ID code: '1LUX' CHIRALITY (03 Nov 1998) Checks the chirality and the naming of substituents of chiral and prochiral centers in nucleic acid structures. The molecular structure is read from a PDB file. Only the first model is evaluated. ---------------------------------------------------------- Center Reference for correct naming ---------------------------------------------------------- C1' alpha/beta nomenclature of anomeric sugars, base in beta position in natural nucleosids. C2' IUPAC. 1983. Eur J Biochem, 131: 9-15. C3' IUPAC. 1983. Eur J Biochem, 131: 9-15. C4' IUPAC. 1983. Eur J Biochem, 131: 9-15. C5' IUPAC. 1983. Eur J Biochem, 131: 9-15. P Brookhaven PDB entry '1BNA', O1P -> major groove, O2P -> minor groove. ---------------------------------------------------------- Author: Peter Slickers (slickers@imb-jena.de) Biocomputing, IMB Jena, Germany --------------------------------------------------------------------------------- Seq No Atom Residue H1' base O4' H1' base C2' --------------------------------------------------------------------------------- 9 C1' C A 27 alpha beta 4 24 10 7 41 C1' C A 28 alpha beta 36 56 42 39 72 C1' A A 29 alpha beta 67 89 73 70 105 C1' G A 30 alpha beta 100 123 106 103 139 C1' A A 31 alpha beta 134 156 140 137 169 C1' OMC A 32 alpha beta 175 186 161 170 206 C1' U A 33 alpha beta 201 221 207 204 237 C1' OMG A 34 alpha beta 231 257 238 234 273 C1' A A 35 alpha beta 268 290 274 271 306 C1' A A 36 alpha beta 301 323 307 304 339 C1' G A 37 alpha beta 334 357 340 337 373 C1' A A 38 alpha beta 368 391 374 371 407 C1' U A 39 alpha beta 402 422 408 405 437 C1' 5MC A 40 alpha beta 432 453 438 435 471 C1' U A 41 alpha beta 466 486 472 469 501 C1' G A 42 alpha beta 496 519 502 499 535 C1' G A 43 alpha beta 530 554 536 533 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 27 OK OK 9 5 22 8 39 C2' C A 28 OK OK 41 37 54 40 70 C2' A A 29 OK OK 72 68 87 71 103 C2' G A 30 OK OK 105 101 121 104 137 C2' A A 31 OK OK 139 135 154 138 170 C2' OMC A 32 OK OK 169 173 187 171 204 C2' U A 33 OK OK 206 202 219 205 234 C2' OMG A 34 OK OK 237 232 253 235 271 C2' A A 35 OK OK 273 269 288 272 304 C2' A A 36 OK OK 306 302 321 305 337 C2' G A 37 OK OK 339 335 355 338 371 C2' A A 38 OK OK 373 369 389 372 405 C2' U A 39 OK OK 407 403 420 406 435 C2' 5MC A 40 OK OK 437 433 451 436 469 C2' U A 41 OK OK 471 467 484 470 499 C2' G A 42 OK OK 501 497 517 500 533 C2' G A 43 OK OK 535 531 552 534 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 27 OK OK 3 21 6 7 37 C3' C A 28 OK OK 35 53 38 39 68 C3' A A 29 OK OK 66 86 69 70 101 C3' G A 30 OK OK 99 120 102 103 135 C3' A A 31 OK OK 133 153 136 137 173 C3' OMC A 32 OK OK 174 191 176 170 202 C3' U A 33 OK OK 200 218 203 204 232 C3' OMG A 34 OK OK 230 252 233 234 269 C3' A A 35 OK OK 267 287 270 271 302 C3' A A 36 OK OK 300 320 303 304 335 C3' G A 37 OK OK 333 354 336 337 369 C3' A A 38 OK OK 367 388 370 371 403 C3' U A 39 OK OK 401 419 404 405 433 C3' 5MC A 40 OK OK 431 450 434 435 467 C3' U A 41 OK OK 465 483 468 469 497 C3' G A 42 OK OK 495 516 498 499 531 C3' G A 43 OK OK 529 550 532 533 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 27 OK OK 5 20 2 4 35 C4' C A 28 OK OK 37 52 34 36 66 C4' A A 29 OK OK 68 85 65 67 99 C4' G A 30 OK OK 101 119 98 100 133 C4' A A 31 OK OK 135 152 132 134 174 C4' OMC A 32 OK OK 173 192 177 175 200 C4' U A 33 OK OK 202 217 199 201 230 C4' OMG A 34 OK OK 232 251 229 231 267 C4' A A 35 OK OK 269 286 266 268 300 C4' A A 36 OK OK 302 319 299 301 333 C4' G A 37 OK OK 335 353 332 334 367 C4' A A 38 OK OK 369 387 366 368 401 C4' U A 39 OK OK 403 418 400 402 431 C4' 5MC A 40 OK OK 433 449 430 432 465 C4' U A 41 OK OK 467 482 464 466 495 C4' G A 42 OK OK 497 515 494 496 529 C4' G A 43 OK OK 531 549 528 530 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 27 OK OK 1 18 19 3 34 C5' C A 28 OK OK 33 50 51 35 65 C5' A A 29 OK OK 64 83 84 66 98 C5' G A 30 OK OK 97 117 118 99 132 C5' A A 31 OK OK 131 150 151 133 177 C5' OMC A 32 OK OK 178 193 194 174 199 C5' U A 33 OK OK 198 215 216 200 229 C5' OMG A 34 OK OK 228 249 250 230 266 C5' A A 35 OK OK 265 284 285 267 299 C5' A A 36 OK OK 298 317 318 300 332 C5' G A 37 OK OK 331 351 352 333 366 C5' A A 38 OK OK 365 385 386 367 400 C5' U A 39 OK OK 399 416 417 401 430 C5' 5MC A 40 OK OK 429 447 448 431 464 C5' U A 41 OK OK 463 480 481 465 494 C5' G A 42 OK OK 493 513 514 495 528 C5' G A 43 OK OK 527 547 548 529 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 30 P C A 28 distorted distorted 6 31 32 33 61 P A A 29 distorted distorted 38 62 63 64 94 P G A 30 distorted distorted 69 95 96 97 128 P A A 31 distorted distorted 102 129 130 131 179 P OMC A 32 distorted distorted 136 180 181 178 195 P U A 33 distorted distorted 176 196 197 198 225 P OMG A 34 distorted distorted 203 226 227 228 262 P A A 35 distorted distorted 233 263 264 265 295 P A A 36 distorted distorted 270 296 297 298 328 P G A 37 distorted distorted 303 329 330 331 362 P A A 38 distorted distorted 336 363 364 365 396 P U A 39 distorted distorted 370 397 398 399 426 P 5MC A 40 distorted distorted 404 427 428 429 460 P U A 41 distorted distorted 434 461 462 463 490 P G A 42 distorted distorted 468 491 492 493 524 P G A 43 distorted distorted 498 525 526 527 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