ID code: '1ZIH' 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' G A 3 alpha beta 73 96 79 76 112 C1' C A 4 alpha beta 107 127 113 110 143 C1' G A 5 alpha beta 138 161 144 141 177 C1' C A 6 alpha beta 172 192 178 175 208 C1' A A 7 alpha beta 203 225 209 206 241 C1' A A 8 alpha beta 236 258 242 239 274 C1' G A 9 alpha beta 269 292 275 272 308 C1' C A 10 alpha beta 303 323 309 306 339 C1' C A 11 alpha beta 334 354 340 337 370 C1' U A 12 alpha beta 365 386 371 368 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 3 OK OK 78 74 94 77 110 C2' C A 4 OK OK 112 108 125 111 141 C2' G A 5 OK OK 143 139 159 142 175 C2' C A 6 OK OK 177 173 190 176 206 C2' A A 7 OK OK 208 204 223 207 239 C2' A A 8 OK OK 241 237 256 240 272 C2' G A 9 OK OK 274 270 290 273 306 C2' C A 10 OK OK 308 304 321 307 337 C2' C A 11 OK OK 339 335 352 338 368 C2' U A 12 OK OK 370 366 384 369 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 72 93 75 76 108 C3' C A 4 OK OK 106 124 109 110 139 C3' G A 5 OK OK 137 158 140 141 173 C3' C A 6 OK OK 171 189 174 175 204 C3' A A 7 OK OK 202 222 205 206 237 C3' A A 8 OK OK 235 255 238 239 270 C3' G A 9 OK OK 268 289 271 272 304 C3' C A 10 OK OK 302 320 305 306 335 C3' C A 11 OK OK 333 351 336 337 366 C3' U A 12 OK OK 364 382 367 368 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 74 92 71 73 106 C4' C A 4 OK OK 108 123 105 107 137 C4' G A 5 OK OK 139 157 136 138 171 C4' C A 6 OK OK 173 188 170 172 202 C4' A A 7 OK OK 204 221 201 203 235 C4' A A 8 OK OK 237 254 234 236 268 C4' G A 9 OK OK 270 288 267 269 302 C4' C A 10 OK OK 304 319 301 303 333 C4' C A 11 OK OK 335 350 332 334 364 C4' U A 12 OK OK 366 381 363 365 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 70 90 91 72 105 C5' C A 4 OK OK 104 121 122 106 136 C5' G A 5 OK OK 135 155 156 137 170 C5' C A 6 OK OK 169 186 187 171 201 C5' A A 7 OK OK 200 219 220 202 234 C5' A A 8 OK OK 233 252 253 235 267 C5' G A 9 OK OK 266 286 287 268 301 C5' C A 10 OK OK 300 317 318 302 332 C5' C A 11 OK OK 331 348 349 333 363 C5' U A 12 OK OK 362 379 380 364 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P G A 3 distorted distorted 41 68 69 70 101 P C A 4 distorted distorted 75 102 103 104 132 P G A 5 distorted distorted 109 133 134 135 166 P C A 6 distorted distorted 140 167 168 169 197 P A A 7 distorted distorted 174 198 199 200 230 P A A 8 distorted distorted 205 231 232 233 263 P G A 9 distorted distorted 238 264 265 266 297 P C A 10 distorted distorted 271 298 299 300 328 P C A 11 distorted distorted 305 329 330 331 359 P U A 12 distorted distorted 336 360 361 362 ---------------------------------------------------------------------------------