ID code: '1RNG' 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' C A 3 alpha beta 73 93 79 76 109 C1' G A 4 alpha beta 104 127 110 107 143 C1' C A 5 alpha beta 138 158 144 141 174 C1' U A 6 alpha beta 169 189 175 172 204 C1' U A 7 alpha beta 199 219 205 202 234 C1' G A 8 alpha beta 229 252 235 232 268 C1' C A 9 alpha beta 263 283 269 266 299 C1' G A 10 alpha beta 294 317 300 297 333 C1' U A 11 alpha beta 328 348 334 331 363 C1' C A 12 alpha beta 358 379 364 361 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 3 OK OK 78 74 91 77 107 C2' G A 4 OK OK 109 105 125 108 141 C2' C A 5 OK OK 143 139 156 142 172 C2' U A 6 OK OK 174 170 187 173 202 C2' U A 7 OK OK 204 200 217 203 232 C2' G A 8 OK OK 234 230 250 233 266 C2' C A 9 OK OK 268 264 281 267 297 C2' G A 10 OK OK 299 295 315 298 331 C2' U A 11 OK OK 333 329 346 332 361 C2' C A 12 OK OK 363 359 377 362 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 72 90 75 76 105 C3' G A 4 OK OK 103 124 106 107 139 C3' C A 5 OK OK 137 155 140 141 170 C3' U A 6 OK OK 168 186 171 172 200 C3' U A 7 OK OK 198 216 201 202 230 C3' G A 8 OK OK 228 249 231 232 264 C3' C A 9 OK OK 262 280 265 266 295 C3' G A 10 OK OK 293 314 296 297 329 C3' U A 11 OK OK 327 345 330 331 359 C3' C A 12 OK OK 357 375 360 361 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 74 89 71 73 103 C4' G A 4 OK OK 105 123 102 104 137 C4' C A 5 OK OK 139 154 136 138 168 C4' U A 6 OK OK 170 185 167 169 198 C4' U A 7 OK OK 200 215 197 199 228 C4' G A 8 OK OK 230 248 227 229 262 C4' C A 9 OK OK 264 279 261 263 293 C4' G A 10 OK OK 295 313 292 294 327 C4' U A 11 OK OK 329 344 326 328 357 C4' C A 12 OK OK 359 374 356 358 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 70 87 88 72 102 C5' G A 4 OK OK 101 121 122 103 136 C5' C A 5 OK OK 135 152 153 137 167 C5' U A 6 OK OK 166 183 184 168 197 C5' U A 7 OK OK 196 213 214 198 227 C5' G A 8 OK OK 226 246 247 228 261 C5' C A 9 OK OK 260 277 278 262 292 C5' G A 10 OK OK 291 311 312 293 326 C5' U A 11 OK OK 325 342 343 327 356 C5' C A 12 OK OK 355 372 373 357 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P C A 3 distorted distorted 41 68 69 70 98 P G A 4 distorted distorted 75 99 100 101 132 P C A 5 distorted distorted 106 133 134 135 163 P U A 6 distorted distorted 140 164 165 166 193 P U A 7 distorted distorted 171 194 195 196 223 P G A 8 distorted distorted 201 224 225 226 257 P C A 9 distorted distorted 231 258 259 260 288 P G A 10 distorted distorted 265 289 290 291 322 P U A 11 distorted distorted 296 323 324 325 352 P C A 12 distorted distorted 330 353 354 355 ---------------------------------------------------------------------------------