ID code: '1ZIG' 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' A A 6 alpha beta 172 194 178 175 210 C1' G A 7 alpha beta 205 228 211 208 244 C1' A A 8 alpha beta 239 261 245 242 277 C1' G A 9 alpha beta 272 295 278 275 311 C1' C A 10 alpha beta 306 326 312 309 342 C1' C A 11 alpha beta 337 357 343 340 373 C1' U A 12 alpha beta 368 389 374 371 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 6 OK OK 177 173 192 176 208 C2' G A 7 OK OK 210 206 226 209 242 C2' A A 8 OK OK 244 240 259 243 275 C2' G A 9 OK OK 277 273 293 276 309 C2' C A 10 OK OK 311 307 324 310 340 C2' C A 11 OK OK 342 338 355 341 371 C2' U A 12 OK OK 373 369 387 372 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 6 OK OK 171 191 174 175 206 C3' G A 7 OK OK 204 225 207 208 240 C3' A A 8 OK OK 238 258 241 242 273 C3' G A 9 OK OK 271 292 274 275 307 C3' C A 10 OK OK 305 323 308 309 338 C3' C A 11 OK OK 336 354 339 340 369 C3' U A 12 OK OK 367 385 370 371 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 6 OK OK 173 190 170 172 204 C4' G A 7 OK OK 206 224 203 205 238 C4' A A 8 OK OK 240 257 237 239 271 C4' G A 9 OK OK 273 291 270 272 305 C4' C A 10 OK OK 307 322 304 306 336 C4' C A 11 OK OK 338 353 335 337 367 C4' U A 12 OK OK 369 384 366 368 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 6 OK OK 169 188 189 171 203 C5' G A 7 OK OK 202 222 223 204 237 C5' A A 8 OK OK 236 255 256 238 270 C5' G A 9 OK OK 269 289 290 271 304 C5' C A 10 OK OK 303 320 321 305 335 C5' C A 11 OK OK 334 351 352 336 366 C5' U A 12 OK OK 365 382 383 367 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 A A 6 distorted distorted 140 167 168 169 199 P G A 7 distorted distorted 174 200 201 202 233 P A A 8 distorted distorted 207 234 235 236 266 P G A 9 distorted distorted 241 267 268 269 300 P C A 10 distorted distorted 274 301 302 303 331 P C A 11 distorted distorted 308 332 333 334 362 P U A 12 distorted distorted 339 363 364 365 ---------------------------------------------------------------------------------