ID code: '2LBJ' 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' G A 1 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' G A 3 alpha beta 73 96 79 76 112 C1' C A 4 alpha beta 107 127 113 110 143 C1' C A 5 alpha beta 138 158 144 141 174 C1' U A 6 alpha beta 169 189 175 172 204 C1' U A 7 alpha beta 199 219 205 202 234 C1' G A 8 alpha beta 229 252 235 232 268 C1' C A 9 alpha beta 263 283 269 266 299 C1' C A 10 alpha beta 294 314 300 297 330 C1' A A 11 alpha beta 325 347 331 328 363 C1' A A 12 alpha beta 358 380 364 361 396 C1' G A 13 alpha beta 391 414 397 394 430 C1' G A 14 alpha beta 425 448 431 428 464 C1' U A 15 alpha beta 459 479 465 462 494 C1' C A 16 alpha beta 489 509 495 492 525 C1' C A 17 alpha beta 520 541 526 523 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' G A 3 OK OK 78 74 94 77 110 C2' C A 4 OK OK 112 108 125 111 141 C2' C A 5 OK OK 143 139 156 142 172 C2' U A 6 OK OK 174 170 187 173 202 C2' U A 7 OK OK 204 200 217 203 232 C2' G A 8 OK OK 234 230 250 233 266 C2' C A 9 OK OK 268 264 281 267 297 C2' C A 10 OK OK 299 295 312 298 328 C2' A A 11 OK OK 330 326 345 329 361 C2' A A 12 OK OK 363 359 378 362 394 C2' G A 13 OK OK 396 392 412 395 428 C2' G A 14 OK OK 430 426 446 429 462 C2' U A 15 OK OK 464 460 477 463 492 C2' C A 16 OK OK 494 490 507 493 523 C2' C A 17 OK OK 525 521 539 524 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' G A 3 OK OK 72 93 75 76 108 C3' C A 4 OK OK 106 124 109 110 139 C3' C A 5 OK OK 137 155 140 141 170 C3' U A 6 OK OK 168 186 171 172 200 C3' U A 7 OK OK 198 216 201 202 230 C3' G A 8 OK OK 228 249 231 232 264 C3' C A 9 OK OK 262 280 265 266 295 C3' C A 10 OK OK 293 311 296 297 326 C3' A A 11 OK OK 324 344 327 328 359 C3' A A 12 OK OK 357 377 360 361 392 C3' G A 13 OK OK 390 411 393 394 426 C3' G A 14 OK OK 424 445 427 428 460 C3' U A 15 OK OK 458 476 461 462 490 C3' C A 16 OK OK 488 506 491 492 521 C3' C A 17 OK OK 519 537 522 523 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' G A 3 OK OK 74 92 71 73 106 C4' C A 4 OK OK 108 123 105 107 137 C4' C A 5 OK OK 139 154 136 138 168 C4' U A 6 OK OK 170 185 167 169 198 C4' U A 7 OK OK 200 215 197 199 228 C4' G A 8 OK OK 230 248 227 229 262 C4' C A 9 OK OK 264 279 261 263 293 C4' C A 10 OK OK 295 310 292 294 324 C4' A A 11 OK OK 326 343 323 325 357 C4' A A 12 OK OK 359 376 356 358 390 C4' G A 13 OK OK 392 410 389 391 424 C4' G A 14 OK OK 426 444 423 425 458 C4' U A 15 OK OK 460 475 457 459 488 C4' C A 16 OK OK 490 505 487 489 519 C4' C A 17 OK OK 521 536 518 520 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' G A 3 OK OK 70 90 91 72 105 C5' C A 4 OK OK 104 121 122 106 136 C5' C A 5 OK OK 135 152 153 137 167 C5' U A 6 OK OK 166 183 184 168 197 C5' U A 7 OK OK 196 213 214 198 227 C5' G A 8 OK OK 226 246 247 228 261 C5' C A 9 OK OK 260 277 278 262 292 C5' C A 10 OK OK 291 308 309 293 323 C5' A A 11 OK OK 322 341 342 324 356 C5' A A 12 OK OK 355 374 375 357 389 C5' G A 13 OK OK 388 408 409 390 423 C5' G A 14 OK OK 422 442 443 424 457 C5' U A 15 OK OK 456 473 474 458 487 C5' C A 16 OK OK 486 503 504 488 518 C5' C A 17 OK OK 517 534 535 519 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P G A 3 distorted distorted 41 68 69 70 101 P C A 4 distorted distorted 75 102 103 104 132 P C A 5 distorted distorted 109 133 134 135 163 P U A 6 distorted distorted 140 164 165 166 193 P U A 7 distorted distorted 171 194 195 196 223 P G A 8 distorted distorted 201 224 225 226 257 P C A 9 distorted distorted 231 258 259 260 288 P C A 10 distorted distorted 265 289 290 291 319 P A A 11 distorted distorted 296 320 321 322 352 P A A 12 distorted distorted 327 353 354 355 385 P G A 13 distorted distorted 360 386 387 388 419 P G A 14 distorted distorted 393 420 421 422 453 P U A 15 distorted distorted 427 454 455 456 483 P C A 16 distorted distorted 461 484 485 486 514 P C A 17 distorted distorted 491 515 516 517 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