ID code: '2KRY' 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' PSU A 1 alpha beta 15 21 5 10 39 C1' C A 2 alpha beta 34 54 40 37 70 C1' G A 3 alpha beta 65 88 71 68 104 C1' G A 4 alpha beta 99 122 105 102 138 C1' G A 5 alpha beta 133 156 139 136 172 C1' C A 6 alpha beta 167 187 173 170 203 C1' C A 7 alpha beta 198 218 204 201 232 C1' RSQ A 8 alpha beta 240 247 224 234 267 C1' A A 9 alpha beta 262 284 268 265 300 C1' U A 10 alpha beta 295 315 301 298 330 C1' A A 11 alpha beta 325 347 331 328 363 C1' C A 12 alpha beta 358 378 364 361 394 C1' C A 13 alpha beta 389 409 395 392 425 C1' C A 14 alpha beta 420 440 426 423 456 C1' C A 15 alpha beta 451 471 457 454 487 C1' G A 16 alpha beta 482 505 488 485 521 C1' A A 17 alpha beta 516 539 522 519 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' PSU A 1 OK OK 9 12 22 11 37 C2' C A 2 OK OK 39 35 52 38 68 C2' G A 3 OK OK 70 66 86 69 102 C2' G A 4 OK OK 104 100 120 103 136 C2' G A 5 OK OK 138 134 154 137 170 C2' C A 6 OK OK 172 168 185 171 201 C2' C A 7 OK OK 203 199 216 202 234 C2' RSQ A 8 OK OK 232 236 248 235 265 C2' A A 9 OK OK 267 263 282 266 298 C2' U A 10 OK OK 300 296 313 299 328 C2' A A 11 OK OK 330 326 345 329 361 C2' C A 12 OK OK 363 359 376 362 392 C2' C A 13 OK OK 394 390 407 393 423 C2' C A 14 OK OK 425 421 438 424 454 C2' C A 15 OK OK 456 452 469 455 485 C2' G A 16 OK OK 487 483 503 486 519 C2' A A 17 OK OK 521 517 537 520 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 12 C3' PSU A 1 OK OK 13 24 14 10 35 C3' C A 2 OK OK 33 51 36 37 66 C3' G A 3 OK OK 64 85 67 68 100 C3' G A 4 OK OK 98 119 101 102 134 C3' G A 5 OK OK 132 153 135 136 168 C3' C A 6 OK OK 166 184 169 170 199 C3' C A 7 OK OK 197 215 200 201 236 C3' RSQ A 8 OK OK 239 251 237 234 263 C3' A A 9 OK OK 261 281 264 265 296 C3' U A 10 OK OK 294 312 297 298 326 C3' A A 11 OK OK 324 344 327 328 359 C3' C A 12 OK OK 357 375 360 361 390 C3' C A 13 OK OK 388 406 391 392 421 C3' C A 14 OK OK 419 437 422 423 452 C3' C A 15 OK OK 450 468 453 454 483 C3' G A 16 OK OK 481 502 484 485 517 C3' A A 17 OK OK 515 535 518 519 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 13 C4' PSU A 1 OK OK 12 25 16 15 33 C4' C A 2 OK OK 35 50 32 34 64 C4' G A 3 OK OK 66 84 63 65 98 C4' G A 4 OK OK 100 118 97 99 132 C4' G A 5 OK OK 134 152 131 133 166 C4' C A 6 OK OK 168 183 165 167 197 C4' C A 7 OK OK 199 214 196 198 239 C4' RSQ A 8 OK OK 236 252 241 240 261 C4' A A 9 OK OK 263 280 260 262 294 C4' U A 10 OK OK 296 311 293 295 324 C4' A A 11 OK OK 326 343 323 325 357 C4' C A 12 OK OK 359 374 356 358 388 C4' C A 13 OK OK 390 405 387 389 419 C4' C A 14 OK OK 421 436 418 420 450 C4' C A 15 OK OK 452 467 449 451 481 C4' G A 16 OK OK 483 501 480 482 515 C4' A A 17 OK OK 517 534 514 516 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 16 C5' PSU A 1 OK OK 17 26 27 13 32 C5' C A 2 OK OK 31 48 49 33 63 C5' G A 3 OK OK 62 82 83 64 97 C5' G A 4 OK OK 96 116 117 98 131 C5' G A 5 OK OK 130 150 151 132 165 C5' C A 6 OK OK 164 181 182 166 196 C5' C A 7 OK OK 195 212 213 197 241 C5' RSQ A 8 242 239 260 C5' A A 9 OK OK 259 278 279 261 293 C5' U A 10 OK OK 292 309 310 294 323 C5' A A 11 OK OK 322 341 342 324 356 C5' C A 12 OK OK 355 372 373 357 387 C5' C A 13 OK OK 386 403 404 388 418 C5' C A 14 OK OK 417 434 435 419 449 C5' C A 15 OK OK 448 465 466 450 480 C5' G A 16 OK OK 479 499 500 481 514 C5' A A 17 OK OK 513 532 533 515 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 28 P C A 2 distorted distorted 14 29 30 31 59 P G A 3 distorted distorted 36 60 61 62 93 P G A 4 distorted distorted 67 94 95 96 127 P G A 5 distorted distorted 101 128 129 130 161 P C A 6 distorted distorted 135 162 163 164 192 P C A 7 distorted distorted 169 193 194 195 223 P RSQ A 8 OK OK 200 243 244 242 256 P A A 9 distorted distorted 237 257 258 259 289 P U A 10 distorted distorted 264 290 291 292 319 P A A 11 distorted distorted 297 320 321 322 352 P C A 12 distorted distorted 327 353 354 355 383 P C A 13 distorted distorted 360 384 385 386 414 P C A 14 distorted distorted 391 415 416 417 445 P C A 15 distorted distorted 422 446 447 448 476 P G A 16 distorted distorted 453 477 478 479 510 P A A 17 distorted distorted 484 511 512 513 ---------------------------------------------------------------------------------