ID code: '1K2Z' 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' C A 3 beta 7 12 10 30 C1' C A 4 beta 26 31 29 49 C1' A A 5 beta 45 50 48 70 C1' A A 6 beta 66 71 69 91 C1' T A 7 beta 87 92 90 111 C1' T A 8 beta 107 112 110 131 C1' G A 9 beta 127 132 130 153 C1' G A 10 beta 149 154 152 176 C1' C B 13 beta 172 177 175 195 C1' C B 14 beta 191 196 194 214 C1' A B 15 beta 210 215 213 235 C1' A B 16 beta 231 236 234 256 C1' T B 17 beta 252 257 255 276 C1' T B 18 beta 272 277 275 296 C1' G B 19 beta 292 297 295 318 C1' G B 20 beta 314 319 317 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' C A 3 11 8 29 C2' C A 4 30 27 48 C2' A A 5 49 46 69 C2' A A 6 70 67 90 C2' T A 7 91 88 110 C2' T A 8 111 108 130 C2' G A 9 131 128 152 C2' G A 10 153 150 175 C2' C B 13 176 173 194 C2' C B 14 195 192 213 C2' A B 15 214 211 234 C2' A B 16 235 232 255 C2' T B 17 256 253 275 C2' T B 18 276 273 295 C2' G B 19 296 293 317 C2' G B 20 318 315 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' C A 3 OK 6 9 10 27 C3' C A 4 OK 25 28 29 46 C3' A A 5 OK 44 47 48 67 C3' A A 6 OK 65 68 69 88 C3' T A 7 OK 86 89 90 108 C3' T A 8 OK 106 109 110 128 C3' G A 9 OK 126 129 130 150 C3' G A 10 OK 148 151 152 173 C3' C B 13 OK 171 174 175 192 C3' C B 14 OK 190 193 194 211 C3' A B 15 OK 209 212 213 232 C3' A B 16 OK 230 233 234 253 C3' T B 17 OK 251 254 255 273 C3' T B 18 OK 271 274 275 293 C3' G B 19 OK 291 294 295 315 C3' G B 20 OK 313 316 317 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' C A 3 OK 8 5 7 25 C4' C A 4 OK 27 24 26 44 C4' A A 5 OK 46 43 45 65 C4' A A 6 OK 67 64 66 86 C4' T A 7 OK 88 85 87 106 C4' T A 8 OK 108 105 107 126 C4' G A 9 OK 128 125 127 148 C4' G A 10 OK 150 147 149 171 C4' C B 13 OK 173 170 172 190 C4' C B 14 OK 192 189 191 209 C4' A B 15 OK 211 208 210 230 C4' A B 16 OK 232 229 231 251 C4' T B 17 OK 253 250 252 271 C4' T B 18 OK 273 270 272 291 C4' G B 19 OK 293 290 292 313 C4' G B 20 OK 315 312 314 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' C A 3 4 6 24 C5' C A 4 23 25 43 C5' A A 5 42 44 64 C5' A A 6 63 65 85 C5' T A 7 84 86 105 C5' T A 8 104 106 125 C5' G A 9 124 126 147 C5' G A 10 146 148 170 C5' C B 13 169 171 189 C5' C B 14 188 190 208 C5' A B 15 207 209 229 C5' A B 16 228 230 250 C5' T B 17 249 251 270 C5' T B 18 269 271 290 C5' G B 19 289 291 312 C5' G B 20 311 313 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P C A 3 distorted distorted 2 3 4 20 P C A 4 distorted distorted 9 21 22 23 39 P A A 5 distorted distorted 28 40 41 42 60 P A A 6 distorted distorted 47 61 62 63 81 P T A 7 distorted distorted 68 82 83 84 101 P T A 8 distorted distorted 89 102 103 104 121 P G A 9 distorted distorted 109 122 123 124 143 P G A 10 distorted distorted 129 144 145 146 166 P C B 13 distorted distorted 167 168 169 185 P C B 14 distorted distorted 174 186 187 188 204 P A B 15 distorted distorted 193 205 206 207 225 P A B 16 distorted distorted 212 226 227 228 246 P T B 17 distorted distorted 233 247 248 249 266 P T B 18 distorted distorted 254 267 268 269 286 P G B 19 distorted distorted 274 287 288 289 308 P G B 20 distorted distorted 294 309 310 311 ---------------------------------------------------------------------------------