ID code: '1ZSE' 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' --------------------------------------------------------------------------------- 12 C1' U R 306 beta 7 13 10 32 C1' G R 307 beta 27 33 30 55 C1' U R 308 beta 50 56 53 75 C1' C R 309 beta 70 76 73 95 C1' U R 310 beta 90 96 93 115 C1' A R 311 beta 110 116 113 137 C1' A R 312 beta 132 138 135 159 C1' G R 313 beta 154 160 157 182 C1' A R 314 beta 177 183 180 204 C1' C R 315 beta 199 205 202 224 C1' A R 316 beta 219 225 222 246 C1' G R 317 beta 241 247 244 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' U R 306 OK 12 8 11 30 C2' G R 307 OK 32 28 31 53 C2' U R 308 OK 55 51 54 73 C2' C R 309 OK 75 71 74 93 C2' U R 310 OK 95 91 94 113 C2' A R 311 OK 115 111 114 135 C2' A R 312 OK 137 133 136 157 C2' G R 313 OK 159 155 158 180 C2' A R 314 OK 182 178 181 202 C2' C R 315 OK 204 200 203 222 C2' A R 316 OK 224 220 223 244 C2' G R 317 OK 246 242 245 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' U R 306 OK 6 9 10 28 C3' G R 307 OK 26 29 30 51 C3' U R 308 OK 49 52 53 71 C3' C R 309 OK 69 72 73 91 C3' U R 310 OK 89 92 93 111 C3' A R 311 OK 109 112 113 133 C3' A R 312 OK 131 134 135 155 C3' G R 313 OK 153 156 157 178 C3' A R 314 OK 176 179 180 200 C3' C R 315 OK 198 201 202 220 C3' A R 316 OK 218 221 222 242 C3' G R 317 OK 240 243 244 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' U R 306 OK 8 5 7 26 C4' G R 307 OK 28 25 27 49 C4' U R 308 OK 51 48 50 69 C4' C R 309 OK 71 68 70 89 C4' U R 310 OK 91 88 90 109 C4' A R 311 OK 111 108 110 131 C4' A R 312 OK 133 130 132 153 C4' G R 313 OK 155 152 154 176 C4' A R 314 OK 178 175 177 198 C4' C R 315 OK 200 197 199 218 C4' A R 316 OK 220 217 219 240 C4' G R 317 OK 242 239 241 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' U R 306 4 6 25 C5' G R 307 24 26 48 C5' U R 308 47 49 68 C5' C R 309 67 69 88 C5' U R 310 87 89 108 C5' A R 311 107 109 130 C5' A R 312 129 131 152 C5' G R 313 151 153 175 C5' A R 314 174 176 197 C5' C R 315 196 198 217 C5' A R 316 216 218 239 C5' G R 317 238 240 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P U R 306 OK OK 2 3 4 21 P G R 307 distorted distorted 9 22 23 24 44 P U R 308 distorted distorted 29 45 46 47 64 P C R 309 distorted distorted 52 65 66 67 84 P U R 310 distorted distorted 72 85 86 87 104 P A R 311 distorted distorted 92 105 106 107 126 P A R 312 distorted distorted 112 127 128 129 148 P G R 313 distorted distorted 134 149 150 151 171 P A R 314 distorted distorted 156 172 173 174 193 P C R 315 distorted distorted 179 194 195 196 213 P A R 316 distorted distorted 201 214 215 216 235 P G R 317 distorted distorted 221 236 237 238 ---------------------------------------------------------------------------------