ID code: '2MNC' 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 8 alpha beta 4 24 10 7 40 C1' C A 9 alpha beta 35 55 41 38 71 C1' G A 10 alpha beta 66 89 72 69 105 C1' U A 11 alpha beta 100 120 106 103 135 C1' U A 12 alpha beta 130 150 136 133 165 C1' G A 13 alpha beta 160 183 166 163 199 C1' A A 14 alpha beta 194 216 200 197 232 C1' A A 15 alpha beta 227 249 233 230 265 C1' U A 16 alpha beta 260 280 266 263 295 C1' C A 17 alpha beta 290 310 296 293 326 C1' U A 18 alpha beta 321 341 327 324 356 C1' C A 19 alpha beta 351 371 357 354 387 C1' A A 20 alpha beta 382 404 388 385 420 C1' C A 21 alpha beta 415 435 421 418 451 C1' G A 22 alpha beta 446 469 452 449 485 C1' G A 23 alpha beta 480 503 486 483 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 8 OK OK 9 5 22 8 38 C2' C A 9 OK OK 40 36 53 39 69 C2' G A 10 OK OK 71 67 87 70 103 C2' U A 11 OK OK 105 101 118 104 133 C2' U A 12 OK OK 135 131 148 134 163 C2' G A 13 OK OK 165 161 181 164 197 C2' A A 14 OK OK 199 195 214 198 230 C2' A A 15 OK OK 232 228 247 231 263 C2' U A 16 OK OK 265 261 278 264 293 C2' C A 17 OK OK 295 291 308 294 324 C2' U A 18 OK OK 326 322 339 325 354 C2' C A 19 OK OK 356 352 369 355 385 C2' A A 20 OK OK 387 383 402 386 418 C2' C A 21 OK OK 420 416 433 419 449 C2' G A 22 OK OK 451 447 467 450 483 C2' G A 23 OK OK 485 481 501 484 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 8 OK OK 3 21 6 7 36 C3' C A 9 OK OK 34 52 37 38 67 C3' G A 10 OK OK 65 86 68 69 101 C3' U A 11 OK OK 99 117 102 103 131 C3' U A 12 OK OK 129 147 132 133 161 C3' G A 13 OK OK 159 180 162 163 195 C3' A A 14 OK OK 193 213 196 197 228 C3' A A 15 OK OK 226 246 229 230 261 C3' U A 16 OK OK 259 277 262 263 291 C3' C A 17 OK OK 289 307 292 293 322 C3' U A 18 OK OK 320 338 323 324 352 C3' C A 19 OK OK 350 368 353 354 383 C3' A A 20 OK OK 381 401 384 385 416 C3' C A 21 OK OK 414 432 417 418 447 C3' G A 22 OK OK 445 466 448 449 481 C3' G A 23 OK OK 479 500 482 483 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 8 OK OK 5 20 2 4 34 C4' C A 9 OK OK 36 51 33 35 65 C4' G A 10 OK OK 67 85 64 66 99 C4' U A 11 OK OK 101 116 98 100 129 C4' U A 12 OK OK 131 146 128 130 159 C4' G A 13 OK OK 161 179 158 160 193 C4' A A 14 OK OK 195 212 192 194 226 C4' A A 15 OK OK 228 245 225 227 259 C4' U A 16 OK OK 261 276 258 260 289 C4' C A 17 OK OK 291 306 288 290 320 C4' U A 18 OK OK 322 337 319 321 350 C4' C A 19 OK OK 352 367 349 351 381 C4' A A 20 OK OK 383 400 380 382 414 C4' C A 21 OK OK 416 431 413 415 445 C4' G A 22 OK OK 447 465 444 446 479 C4' G A 23 OK OK 481 499 478 480 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 8 OK OK 1 18 19 3 33 C5' C A 9 OK OK 32 49 50 34 64 C5' G A 10 OK OK 63 83 84 65 98 C5' U A 11 OK OK 97 114 115 99 128 C5' U A 12 OK OK 127 144 145 129 158 C5' G A 13 OK OK 157 177 178 159 192 C5' A A 14 OK OK 191 210 211 193 225 C5' A A 15 OK OK 224 243 244 226 258 C5' U A 16 OK OK 257 274 275 259 288 C5' C A 17 OK OK 287 304 305 289 319 C5' U A 18 OK OK 318 335 336 320 349 C5' C A 19 OK OK 348 365 366 350 380 C5' A A 20 OK OK 379 398 399 381 413 C5' C A 21 OK OK 412 429 430 414 444 C5' G A 22 OK OK 443 463 464 445 478 C5' G A 23 OK OK 477 497 498 479 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 29 P C A 9 distorted distorted 6 30 31 32 60 P G A 10 distorted distorted 37 61 62 63 94 P U A 11 distorted distorted 68 95 96 97 124 P U A 12 distorted distorted 102 125 126 127 154 P G A 13 distorted distorted 132 155 156 157 188 P A A 14 distorted distorted 162 189 190 191 221 P A A 15 distorted distorted 196 222 223 224 254 P U A 16 distorted distorted 229 255 256 257 284 P C A 17 distorted distorted 262 285 286 287 315 P U A 18 distorted distorted 292 316 317 318 345 P C A 19 distorted distorted 323 346 347 348 376 P A A 20 distorted distorted 353 377 378 379 409 P C A 21 distorted distorted 384 410 411 412 440 P G A 22 distorted distorted 417 441 442 443 474 P G A 23 distorted distorted 448 475 476 477 ---------------------------------------------------------------------------------