ID code: '1WNE' 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 B 902 beta 4 10 7 29 C1' A B 903 beta 24 30 27 51 C1' U B 904 beta 46 52 49 71 C1' G B 905 beta 66 72 69 94 C1' G B 906 beta 89 95 92 117 C1' G B 907 beta 112 118 115 140 C1' C B 908 beta 135 141 138 160 C1' C B 909 beta 155 161 158 178 C1' G C 916 beta 173 179 176 201 C1' G C 917 beta 196 202 199 224 C1' C C 918 beta 219 225 222 244 C1' C C 919 beta 239 245 242 264 C1' C C 920 beta 259 265 262 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C B 902 OK 9 5 8 27 C2' A B 903 OK 29 25 28 49 C2' U B 904 OK 51 47 50 69 C2' G B 905 OK 71 67 70 92 C2' G B 906 OK 94 90 93 115 C2' G B 907 OK 117 113 116 138 C2' C B 908 OK 140 136 139 158 C2' C B 909 OK 160 156 159 176 C2' G C 916 OK 178 174 177 199 C2' G C 917 OK 201 197 200 222 C2' C C 918 OK 224 220 223 242 C2' C C 919 OK 244 240 243 262 C2' C C 920 OK 264 260 263 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C B 902 OK 3 6 7 25 C3' A B 903 OK 23 26 27 47 C3' U B 904 OK 45 48 49 67 C3' G B 905 OK 65 68 69 90 C3' G B 906 OK 88 91 92 113 C3' G B 907 OK 111 114 115 136 C3' C B 908 OK 134 137 138 156 C3' C B 909 OK 154 157 158 174 C3' G C 916 OK 172 175 176 197 C3' G C 917 OK 195 198 199 220 C3' C C 918 OK 218 221 222 240 C3' C C 919 OK 238 241 242 260 C3' C C 920 OK 258 261 262 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C B 902 OK 5 2 4 23 C4' A B 903 OK 25 22 24 45 C4' U B 904 OK 47 44 46 65 C4' G B 905 OK 67 64 66 88 C4' G B 906 OK 90 87 89 111 C4' G B 907 OK 113 110 112 134 C4' C B 908 OK 136 133 135 154 C4' C B 909 OK 156 153 155 172 C4' G C 916 OK 174 171 173 195 C4' G C 917 OK 197 194 196 218 C4' C C 918 OK 220 217 219 238 C4' C C 919 OK 240 237 239 258 C4' C C 920 OK 260 257 259 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C B 902 1 3 22 C5' A B 903 21 23 44 C5' U B 904 43 45 64 C5' G B 905 63 65 87 C5' G B 906 86 88 110 C5' G B 907 109 111 133 C5' C B 908 132 134 153 C5' C B 909 152 154 171 C5' G C 916 170 172 194 C5' G C 917 193 195 217 C5' C C 918 216 218 237 C5' C C 919 236 238 257 C5' C C 920 256 258 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P A B 903 distorted distorted 6 19 20 21 40 P U B 904 distorted distorted 26 41 42 43 60 P G B 905 distorted distorted 48 61 62 63 83 P G B 906 distorted distorted 68 84 85 86 106 P G B 907 distorted distorted 91 107 108 109 129 P C B 908 distorted distorted 114 130 131 132 149 P C B 909 distorted distorted 137 150 151 152 190 P G C 917 distorted distorted 175 191 192 193 213 P C C 918 distorted distorted 198 214 215 216 233 P C C 919 distorted distorted 221 234 235 236 253 P C C 920 distorted distorted 241 254 255 256 ---------------------------------------------------------------------------------