ID code: '1ZBI' 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 C 1 beta 4 10 7 32 C1' A C 2 beta 27 33 30 54 C1' C C 3 beta 49 55 52 74 C1' A C 4 beta 69 75 72 96 C1' C C 5 beta 91 97 94 116 C1' C C 6 beta 111 117 114 136 C1' U C 7 beta 131 137 134 156 C1' G C 8 beta 151 157 154 179 C1' A C 9 beta 174 180 177 201 C1' U C 10 beta 196 202 199 221 C1' U C 11 beta 216 222 219 241 C1' C C 12 beta 236 242 239 258 C1' DG D 1 beta 254 259 257 280 C1' DA D 2 beta 276 281 279 301 C1' DA D 3 beta 297 302 300 322 C1' DT D 4 beta 318 323 321 342 C1' DC D 5 beta 338 343 341 361 C1' DA D 6 beta 357 362 360 382 C1' DG D 7 beta 378 383 381 404 C1' DG D 8 beta 400 405 403 426 C1' DT D 9 beta 422 427 425 446 C1' DG D 10 beta 442 447 445 468 C1' DT D 11 beta 464 469 467 488 C1' DC D 12 beta 484 489 487 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G C 1 OK 9 5 8 30 C2' A C 2 OK 32 28 31 52 C2' C C 3 OK 54 50 53 72 C2' A C 4 OK 74 70 73 94 C2' C C 5 OK 96 92 95 114 C2' C C 6 OK 116 112 115 134 C2' U C 7 OK 136 132 135 154 C2' G C 8 OK 156 152 155 177 C2' A C 9 OK 179 175 178 199 C2' U C 10 OK 201 197 200 219 C2' U C 11 OK 221 217 220 239 C2' C C 12 OK 241 237 240 257 C2' DG D 1 258 255 279 C2' DA D 2 280 277 300 C2' DA D 3 301 298 321 C2' DT D 4 322 319 341 C2' DC D 5 342 339 360 C2' DA D 6 361 358 381 C2' DG D 7 382 379 403 C2' DG D 8 404 401 425 C2' DT D 9 426 423 445 C2' DG D 10 446 443 467 C2' DT D 11 468 465 487 C2' DC D 12 488 485 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G C 1 OK 3 6 7 28 C3' A C 2 OK 26 29 30 50 C3' C C 3 OK 48 51 52 70 C3' A C 4 OK 68 71 72 92 C3' C C 5 OK 90 93 94 112 C3' C C 6 OK 110 113 114 132 C3' U C 7 OK 130 133 134 152 C3' G C 8 OK 150 153 154 175 C3' A C 9 OK 173 176 177 197 C3' U C 10 OK 195 198 199 217 C3' U C 11 OK 215 218 219 237 C3' C C 12 OK 235 238 239 255 C3' DG D 1 OK 253 256 257 277 C3' DA D 2 OK 275 278 279 298 C3' DA D 3 OK 296 299 300 319 C3' DT D 4 OK 317 320 321 339 C3' DC D 5 OK 337 340 341 358 C3' DA D 6 OK 356 359 360 379 C3' DG D 7 OK 377 380 381 401 C3' DG D 8 OK 399 402 403 423 C3' DT D 9 OK 421 424 425 443 C3' DG D 10 OK 441 444 445 465 C3' DT D 11 OK 463 466 467 485 C3' DC D 12 OK 483 486 487 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G C 1 OK 5 2 4 26 C4' A C 2 OK 28 25 27 48 C4' C C 3 OK 50 47 49 68 C4' A C 4 OK 70 67 69 90 C4' C C 5 OK 92 89 91 110 C4' C C 6 OK 112 109 111 130 C4' U C 7 OK 132 129 131 150 C4' G C 8 OK 152 149 151 173 C4' A C 9 OK 175 172 174 195 C4' U C 10 OK 197 194 196 215 C4' U C 11 OK 217 214 216 235 C4' C C 12 OK 237 234 236 253 C4' DG D 1 OK 255 252 254 275 C4' DA D 2 OK 277 274 276 296 C4' DA D 3 OK 298 295 297 317 C4' DT D 4 OK 319 316 318 337 C4' DC D 5 OK 339 336 338 356 C4' DA D 6 OK 358 355 357 377 C4' DG D 7 OK 379 376 378 399 C4' DG D 8 OK 401 398 400 421 C4' DT D 9 OK 423 420 422 441 C4' DG D 10 OK 443 440 442 463 C4' DT D 11 OK 465 462 464 483 C4' DC D 12 OK 485 482 484 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G C 1 1 3 25 C5' A C 2 24 26 47 C5' C C 3 46 48 67 C5' A C 4 66 68 89 C5' C C 5 88 90 109 C5' C C 6 108 110 129 C5' U C 7 128 130 149 C5' G C 8 148 150 172 C5' A C 9 171 173 194 C5' U C 10 193 195 214 C5' U C 11 213 215 234 C5' C C 12 233 235 252 C5' DG D 1 251 253 274 C5' DA D 2 273 275 295 C5' DA D 3 294 296 316 C5' DT D 4 315 317 336 C5' DC D 5 335 337 355 C5' DA D 6 354 356 376 C5' DG D 7 375 377 398 C5' DG D 8 397 399 420 C5' DT D 9 419 421 440 C5' DG D 10 439 441 462 C5' DT D 11 461 463 482 C5' DC D 12 481 483 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P A C 2 distorted distorted 6 22 23 24 43 P C C 3 distorted distorted 29 44 45 46 63 P A C 4 distorted distorted 51 64 65 66 85 P C C 5 distorted distorted 71 86 87 88 105 P C C 6 distorted distorted 93 106 107 108 125 P U C 7 distorted distorted 113 126 127 128 145 P G C 8 distorted distorted 133 146 147 148 168 P A C 9 distorted distorted 153 169 170 171 190 P U C 10 distorted distorted 176 191 192 193 210 P U C 11 distorted distorted 198 211 212 213 230 P C C 12 distorted distorted 218 231 232 233 270 P DA D 2 distorted distorted 256 271 272 273 291 P DA D 3 distorted distorted 278 292 293 294 312 P DT D 4 distorted distorted 299 313 314 315 332 P DC D 5 distorted distorted 320 333 334 335 351 P DA D 6 distorted distorted 340 352 353 354 372 P DG D 7 distorted distorted 359 373 374 375 394 P DG D 8 distorted distorted 380 395 396 397 416 P DT D 9 distorted distorted 402 417 418 419 436 P DG D 10 distorted distorted 424 437 438 439 458 P DT D 11 distorted distorted 444 459 460 461 478 P DC D 12 distorted distorted 466 479 480 481 ---------------------------------------------------------------------------------