ID code: '2KRV' 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' C A 1 alpha beta 4 24 10 7 40 C1' U A 2 alpha beta 35 55 41 38 70 C1' C A 3 alpha beta 65 85 71 68 101 C1' G A 4 alpha beta 96 119 102 99 135 C1' G A 5 alpha beta 130 153 136 133 167 C1' RSP A 6 alpha beta 173 181 159 168 200 C1' U A 7 alpha beta 195 215 201 198 230 C1' I A 8 alpha beta 225 247 231 228 262 C1' C A 9 alpha beta 257 277 263 260 293 C1' G A 10 alpha beta 288 311 294 291 327 C1' A A 11 alpha beta 322 344 328 325 360 C1' A A 12 alpha beta 355 377 361 358 393 C1' C A 13 alpha beta 388 408 394 391 424 C1' C A 14 alpha beta 419 439 425 422 455 C1' G A 15 alpha beta 450 473 456 453 489 C1' A A 16 alpha beta 484 506 490 487 522 C1' G A 17 alpha beta 517 541 523 520 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 1 OK OK 9 5 22 8 38 C2' U A 2 OK OK 40 36 53 39 68 C2' C A 3 OK OK 70 66 83 69 99 C2' G A 4 OK OK 101 97 117 100 133 C2' G A 5 OK OK 135 131 151 134 168 C2' RSP A 6 OK OK 167 170 182 169 198 C2' U A 7 OK OK 200 196 213 199 228 C2' I A 8 OK OK 230 226 245 229 260 C2' C A 9 OK OK 262 258 275 261 291 C2' G A 10 OK OK 293 289 309 292 325 C2' A A 11 OK OK 327 323 342 326 358 C2' A A 12 OK OK 360 356 375 359 391 C2' C A 13 OK OK 393 389 406 392 422 C2' C A 14 OK OK 424 420 437 423 453 C2' G A 15 OK OK 455 451 471 454 487 C2' A A 16 OK OK 489 485 504 488 520 C2' G A 17 OK OK 522 518 539 521 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK OK 3 21 6 7 36 C3' U A 2 OK OK 34 52 37 38 66 C3' C A 3 OK OK 64 82 67 68 97 C3' G A 4 OK OK 95 116 98 99 131 C3' G A 5 OK OK 129 150 132 133 170 C3' RSP A 6 OK OK 172 184 171 168 196 C3' U A 7 OK OK 194 212 197 198 226 C3' I A 8 OK OK 224 244 227 228 258 C3' C A 9 OK OK 256 274 259 260 289 C3' G A 10 OK OK 287 308 290 291 323 C3' A A 11 OK OK 321 341 324 325 356 C3' A A 12 OK OK 354 374 357 358 389 C3' C A 13 OK OK 387 405 390 391 420 C3' C A 14 OK OK 418 436 421 422 451 C3' G A 15 OK OK 449 470 452 453 485 C3' A A 16 OK OK 483 503 486 487 518 C3' G A 17 OK OK 516 537 519 520 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK OK 5 20 2 4 34 C4' U A 2 OK OK 36 51 33 35 64 C4' C A 3 OK OK 66 81 63 65 95 C4' G A 4 OK OK 97 115 94 96 129 C4' G A 5 OK OK 131 149 128 130 172 C4' RSP A 6 OK OK 170 185 174 173 194 C4' U A 7 OK OK 196 211 193 195 224 C4' I A 8 OK OK 226 243 223 225 256 C4' C A 9 OK OK 258 273 255 257 287 C4' G A 10 OK OK 289 307 286 288 321 C4' A A 11 OK OK 323 340 320 322 354 C4' A A 12 OK OK 356 373 353 355 387 C4' C A 13 OK OK 389 404 386 388 418 C4' C A 14 OK OK 420 435 417 419 449 C4' G A 15 OK OK 451 469 448 450 483 C4' A A 16 OK OK 485 502 482 484 516 C4' G A 17 OK OK 518 536 515 517 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 OK OK 1 18 19 3 33 C5' U A 2 OK OK 32 49 50 34 63 C5' C A 3 OK OK 62 79 80 64 94 C5' G A 4 OK OK 93 113 114 95 128 C5' G A 5 OK OK 127 147 148 129 174 C5' RSP A 6 175 172 193 C5' U A 7 OK OK 192 209 210 194 223 C5' I A 8 OK OK 222 241 242 224 255 C5' C A 9 OK OK 254 271 272 256 286 C5' G A 10 OK OK 285 305 306 287 320 C5' A A 11 OK OK 319 338 339 321 353 C5' A A 12 OK OK 352 371 372 354 386 C5' C A 13 OK OK 385 402 403 387 417 C5' C A 14 OK OK 416 433 434 418 448 C5' G A 15 OK OK 447 467 468 449 482 C5' A A 16 OK OK 481 500 501 483 515 C5' G A 17 OK OK 514 534 535 516 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 29 P U A 2 distorted distorted 6 30 31 32 59 P C A 3 distorted distorted 37 60 61 62 90 P G A 4 distorted distorted 67 91 92 93 124 P G A 5 distorted distorted 98 125 126 127 158 P RSP A 6 OK OK 132 176 177 175 189 P U A 7 distorted distorted 171 190 191 192 219 P I A 8 distorted distorted 197 220 221 222 251 P C A 9 distorted distorted 227 252 253 254 282 P G A 10 distorted distorted 259 283 284 285 316 P A A 11 distorted distorted 290 317 318 319 349 P A A 12 distorted distorted 324 350 351 352 382 P C A 13 distorted distorted 357 383 384 385 413 P C A 14 distorted distorted 390 414 415 416 444 P G A 15 distorted distorted 421 445 446 447 478 P A A 16 distorted distorted 452 479 480 481 511 P G A 17 distorted distorted 486 512 513 514 ---------------------------------------------------------------------------------