ID code: '2KD4' 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' C A 2 alpha beta 39 59 45 42 75 C1' C A 3 alpha beta 70 90 76 73 106 C1' G A 4 alpha beta 101 124 107 104 140 C1' C A 5 alpha beta 135 155 141 138 171 C1' G A 6 alpha beta 166 189 172 169 205 C1' G A 7 alpha beta 200 223 206 203 239 C1' C A 8 alpha beta 234 255 240 237 269 C1' G B 1 alpha beta 264 287 270 267 304 C1' C B 2 alpha beta 299 319 305 302 335 C1' C B 3 alpha beta 330 350 336 333 366 C1' G B 4 alpha beta 361 384 367 364 400 C1' C B 5 alpha beta 395 415 401 398 431 C1' G B 6 alpha beta 426 449 432 429 465 C1' G B 7 alpha beta 460 483 466 463 499 C1' C B 8 alpha beta 494 515 500 497 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 26 8 42 C2' C A 2 OK OK 44 40 58 43 73 C2' C A 3 OK OK 75 71 89 74 104 C2' G A 4 OK OK 106 102 123 105 138 C2' C A 5 OK OK 140 136 154 139 169 C2' G A 6 OK OK 171 167 188 170 203 C2' G A 7 OK OK 205 201 222 204 237 C2' C A 8 OK OK 239 235 253 238 267 C2' G B 1 OK OK 269 265 286 268 302 C2' C B 2 OK OK 304 300 318 303 333 C2' C B 3 OK OK 335 331 349 334 364 C2' G B 4 OK OK 366 362 383 365 398 C2' C B 5 OK OK 400 396 414 399 429 C2' G B 6 OK OK 431 427 448 430 463 C2' G B 7 OK OK 465 461 482 464 497 C2' C B 8 OK OK 499 495 513 498 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' C A 2 OK OK 38 56 41 42 71 C3' C A 3 OK OK 69 87 72 73 102 C3' G A 4 OK OK 100 121 103 104 136 C3' C A 5 OK OK 134 152 137 138 167 C3' G A 6 OK OK 165 186 168 169 201 C3' G A 7 OK OK 199 220 202 203 235 C3' C A 8 OK OK 233 251 236 237 265 C3' G B 1 OK OK 263 284 266 267 300 C3' C B 2 OK OK 298 316 301 302 331 C3' C B 3 OK OK 329 347 332 333 362 C3' G B 4 OK OK 360 381 363 364 396 C3' C B 5 OK OK 394 412 397 398 427 C3' G B 6 OK OK 425 446 428 429 461 C3' G B 7 OK OK 459 480 462 463 495 C3' C B 8 OK OK 493 511 496 497 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' C A 2 OK OK 40 55 37 39 69 C4' C A 3 OK OK 71 86 68 70 100 C4' G A 4 OK OK 102 120 99 101 134 C4' C A 5 OK OK 136 151 133 135 165 C4' G A 6 OK OK 167 185 164 166 199 C4' G A 7 OK OK 201 219 198 200 233 C4' C A 8 OK OK 235 250 232 234 263 C4' G B 1 OK OK 265 283 262 264 298 C4' C B 2 OK OK 300 315 297 299 329 C4' C B 3 OK OK 331 346 328 330 360 C4' G B 4 OK OK 362 380 359 361 394 C4' C B 5 OK OK 396 411 393 395 425 C4' G B 6 OK OK 427 445 424 426 459 C4' G B 7 OK OK 461 479 458 460 493 C4' C B 8 OK OK 495 510 492 494 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 2 OK OK 36 53 54 38 68 C5' C A 3 OK OK 67 84 85 69 99 C5' G A 4 OK OK 98 118 119 100 133 C5' C A 5 OK OK 132 149 150 134 164 C5' G A 6 OK OK 163 183 184 165 198 C5' G A 7 OK OK 197 217 218 199 232 C5' C A 8 OK OK 231 248 249 233 262 C5' G B 1 OK OK 261 281 282 263 297 C5' C B 2 OK OK 296 313 314 298 328 C5' C B 3 OK OK 327 344 345 329 359 C5' G B 4 OK OK 358 378 379 360 393 C5' C B 5 OK OK 392 409 410 394 424 C5' G B 6 OK OK 423 443 444 425 458 C5' G B 7 OK OK 457 477 478 459 492 C5' C B 8 OK OK 491 508 509 493 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P C A 2 OK OK 34 35 36 64 P C A 3 OK OK 65 66 67 95 P G A 4 OK OK 96 97 98 129 P C A 5 OK OK 130 131 132 160 P G A 6 OK OK 161 162 163 194 P G A 7 OK OK 195 196 197 228 P C A 8 OK OK 229 230 231 293 P C B 2 OK OK 294 295 296 324 P C B 3 OK OK 325 326 327 355 P G B 4 OK OK 356 357 358 389 P C B 5 OK OK 390 391 392 420 P G B 6 OK OK 421 422 423 454 P G B 7 OK OK 455 456 457 488 P C B 8 OK OK 489 490 491 ---------------------------------------------------------------------------------