ID code: '3CJZ' 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 beta 4 10 7 32 C1' G A 2 beta 27 33 30 55 C1' A A 3 beta 50 56 53 77 C1' C A 4 beta 72 78 75 97 C1' G A 5 beta 92 98 95 120 C1' M2G A 6 beta 115 121 118 145 C1' A A 7 beta 140 146 143 167 C1' C A 8 beta 162 168 165 187 C1' G A 9 beta 182 188 185 210 C1' U A 10 beta 205 211 208 230 C1' C A 11 beta 225 231 228 250 C1' C A 12 beta 245 251 248 270 C1' U A 13 beta 265 271 268 288 C1' G B 14 beta 283 289 286 311 C1' G B 15 beta 306 312 309 334 C1' A B 16 beta 329 335 332 356 C1' C B 17 beta 351 357 354 376 C1' G B 18 beta 371 377 374 399 C1' M2G B 19 beta 394 400 397 424 C1' A B 20 beta 419 425 422 446 C1' C B 21 beta 441 447 444 466 C1' G B 22 beta 461 467 464 489 C1' U B 23 beta 484 490 487 509 C1' C B 24 beta 504 510 507 529 C1' C B 25 beta 524 530 527 549 C1' U B 26 beta 544 550 547 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 9 5 8 30 C2' G A 2 OK 32 28 31 53 C2' A A 3 OK 55 51 54 75 C2' C A 4 OK 77 73 76 95 C2' G A 5 OK 97 93 96 118 C2' M2G A 6 OK 120 116 119 143 C2' A A 7 OK 145 141 144 165 C2' C A 8 OK 167 163 166 185 C2' G A 9 OK 187 183 186 208 C2' U A 10 OK 210 206 209 228 C2' C A 11 OK 230 226 229 248 C2' C A 12 OK 250 246 249 268 C2' U A 13 OK 270 266 269 286 C2' G B 14 OK 288 284 287 309 C2' G B 15 OK 311 307 310 332 C2' A B 16 OK 334 330 333 354 C2' C B 17 OK 356 352 355 374 C2' G B 18 OK 376 372 375 397 C2' M2G B 19 OK 399 395 398 422 C2' A B 20 OK 424 420 423 444 C2' C B 21 OK 446 442 445 464 C2' G B 22 OK 466 462 465 487 C2' U B 23 OK 489 485 488 507 C2' C B 24 OK 509 505 508 527 C2' C B 25 OK 529 525 528 547 C2' U B 26 OK 549 545 548 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 28 C3' G A 2 OK 26 29 30 51 C3' A A 3 OK 49 52 53 73 C3' C A 4 OK 71 74 75 93 C3' G A 5 OK 91 94 95 116 C3' M2G A 6 OK 114 117 118 141 C3' A A 7 OK 139 142 143 163 C3' C A 8 OK 161 164 165 183 C3' G A 9 OK 181 184 185 206 C3' U A 10 OK 204 207 208 226 C3' C A 11 OK 224 227 228 246 C3' C A 12 OK 244 247 248 266 C3' U A 13 OK 264 267 268 284 C3' G B 14 OK 282 285 286 307 C3' G B 15 OK 305 308 309 330 C3' A B 16 OK 328 331 332 352 C3' C B 17 OK 350 353 354 372 C3' G B 18 OK 370 373 374 395 C3' M2G B 19 OK 393 396 397 420 C3' A B 20 OK 418 421 422 442 C3' C B 21 OK 440 443 444 462 C3' G B 22 OK 460 463 464 485 C3' U B 23 OK 483 486 487 505 C3' C B 24 OK 503 506 507 525 C3' C B 25 OK 523 526 527 545 C3' U B 26 OK 543 546 547 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 26 C4' G A 2 OK 28 25 27 49 C4' A A 3 OK 51 48 50 71 C4' C A 4 OK 73 70 72 91 C4' G A 5 OK 93 90 92 114 C4' M2G A 6 OK 116 113 115 139 C4' A A 7 OK 141 138 140 161 C4' C A 8 OK 163 160 162 181 C4' G A 9 OK 183 180 182 204 C4' U A 10 OK 206 203 205 224 C4' C A 11 OK 226 223 225 244 C4' C A 12 OK 246 243 245 264 C4' U A 13 OK 266 263 265 282 C4' G B 14 OK 284 281 283 305 C4' G B 15 OK 307 304 306 328 C4' A B 16 OK 330 327 329 350 C4' C B 17 OK 352 349 351 370 C4' G B 18 OK 372 369 371 393 C4' M2G B 19 OK 395 392 394 418 C4' A B 20 OK 420 417 419 440 C4' C B 21 OK 442 439 441 460 C4' G B 22 OK 462 459 461 483 C4' U B 23 OK 485 482 484 503 C4' C B 24 OK 505 502 504 523 C4' C B 25 OK 525 522 524 543 C4' U B 26 OK 545 542 544 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 25 C5' G A 2 24 26 48 C5' A A 3 47 49 70 C5' C A 4 69 71 90 C5' G A 5 89 91 113 C5' M2G A 6 112 114 138 C5' A A 7 137 139 160 C5' C A 8 159 161 180 C5' G A 9 179 181 203 C5' U A 10 202 204 223 C5' C A 11 222 224 243 C5' C A 12 242 244 263 C5' U A 13 262 264 281 C5' G B 14 280 282 304 C5' G B 15 303 305 327 C5' A B 16 326 328 349 C5' C B 17 348 350 369 C5' G B 18 368 370 392 C5' M2G B 19 391 393 417 C5' A B 20 416 418 439 C5' C B 21 438 440 459 C5' G B 22 458 460 482 C5' U B 23 481 483 502 C5' C B 24 501 503 522 C5' C B 25 521 523 542 C5' U B 26 541 543 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P G A 2 distorted distorted 6 22 23 24 44 P A A 3 distorted distorted 29 45 46 47 66 P C A 4 distorted distorted 52 67 68 69 86 P G A 5 distorted distorted 74 87 88 89 109 P M2G A 6 distorted distorted 94 110 111 112 134 P A A 7 distorted distorted 117 135 136 137 156 P C A 8 distorted distorted 142 157 158 159 176 P G A 9 distorted distorted 164 177 178 179 199 P U A 10 distorted distorted 184 200 201 202 219 P C A 11 distorted distorted 207 220 221 222 239 P C A 12 distorted distorted 227 240 241 242 259 P U A 13 distorted distorted 247 260 261 262 300 P G B 15 distorted distorted 285 301 302 303 323 P A B 16 distorted distorted 308 324 325 326 345 P C B 17 distorted distorted 331 346 347 348 365 P G B 18 distorted distorted 353 366 367 368 388 P M2G B 19 distorted distorted 373 389 390 391 413 P A B 20 distorted distorted 396 414 415 416 435 P C B 21 distorted distorted 421 436 437 438 455 P G B 22 distorted distorted 443 456 457 458 478 P U B 23 distorted distorted 463 479 480 481 498 P C B 24 distorted distorted 486 499 500 501 518 P C B 25 distorted distorted 506 519 520 521 538 P U B 26 distorted distorted 526 539 540 541 ---------------------------------------------------------------------------------