ID code: '3CZW' 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' G X 3 beta 8 14 11 36 C1' G X 4 beta 31 37 34 59 C1' U X 5 beta 54 60 57 79 C1' C X 6 beta 74 80 77 99 C1' U X 7 beta 94 100 97 119 C1' G X 8 beta 114 120 117 142 C1' A X 9 beta 137 143 140 164 C1' U X 10 beta 159 165 162 184 C1' G X 11 beta 179 185 182 207 C1' A X 12 beta 202 208 205 229 C1' G X 13 beta 224 230 227 252 C1' G X 14 beta 247 253 250 275 C1' C X 15 beta 270 276 273 295 C1' C X 16 beta 290 296 293 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G X 3 OK 13 9 12 34 C2' G X 4 OK 36 32 35 57 C2' U X 5 OK 59 55 58 77 C2' C X 6 OK 79 75 78 97 C2' U X 7 OK 99 95 98 117 C2' G X 8 OK 119 115 118 140 C2' A X 9 OK 142 138 141 162 C2' U X 10 OK 164 160 163 182 C2' G X 11 OK 184 180 183 205 C2' A X 12 OK 207 203 206 227 C2' G X 13 OK 229 225 228 250 C2' G X 14 OK 252 248 251 273 C2' C X 15 OK 275 271 274 293 C2' C X 16 OK 295 291 294 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G X 3 OK 7 10 11 32 C3' G X 4 OK 30 33 34 55 C3' U X 5 OK 53 56 57 75 C3' C X 6 OK 73 76 77 95 C3' U X 7 OK 93 96 97 115 C3' G X 8 OK 113 116 117 138 C3' A X 9 OK 136 139 140 160 C3' U X 10 OK 158 161 162 180 C3' G X 11 OK 178 181 182 203 C3' A X 12 OK 201 204 205 225 C3' G X 13 OK 223 226 227 248 C3' G X 14 OK 246 249 250 271 C3' C X 15 OK 269 272 273 291 C3' C X 16 OK 289 292 293 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G X 3 OK 9 6 8 30 C4' G X 4 OK 32 29 31 53 C4' U X 5 OK 55 52 54 73 C4' C X 6 OK 75 72 74 93 C4' U X 7 OK 95 92 94 113 C4' G X 8 OK 115 112 114 136 C4' A X 9 OK 138 135 137 158 C4' U X 10 OK 160 157 159 178 C4' G X 11 OK 180 177 179 201 C4' A X 12 OK 203 200 202 223 C4' G X 13 OK 225 222 224 246 C4' G X 14 OK 248 245 247 269 C4' C X 15 OK 271 268 270 289 C4' C X 16 OK 291 288 290 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G X 3 5 7 29 C5' G X 4 28 30 52 C5' U X 5 51 53 72 C5' C X 6 71 73 92 C5' U X 7 91 93 112 C5' G X 8 111 113 135 C5' A X 9 134 136 157 C5' U X 10 156 158 177 C5' G X 11 176 178 200 C5' A X 12 199 201 222 C5' G X 13 221 223 245 C5' G X 14 244 246 268 C5' C X 15 267 269 288 C5' C X 16 287 289 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G X 3 distorted distorted 1 3 4 5 25 P G X 4 distorted distorted 10 26 27 28 48 P U X 5 distorted distorted 33 49 50 51 68 P C X 6 distorted distorted 56 69 70 71 88 P U X 7 distorted distorted 76 89 90 91 108 P G X 8 distorted distorted 96 109 110 111 131 P A X 9 distorted distorted 116 132 133 134 153 P U X 10 distorted distorted 139 154 155 156 173 P G X 11 distorted distorted 161 174 175 176 196 P A X 12 distorted distorted 181 197 198 199 218 P G X 13 distorted distorted 204 219 220 221 241 P G X 14 distorted distorted 226 242 243 244 264 P C X 15 distorted distorted 249 265 266 267 284 P C X 16 distorted distorted 272 285 286 287 ---------------------------------------------------------------------------------