ID code: '1O3Z' 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' C A 1 beta 4 10 7 29 C1' U A 2 beta 24 30 27 49 C1' U A 3 beta 44 50 47 69 C1' G A 4 beta 64 70 67 92 C1' C A 5 beta 87 93 90 112 C1' U A 6 beta 107 113 110 132 C1' G A 7 beta 127 133 130 156 C1' C B 17 beta 151 157 154 176 C1' A B 18 beta 171 177 174 198 C1' G B 19 beta 193 199 196 221 C1' C B 20 beta 216 222 219 241 C1' A B 21 beta 236 242 239 263 C1' A B 22 beta 258 264 261 285 C1' G B 23 beta 280 286 283 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 1 OK 9 5 8 27 C2' U A 2 OK 29 25 28 47 C2' U A 3 OK 49 45 48 67 C2' G A 4 OK 69 65 68 90 C2' C A 5 OK 92 88 91 110 C2' U A 6 OK 112 108 111 130 C2' G A 7 OK 132 128 131 154 C2' C B 17 OK 156 152 155 174 C2' A B 18 OK 176 172 175 196 C2' G B 19 OK 198 194 197 219 C2' C B 20 OK 221 217 220 239 C2' A B 21 OK 241 237 240 261 C2' A B 22 OK 263 259 262 283 C2' G B 23 OK 285 281 284 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK 3 6 7 25 C3' U A 2 OK 23 26 27 45 C3' U A 3 OK 43 46 47 65 C3' G A 4 OK 63 66 67 88 C3' C A 5 OK 86 89 90 108 C3' U A 6 OK 106 109 110 128 C3' G A 7 OK 126 129 130 152 C3' C B 17 OK 150 153 154 172 C3' A B 18 OK 170 173 174 194 C3' G B 19 OK 192 195 196 217 C3' C B 20 OK 215 218 219 237 C3' A B 21 OK 235 238 239 259 C3' A B 22 OK 257 260 261 281 C3' G B 23 OK 279 282 283 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK 5 2 4 23 C4' U A 2 OK 25 22 24 43 C4' U A 3 OK 45 42 44 63 C4' G A 4 OK 65 62 64 86 C4' C A 5 OK 88 85 87 106 C4' U A 6 OK 108 105 107 126 C4' G A 7 OK 128 125 127 150 C4' C B 17 OK 152 149 151 170 C4' A B 18 OK 172 169 171 192 C4' G B 19 OK 194 191 193 215 C4' C B 20 OK 217 214 216 235 C4' A B 21 OK 237 234 236 257 C4' A B 22 OK 259 256 258 279 C4' G B 23 OK 281 278 280 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 1 3 22 C5' U A 2 21 23 42 C5' U A 3 41 43 62 C5' G A 4 61 63 85 C5' C A 5 84 86 105 C5' U A 6 104 106 125 C5' G A 7 124 126 149 C5' C B 17 148 150 169 C5' A B 18 168 170 191 C5' G B 19 190 192 214 C5' C B 20 213 215 234 C5' A B 21 233 235 256 C5' A B 22 255 257 278 C5' G B 23 277 279 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P U A 2 distorted distorted 6 19 20 21 38 P U A 3 distorted distorted 26 39 40 41 58 P G A 4 distorted distorted 46 59 60 61 81 P C A 5 distorted distorted 66 82 83 84 101 P U A 6 distorted distorted 89 102 103 104 121 P G A 7 distorted distorted 109 122 123 124 145 P C B 17 distorted distorted 146 147 148 165 P A B 18 distorted distorted 153 166 167 168 187 P G B 19 distorted distorted 173 188 189 190 210 P C B 20 distorted distorted 195 211 212 213 230 P A B 21 distorted distorted 218 231 232 233 252 P A B 22 distorted distorted 238 253 254 255 274 P G B 23 distorted distorted 260 275 276 277 ---------------------------------------------------------------------------------