ID code: '2MN0' 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' G A 2 alpha beta 39 62 45 42 78 C1' A A 3 alpha beta 73 95 79 76 111 C1' G A 4 alpha beta 106 129 112 109 145 C1' A A 5 alpha beta 140 162 146 143 178 C1' G A 6 alpha beta 173 196 179 176 210 C1' H2U A 7 alpha beta 207 225 213 211 244 C1' G A 8 alpha beta 239 262 245 242 278 C1' G A 9 alpha beta 273 296 279 276 312 C1' A A 10 alpha beta 307 329 313 310 345 C1' A A 11 alpha beta 340 362 346 343 378 C1' C A 12 alpha beta 373 393 379 376 409 C1' U A 13 alpha beta 404 424 410 407 439 C1' C A 14 alpha beta 434 454 440 437 470 C1' C A 15 alpha beta 465 486 471 468 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' A A 3 OK OK 78 74 93 77 109 C2' G A 4 OK OK 111 107 127 110 143 C2' A A 5 OK OK 145 141 160 144 176 C2' G A 6 OK OK 178 174 194 177 211 C2' H2U A 7 OK OK 210 208 226 212 242 C2' G A 8 OK OK 244 240 260 243 276 C2' G A 9 OK OK 278 274 294 277 310 C2' A A 10 OK OK 312 308 327 311 343 C2' A A 11 OK OK 345 341 360 344 376 C2' C A 12 OK OK 378 374 391 377 407 C2' U A 13 OK OK 409 405 422 408 437 C2' C A 14 OK OK 439 435 452 438 468 C2' C A 15 OK OK 470 466 484 469 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' A A 3 OK OK 72 92 75 76 107 C3' G A 4 OK OK 105 126 108 109 141 C3' A A 5 OK OK 139 159 142 143 174 C3' G A 6 OK OK 172 193 175 176 208 C3' H2U A 7 OK OK 206 224 209 211 240 C3' G A 8 OK OK 238 259 241 242 274 C3' G A 9 OK OK 272 293 275 276 308 C3' A A 10 OK OK 306 326 309 310 341 C3' A A 11 OK OK 339 359 342 343 374 C3' C A 12 OK OK 372 390 375 376 405 C3' U A 13 OK OK 403 421 406 407 435 C3' C A 14 OK OK 433 451 436 437 466 C3' C A 15 OK OK 464 482 467 468 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' A A 3 OK OK 74 91 71 73 105 C4' G A 4 OK OK 107 125 104 106 139 C4' A A 5 OK OK 141 158 138 140 172 C4' G A 6 OK OK 174 192 171 173 206 C4' H2U A 7 OK OK 208 223 205 207 238 C4' G A 8 OK OK 240 258 237 239 272 C4' G A 9 OK OK 274 292 271 273 306 C4' A A 10 OK OK 308 325 305 307 339 C4' A A 11 OK OK 341 358 338 340 372 C4' C A 12 OK OK 374 389 371 373 403 C4' U A 13 OK OK 405 420 402 404 433 C4' C A 14 OK OK 435 450 432 434 464 C4' C A 15 OK OK 466 481 463 465 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 2 OK OK 36 56 57 38 71 C5' A A 3 OK OK 70 89 90 72 104 C5' G A 4 OK OK 103 123 124 105 138 C5' A A 5 OK OK 137 156 157 139 171 C5' G A 6 OK OK 170 190 191 172 205 C5' H2U A 7 distorted distorted 204 221 222 206 237 C5' G A 8 OK OK 236 256 257 238 271 C5' G A 9 OK OK 270 290 291 272 305 C5' A A 10 OK OK 304 323 324 306 338 C5' A A 11 OK OK 337 356 357 339 371 C5' C A 12 OK OK 370 387 388 372 402 C5' U A 13 OK OK 401 418 419 403 432 C5' C A 14 OK OK 431 448 449 433 463 C5' C A 15 OK OK 462 479 480 464 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P A A 3 distorted distorted 41 68 69 70 100 P G A 4 distorted distorted 75 101 102 103 134 P A A 5 distorted distorted 108 135 136 137 167 P G A 6 distorted distorted 142 168 169 170 201 P H2U A 7 distorted distorted 175 202 203 204 233 P G A 8 distorted distorted 209 234 235 236 267 P G A 9 distorted distorted 241 268 269 270 301 P A A 10 distorted distorted 275 302 303 304 334 P A A 11 distorted distorted 309 335 336 337 367 P C A 12 distorted distorted 342 368 369 370 398 P U A 13 distorted distorted 375 399 400 401 428 P C A 14 distorted distorted 406 429 430 431 459 P C A 15 distorted distorted 436 460 461 462 ---------------------------------------------------------------------------------