ID code: '2KRZ' 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 198 218 204 201 234 C1' C A 8 alpha beta 229 249 235 232 265 C1' A A 9 alpha beta 260 282 266 263 298 C1' U A 10 alpha beta 293 313 299 296 328 C1' A A 11 alpha beta 323 345 329 326 361 C1' C A 12 alpha beta 356 376 362 359 392 C1' C A 13 alpha beta 387 407 393 390 423 C1' C A 14 alpha beta 418 438 424 421 454 C1' C A 15 alpha beta 449 469 455 452 485 C1' G A 16 alpha beta 480 503 486 483 519 C1' A A 17 alpha beta 514 537 520 517 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 203 199 216 202 232 C2' C A 8 OK OK 234 230 247 233 263 C2' A A 9 OK OK 265 261 280 264 296 C2' U A 10 OK OK 298 294 311 297 326 C2' A A 11 OK OK 328 324 343 327 359 C2' C A 12 OK OK 361 357 374 360 390 C2' C A 13 OK OK 392 388 405 391 421 C2' C A 14 OK OK 423 419 436 422 452 C2' C A 15 OK OK 454 450 467 453 483 C2' G A 16 OK OK 485 481 501 484 517 C2' A A 17 OK OK 519 515 535 518 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 197 215 200 201 230 C3' C A 8 OK OK 228 246 231 232 261 C3' A A 9 OK OK 259 279 262 263 294 C3' U A 10 OK OK 292 310 295 296 324 C3' A A 11 OK OK 322 342 325 326 357 C3' C A 12 OK OK 355 373 358 359 388 C3' C A 13 OK OK 386 404 389 390 419 C3' C A 14 OK OK 417 435 420 421 450 C3' C A 15 OK OK 448 466 451 452 481 C3' G A 16 OK OK 479 500 482 483 515 C3' A A 17 OK OK 513 533 516 517 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 199 214 196 198 228 C4' C A 8 OK OK 230 245 227 229 259 C4' A A 9 OK OK 261 278 258 260 292 C4' U A 10 OK OK 294 309 291 293 322 C4' A A 11 OK OK 324 341 321 323 355 C4' C A 12 OK OK 357 372 354 356 386 C4' C A 13 OK OK 388 403 385 387 417 C4' C A 14 OK OK 419 434 416 418 448 C4' C A 15 OK OK 450 465 447 449 479 C4' G A 16 OK OK 481 499 478 480 513 C4' A A 17 OK OK 515 532 512 514 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 195 212 213 197 227 C5' C A 8 OK OK 226 243 244 228 258 C5' A A 9 OK OK 257 276 277 259 291 C5' U A 10 OK OK 290 307 308 292 321 C5' A A 11 OK OK 320 339 340 322 354 C5' C A 12 OK OK 353 370 371 355 385 C5' C A 13 OK OK 384 401 402 386 416 C5' C A 14 OK OK 415 432 433 417 447 C5' C A 15 OK OK 446 463 464 448 478 C5' G A 16 OK OK 477 497 498 479 512 C5' A A 17 OK OK 511 530 531 513 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 C A 8 distorted distorted 200 224 225 226 254 P A A 9 distorted distorted 231 255 256 257 287 P U A 10 distorted distorted 262 288 289 290 317 P A A 11 distorted distorted 295 318 319 320 350 P C A 12 distorted distorted 325 351 352 353 381 P C A 13 distorted distorted 358 382 383 384 412 P C A 14 distorted distorted 389 413 414 415 443 P C A 15 distorted distorted 420 444 445 446 474 P G A 16 distorted distorted 451 475 476 477 508 P A A 17 distorted distorted 482 509 510 511 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