ID code: '1MQ2' 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' --------------------------------------------------------------------------------- 11 C1' T T 7 beta 7 12 10 31 C1' C T 8 beta 27 32 30 50 C1' G T 9 beta 46 51 49 72 C1' C T 10 beta 68 73 71 91 C1' A T 11 beta 87 92 90 112 C1' T T 12 beta 108 113 111 132 C1' C T 13 beta 128 133 131 151 C1' A T 14 beta 147 152 150 172 C1' G T 15 beta 168 173 171 194 C1' C T 16 beta 190 195 193 211 C1' G P 1 beta 207 212 210 233 C1' C P 2 beta 229 234 232 252 C1' T P 3 beta 248 253 251 272 C1' G P 4 beta 268 273 271 294 C1' A P 5 beta 290 295 293 315 C1' T P 6 beta 311 316 314 335 C1' G P 7 beta 331 336 334 357 C1' C P 8 beta 353 358 356 376 C1' G P 9 beta 372 377 375 397 C1' 2DA P 10 beta 394 398 396 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' T T 7 11 8 30 C2' C T 8 31 28 49 C2' G T 9 50 47 71 C2' C T 10 72 69 90 C2' A T 11 91 88 111 C2' T T 12 112 109 131 C2' C T 13 132 129 150 C2' A T 14 151 148 171 C2' G T 15 172 169 193 C2' C T 16 194 191 210 C2' G P 1 211 208 232 C2' C P 2 233 230 251 C2' T P 3 252 249 271 C2' G P 4 272 269 293 C2' A P 5 294 291 314 C2' T P 6 315 312 334 C2' G P 7 335 332 356 C2' C P 8 357 354 375 C2' G P 9 376 373 396 C2' 2DA P 10 397 395 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' T T 7 OK 6 9 10 28 C3' C T 8 OK 26 29 30 47 C3' G T 9 OK 45 48 49 69 C3' C T 10 OK 67 70 71 88 C3' A T 11 OK 86 89 90 109 C3' T T 12 OK 107 110 111 129 C3' C T 13 OK 127 130 131 148 C3' A T 14 OK 146 149 150 169 C3' G T 15 OK 167 170 171 191 C3' C T 16 OK 189 192 193 208 C3' G P 1 OK 206 209 210 230 C3' C P 2 OK 228 231 232 249 C3' T P 3 OK 247 250 251 269 C3' G P 4 OK 267 270 271 291 C3' A P 5 OK 289 292 293 312 C3' T P 6 OK 310 313 314 332 C3' G P 7 OK 330 333 334 354 C3' C P 8 OK 352 355 356 373 C3' G P 9 OK 371 374 375 395 C3' 2DA P 10 393 396 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' T T 7 OK 8 5 7 26 C4' C T 8 OK 28 25 27 45 C4' G T 9 OK 47 44 46 67 C4' C T 10 OK 69 66 68 86 C4' A T 11 OK 88 85 87 107 C4' T T 12 OK 109 106 108 127 C4' C T 13 OK 129 126 128 146 C4' A T 14 OK 148 145 147 167 C4' G T 15 OK 169 166 168 189 C4' C T 16 OK 191 188 190 206 C4' G P 1 OK 208 205 207 228 C4' C P 2 OK 230 227 229 247 C4' T P 3 OK 249 246 248 267 C4' G P 4 OK 269 266 268 289 C4' A P 5 OK 291 288 290 310 C4' T P 6 OK 312 309 311 330 C4' G P 7 OK 332 329 331 352 C4' C P 8 OK 354 351 353 371 C4' G P 9 OK 373 370 372 393 C4' 2DA P 10 OK 395 392 394 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' T T 7 4 6 25 C5' C T 8 24 26 44 C5' G T 9 43 45 66 C5' C T 10 65 67 85 C5' A T 11 84 86 106 C5' T T 12 105 107 126 C5' C T 13 125 127 145 C5' A T 14 144 146 166 C5' G T 15 165 167 188 C5' C T 16 187 189 205 C5' G P 1 204 206 227 C5' C P 2 226 228 246 C5' T P 3 245 247 266 C5' G P 4 265 267 288 C5' A P 5 287 289 309 C5' T P 6 308 310 329 C5' G P 7 328 330 351 C5' C P 8 350 352 370 C5' G P 9 369 371 392 C5' 2DA P 10 391 393 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P T T 7 distorted distorted 2 3 4 21 P C T 8 distorted distorted 9 22 23 24 40 P G T 9 distorted distorted 29 41 42 43 62 P C T 10 distorted distorted 48 63 64 65 81 P A T 11 distorted distorted 70 82 83 84 102 P T T 12 distorted distorted 89 103 104 105 122 P C T 13 distorted distorted 110 123 124 125 141 P A T 14 distorted distorted 130 142 143 144 162 P G T 15 distorted distorted 149 163 164 165 184 P C T 16 distorted distorted 170 185 186 187 223 P C P 2 distorted distorted 209 224 225 226 242 P T P 3 distorted distorted 231 243 244 245 262 P G P 4 distorted distorted 250 263 264 265 284 P A P 5 distorted distorted 270 285 286 287 305 P T P 6 distorted distorted 292 306 307 308 325 P G P 7 distorted distorted 313 326 327 328 347 P C P 8 distorted distorted 333 348 349 350 366 P G P 9 distorted distorted 355 367 368 369 388 P 2DA P 10 OK OK 374 389 390 391 ---------------------------------------------------------------------------------