129 A LEU 130 n 108 LEU 130 A THR 131 n 109 THR 131 A GLU 132 n 110 GLU 132 A ARG 133 n 111 ARG 133 A LEU 134 n 112 LEU 134 A GLU 135 n 113 GLU 135 A GLU 136 n 114 GLU 136 A TRP 137 n 115 TRP 137 A ILE 138 n 116 ILE 138 A CYS 139 n 117 CYS 139 A GLY 140 n 118 GLY 140 A GLU 141 n 119 GLU 141 A GLY 142 n 120 GLY 142 A ALA 143 n 121 ALA 143 A SER 144 n 122 SER 144 A ALA 145 n 123 ALA 145 A GLN 146 n 124 GLN 146 A ILE 147 n 125 ILE 147 A ASP 148 n 126 ASP 148 A THR 149 n 127 THR 149 A GLN 150 n 128 GLN 150 A GLY 151 n 129 GLY 151 A ILE 152 n 130 ILE 152 A HIS 153 n 131 HIS 153 A LEU 154 n 132 LEU 154 A LEU 155 n 133 LEU 155 A ALA 156 n 134 ALA 156 A DT 1 n 1 DT 1 F DA 2 n 2 DA 2 F DG 3 n 3 DG 3 F DG 4 n 4 DG 4 F DC 5 n 5 DC 5 F 5CM 6 n 6 5CM 6 F DT 7 n 7 DT 7 F DG 8 n 8 DG 8 F DG 9 n 9 DG 9 F DA 10 n 10 DA 10 F DT 11 n 11 DT 11 F DC 12 n 12 DC 12 F DT 1 n 1 DT 1 W DA 2 n 2 DA 2 W DG 3 n 3 DG 3 W DG 4 n 4 DG 4 W DC 5 n 5 DC 5 W 5CM 6 n 6 5CM 6 W DT 7 n 7 DT 7 W DG 8 n 8 DG 8 W DG 9 n 9 DG 9 W DA 10 n 10 DA 10 W DT 11 n 11 DT 11 W DC 12 n 12 DC 12 W author_and_software_defined_assembly PQS 3 trimeric A CYS 66 A SG CYS 44 1_555 A ZN 200 D ZN ZN 1_555 A HIS 71 A ND1 HIS 49 1_555 113.7 A CYS 66 A SG CYS 44 1_555 A ZN 200 D ZN ZN 1_555 A CYS 73 A SG CYS 51 1_555 99.1 A HIS 71 A ND1 HIS 49 1_555 A ZN 200 D ZN ZN 1_555 A CYS 73 A SG CYS 51 1_555 124.2 A CYS 66 A SG CYS 44 1_555 A ZN 200 D ZN ZN 1_555 A CYS 117 A SG CYS 95 1_555 104.2 A HIS 71 A ND1 HIS 49 1_555 A ZN 200 D ZN ZN 1_555 A CYS 117 A SG CYS 95 1_555 100.1 A CYS 73 A SG CYS 51 1_555 A ZN 200 D ZN ZN 1_555 A CYS 117 A SG CYS 95 1_555 114.5 F 5CM 6 B 5CM 6 DC W 5CM 6 C 5CM 6 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 ARG 40 A N ARG 18 A O VAL 53 A O VAL 31 A N VAL 54 A N VAL 32 A O CYS 59 A O CYS 37 A N VAL 60 A N VAL 38 A O ARG 110 A O ARG 88 A N ILE 113 A N ILE 91 A O ALA 145 A O ALA 123 A N ASP 148 A N ASP 126 A O GLY 151 A O GLY 129 1 A CG LYS 77 A CG LYS 55 1 Y 1 A CD LYS 77 A CD LYS 55 1 Y 1 A CE LYS 77 A CE LYS 55 1 Y 1 A NZ LYS 77 A NZ LYS 55 1 Y 1 A F O O HOH HOH 2014 2017 2.13 1 F DG 8 0.065 SIDE CHAIN 1 F DG 9 0.054 SIDE CHAIN 1 F F P OP3 DT DT 1 1 -0.085 0.012 1.607 1.522 N 1 W W P OP3 DT DT 1 1 -0.091 0.012 1.607 1.516 N 1 A ILE 24 -152.07 -22.59 1 A ARG 27 -31.57 -39.33 1 A LEU 37 -4.33 117.32 1 A GLN 42 20.72 85.71 1 A PRO 47 -49.51 155.89 1 A ARG 49 26.45 78.26 1 A PRO 50 -47.20 169.74 1 A TYR 57 -155.85 0.13 1 A THR 63 -117.93 75.98 1 A HIS 70 39.24 66.50 1 A CYS 117 -46.86 -18.66 1 A LEU 119 -148.53 -0.61 1 A ARG 122 -76.05 47.95 1 A GLU 123 -173.87 -3.81 1 A ASP 127 -44.81 -15.26 1 A ALA 129 -34.05 -35.64 1 A LEU 130 -63.90 -70.74 1 A TRP 137 -92.86 -99.98 1 A ILE 138 -7.46 -63.26 1 A GLU 141 47.60 174.26 PROTEIN_REP.PARAM PROTEIN.TOP LHP_DNA-RNA.PARAM LHP_DNA-RNA.TOP WATER_REP.PARAM WATER.TOP ION.PARAM ION.TOP -15.190 -6.172 0.0 -15.190 0.0 30.380 0.3561 0.2873 0.2873 2.8 24.7 923 9535 10.0 98.7 RANDOM 1 RESTRAINED THROUGHOUT 0.0 MOLECULAR REPLACEMENT PDB ENTRY 1CW0 FLAT MODEL 74.25 0.318 2.8 24.7 81 1672 1 498 1092 0.008265 1.30641 1.372 1.5 2.381 2.0 2.325 2.0 3.963 2.5 105 2.750 50.000 1ODG 10084 0.07000 1 6.9000 4.900 99.0 0.38400 2.75 2.90 2.000 1 5.00 100.0 refinement CNS 1.0 data reduction MOSFLM data scaling SCALA phasing AMoRE Very-short-patch DNA repair endonuclease bound to its reaction product site 1 N N 2 N N 2 N N 3 N N 4 N N 4 N N 4 N N THE TRIMERIC ASSEMBLY DESCRIBED HERE IS FORMED BYTHE COMPLEX OF PROTEIN CHAIN A WITH DNA CHAINS F,W A ILE 24 A ILE 2 HELX_P A THR 33 A THR 11 1 1 10 A GLY 34 A GLY 12 HELX_P A GLY 36 A GLY 14 5 2 3 A ARG 82 A ARG 60 HELX_P A LEU 107 A LEU 85 1 3 26 A GLU 116 A GLU 94 HELX_P A LEU 119 A LEU 97 5 4 4 A THR 126 A THR 104 HELX_P A CYS 139 A CYS 117 1 5 14 covale 1.610 both F DC 5 B O3' DC 5 1_555 F 5CM 6 B P 5CM 6 1_555 covale 1.615 both F 5CM 6 B O3' 5CM 6 1_555 F DT 7 B P DT 7 1_555 covale 1.614 both W DC 5 C O3' DC 5 1_555 W 5CM 6 C P 5CM 6 1_555 covale 1.620 both W 5CM 6 C O3' 5CM 6 1_555 W DT 7 C P DT 7 1_555 metalc 2.145 A CYS 66 A SG CYS 44 1_555 A ZN 200 D ZN ZN 1_555 metalc 1.859 A HIS 71 A ND1 HIS 49 1_555 A ZN 200 D ZN ZN 1_555 metalc 1.948 A CYS 73 A SG CYS 51 1_555 A ZN 200 D ZN ZN 1_555 metalc 2.508 A CYS 117 A SG CYS 95 1_555 A ZN 200 D ZN ZN 1_555 hydrog TYPE_28_PAIR F DT 1 B N3 DT 1 1_555 W DG 8 C O6 DG 8 1_555 hydrog TYPE_28_PAIR F DT 1 B O2 DT 1 1_555 W DG 8 C N1 DG 8 1_555 hydrog HOOGSTEEN F DA 2 B N6 DA 2 1_555 W DT 7 C O4 DT 7 1_555 hydrog HOOGSTEEN F DA 2 B N7 DA 2 1_555 W DT 7 C N3 DT 7 1_555 hydrog WATSON-CRICK F DG 3 B N1 DG 3 1_555 W 5CM 6 C N3 5CM 6 1_555 hydrog WATSON-CRICK F DG 3 B N2 DG 3 1_555 W 5CM 6 C O2 5CM 6 1_555 hydrog WATSON-CRICK F DG 3 B O6 DG 3 1_555 W 5CM 6 C N4 5CM 6 1_555 hydrog WATSON-CRICK F DG 4 B N1 DG 4 1_555 W DC 5 C N3 DC 5 1_555 hydrog WATSON-CRICK F DG 4 B N2 DG 4 1_555 W DC 5 C O2 DC 5 1_555 hydrog WATSON-CRICK F DG 4 B O6 DG 4 1_555 W DC 5 C N4 DC 5 1_555 hydrog WATSON-CRICK F DC 5 B N3 DC 5 1_555 W DG 4 C N1 DG 4 1_555 hydrog WATSON-CRICK F DC 5 B N4 DC 5 1_555 W DG 4 C O6 DG 4 1_555 hydrog WATSON-CRICK F DC 5 B O2 DC 5 1_555 W DG 4 C N2 DG 4 1_555 hydrog WATSON-CRICK F 5CM 6 B N3 5CM 6 1_555 W DG 3 C N1 DG 3 1_555 hydrog WATSON-CRICK F 5CM 6 B N4 5CM 6 1_555 W DG 3 C O6 DG 3 1_555 hydrog WATSON-CRICK F 5CM 6 B O2 5CM 6 1_555 W DG 3 C N2 DG 3 1_555 hydrog HOOGSTEEN F DT 7 B N3 DT 7 1_555 W DA 2 C N7 DA 2 1_555 hydrog HOOGSTEEN F DT 7 B O4 DT 7 1_555 W DA 2 C N6 DA 2 1_555 hydrog TYPE_28_PAIR F DG 8 B N1 DG 8 1_555 W DT 1 C O2 DT 1 1_555 hydrog TYPE_28_PAIR F DG 8 B O6 DG 8 1_555 W DT 1 C N3 DT 1 1_555 HYDROLASE HYDROLASE, DNA REPAIR, ENDONUCLEASE, VERY SHORT PATCH REPAIR, DNA REPAI HYDROLASE, NUCLEASE, ZINC, METAL-BINDING VSR_ECOLI UNP 1 P09184 1ODG PDB 2 1ODG 22 155 1ODG 23 156 P09184 A 1 1 134 1 12 1ODG 1 12 1ODG F 2 1 12 1 12 1ODG 1 12 1ODG W 2 1 12 6 anti-parallel anti-parallel parallel parallel anti-parallel A PHE 39 A PHE 17 A VAL 41 A VAL 19 A PHE 52 A PHE 30 A VAL 54 A VAL 32 A CYS 59 A CYS 37 A PHE 62 A PHE 40 A ARG 110 A ARG 88 A VAL 114 A VAL 92 A ALA 145 A ALA 123 A ASP 148 A ASP 126 A GLY 151 A GLY 129 A LEU 154 A LEU 132 BINDING SITE FOR RESIDUE ZN A 200 A ZN 200 Software 4 A CYS 66 A CYS 44 4 1_555 A HIS 71 A HIS 49 4 1_555 A CYS 73 A CYS 51 4 1_555 A CYS 117 A CYS 95 4 1_555 169 P 61