ID code: '2KM8' 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' --------------------------------------------------------------------------------- 13 C1' U A 1 alpha beta 8 28 14 11 44 C1' A A 2 alpha beta 39 61 45 42 77 C1' U A 3 alpha beta 72 92 78 75 107 C1' A A 4 alpha beta 102 124 108 105 140 C1' U A 5 alpha beta 135 155 141 138 170 C1' A A 6 alpha beta 165 187 171 168 203 C1' U A 7 alpha beta 198 218 204 201 233 C1' A A 8 alpha beta 228 250 234 231 266 C1' A A 9 alpha beta 261 283 267 264 299 C1' U A 10 alpha beta 294 314 300 297 329 C1' A A 11 alpha beta 324 346 330 327 362 C1' A A 12 alpha beta 357 379 363 360 395 C1' U A 13 alpha beta 390 411 396 393 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' U A 1 OK OK 13 9 26 12 42 C2' A A 2 OK OK 44 40 59 43 75 C2' U A 3 OK OK 77 73 90 76 105 C2' A A 4 OK OK 107 103 122 106 138 C2' U A 5 OK OK 140 136 153 139 168 C2' A A 6 OK OK 170 166 185 169 201 C2' U A 7 OK OK 203 199 216 202 231 C2' A A 8 OK OK 233 229 248 232 264 C2' A A 9 OK OK 266 262 281 265 297 C2' U A 10 OK OK 299 295 312 298 327 C2' A A 11 OK OK 329 325 344 328 360 C2' A A 12 OK OK 362 358 377 361 393 C2' U A 13 OK OK 395 391 409 394 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' U A 1 OK OK 7 25 10 11 40 C3' A A 2 OK OK 38 58 41 42 73 C3' U A 3 OK OK 71 89 74 75 103 C3' A A 4 OK OK 101 121 104 105 136 C3' U A 5 OK OK 134 152 137 138 166 C3' A A 6 OK OK 164 184 167 168 199 C3' U A 7 OK OK 197 215 200 201 229 C3' A A 8 OK OK 227 247 230 231 262 C3' A A 9 OK OK 260 280 263 264 295 C3' U A 10 OK OK 293 311 296 297 325 C3' A A 11 OK OK 323 343 326 327 358 C3' A A 12 OK OK 356 376 359 360 391 C3' U A 13 OK OK 389 407 392 393 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' U A 1 OK OK 9 24 6 8 38 C4' A A 2 OK OK 40 57 37 39 71 C4' U A 3 OK OK 73 88 70 72 101 C4' A A 4 OK OK 103 120 100 102 134 C4' U A 5 OK OK 136 151 133 135 164 C4' A A 6 OK OK 166 183 163 165 197 C4' U A 7 OK OK 199 214 196 198 227 C4' A A 8 OK OK 229 246 226 228 260 C4' A A 9 OK OK 262 279 259 261 293 C4' U A 10 OK OK 295 310 292 294 323 C4' A A 11 OK OK 325 342 322 324 356 C4' A A 12 OK OK 358 375 355 357 389 C4' U A 13 OK OK 391 406 388 390 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' U A 1 OK OK 5 22 23 7 37 C5' A A 2 OK OK 36 55 56 38 70 C5' U A 3 OK OK 69 86 87 71 100 C5' A A 4 OK OK 99 118 119 101 133 C5' U A 5 OK OK 132 149 150 134 163 C5' A A 6 OK OK 162 181 182 164 196 C5' U A 7 OK OK 195 212 213 197 226 C5' A A 8 OK OK 225 244 245 227 259 C5' A A 9 OK OK 258 277 278 260 292 C5' U A 10 OK OK 291 308 309 293 322 C5' A A 11 OK OK 321 340 341 323 355 C5' A A 12 OK OK 354 373 374 356 388 C5' U A 13 OK OK 387 404 405 389 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P U A 1 OK OK 3 4 5 33 P A A 2 distorted distorted 10 34 35 36 66 P U A 3 distorted distorted 41 67 68 69 96 P A A 4 distorted distorted 74 97 98 99 129 P U A 5 distorted distorted 104 130 131 132 159 P A A 6 distorted distorted 137 160 161 162 192 P U A 7 distorted distorted 167 193 194 195 222 P A A 8 distorted distorted 200 223 224 225 255 P A A 9 distorted distorted 230 256 257 258 288 P U A 10 distorted distorted 263 289 290 291 318 P A A 11 distorted distorted 296 319 320 321 351 P A A 12 distorted distorted 326 352 353 354 384 P U A 13 distorted distorted 359 385 386 387 ---------------------------------------------------------------------------------