ID code: '1BZU' 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' U A 27 alpha beta 4 24 10 7 40 C1' C A 28 alpha beta 35 55 41 38 71 C1' A A 29 alpha beta 66 88 72 69 104 C1' G A 30 alpha beta 99 122 105 102 138 C1' A A 31 alpha beta 133 155 139 136 171 C1' C A 32 alpha beta 166 186 172 169 202 C1' U A 33 alpha beta 197 217 203 200 232 C1' U A 34 alpha beta 227 247 233 230 262 C1' U A 35 alpha beta 257 277 263 260 292 C1' U A 36 alpha beta 287 307 293 290 322 C1' A A 37 alpha beta 317 339 323 320 355 C1' A A 38 alpha beta 350 372 356 353 385 C1' PSU A 39 alpha beta 391 400 381 386 418 C1' C A 40 alpha beta 413 433 419 416 449 C1' U A 41 alpha beta 444 464 450 447 479 C1' G A 42 alpha beta 474 497 480 477 513 C1' A A 43 alpha beta 508 531 514 511 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U A 27 OK OK 9 5 22 8 38 C2' C A 28 OK OK 40 36 53 39 69 C2' A A 29 OK OK 71 67 86 70 102 C2' G A 30 OK OK 104 100 120 103 136 C2' A A 31 OK OK 138 134 153 137 169 C2' C A 32 OK OK 171 167 184 170 200 C2' U A 33 OK OK 202 198 215 201 230 C2' U A 34 OK OK 232 228 245 231 260 C2' U A 35 OK OK 262 258 275 261 290 C2' U A 36 OK OK 292 288 305 291 320 C2' A A 37 OK OK 322 318 337 321 353 C2' A A 38 OK OK 355 351 370 354 386 C2' PSU A 39 OK OK 385 388 401 387 416 C2' C A 40 OK OK 418 414 431 417 447 C2' U A 41 OK OK 449 445 462 448 477 C2' G A 42 OK OK 479 475 495 478 511 C2' A A 43 OK OK 513 509 529 512 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U A 27 OK OK 3 21 6 7 36 C3' C A 28 OK OK 34 52 37 38 67 C3' A A 29 OK OK 65 85 68 69 100 C3' G A 30 OK OK 98 119 101 102 134 C3' A A 31 OK OK 132 152 135 136 167 C3' C A 32 OK OK 165 183 168 169 198 C3' U A 33 OK OK 196 214 199 200 228 C3' U A 34 OK OK 226 244 229 230 258 C3' U A 35 OK OK 256 274 259 260 288 C3' U A 36 OK OK 286 304 289 290 318 C3' A A 37 OK OK 316 336 319 320 351 C3' A A 38 OK OK 349 369 352 353 388 C3' PSU A 39 OK OK 389 403 390 386 414 C3' C A 40 OK OK 412 430 415 416 445 C3' U A 41 OK OK 443 461 446 447 475 C3' G A 42 OK OK 473 494 476 477 509 C3' A A 43 OK OK 507 527 510 511 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U A 27 OK OK 5 20 2 4 34 C4' C A 28 OK OK 36 51 33 35 65 C4' A A 29 OK OK 67 84 64 66 98 C4' G A 30 OK OK 100 118 97 99 132 C4' A A 31 OK OK 134 151 131 133 165 C4' C A 32 OK OK 167 182 164 166 196 C4' U A 33 OK OK 198 213 195 197 226 C4' U A 34 OK OK 228 243 225 227 256 C4' U A 35 OK OK 258 273 255 257 286 C4' U A 36 OK OK 288 303 285 287 316 C4' A A 37 OK OK 318 335 315 317 349 C4' A A 38 OK OK 351 368 348 350 389 C4' PSU A 39 OK OK 388 404 392 391 412 C4' C A 40 OK OK 414 429 411 413 443 C4' U A 41 OK OK 445 460 442 444 473 C4' G A 42 OK OK 475 493 472 474 507 C4' A A 43 OK OK 509 526 506 508 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U A 27 OK OK 1 18 19 3 33 C5' C A 28 OK OK 32 49 50 34 64 C5' A A 29 OK OK 63 82 83 65 97 C5' G A 30 OK OK 96 116 117 98 131 C5' A A 31 OK OK 130 149 150 132 164 C5' C A 32 OK OK 163 180 181 165 195 C5' U A 33 OK OK 194 211 212 196 225 C5' U A 34 OK OK 224 241 242 226 255 C5' U A 35 OK OK 254 271 272 256 285 C5' U A 36 OK OK 284 301 302 286 315 C5' A A 37 OK OK 314 333 334 316 348 C5' A A 38 OK OK 347 366 367 349 392 C5' PSU A 39 OK OK 393 405 406 389 411 C5' C A 40 OK OK 410 427 428 412 442 C5' U A 41 OK OK 441 458 459 443 472 C5' G A 42 OK OK 471 491 492 473 506 C5' A A 43 OK OK 505 524 525 507 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 29 P C A 28 distorted distorted 6 30 31 32 60 P A A 29 distorted distorted 37 61 62 63 93 P G A 30 distorted distorted 68 94 95 96 127 P A A 31 distorted distorted 101 128 129 130 160 P C A 32 distorted distorted 135 161 162 163 191 P U A 33 distorted distorted 168 192 193 194 221 P U A 34 distorted distorted 199 222 223 224 251 P U A 35 distorted distorted 229 252 253 254 281 P U A 36 distorted distorted 259 282 283 284 311 P A A 37 distorted distorted 289 312 313 314 344 P A A 38 distorted distorted 319 345 346 347 394 P PSU A 39 distorted distorted 352 395 396 393 407 P C A 40 distorted distorted 390 408 409 410 438 P U A 41 distorted distorted 415 439 440 441 468 P G A 42 distorted distorted 446 469 470 471 502 P A A 43 distorted distorted 476 503 504 505 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