ID code: '1WPU' 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' U C 1 beta 4 10 7 29 C1' U C 2 beta 24 30 27 49 C1' G C 3 beta 44 50 47 72 C1' A C 4 beta 67 73 70 94 C1' G C 5 beta 89 95 92 117 C1' U C 6 beta 112 118 115 137 C1' U C 7 beta 132 138 135 155 C1' U D 1 beta 150 156 153 175 C1' U D 2 beta 170 176 173 195 C1' G D 3 beta 190 196 193 218 C1' A D 4 beta 213 219 216 240 C1' G D 5 beta 235 241 238 263 C1' U D 6 beta 258 264 261 283 C1' U D 7 beta 278 284 281 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U C 1 OK 9 5 8 27 C2' U C 2 OK 29 25 28 47 C2' G C 3 OK 49 45 48 70 C2' A C 4 OK 72 68 71 92 C2' G C 5 OK 94 90 93 115 C2' U C 6 OK 117 113 116 135 C2' U C 7 OK 137 133 136 153 C2' U D 1 OK 155 151 154 173 C2' U D 2 OK 175 171 174 193 C2' G D 3 OK 195 191 194 216 C2' A D 4 OK 218 214 217 238 C2' G D 5 OK 240 236 239 261 C2' U D 6 OK 263 259 262 281 C2' U D 7 OK 283 279 282 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U C 1 OK 3 6 7 25 C3' U C 2 OK 23 26 27 45 C3' G C 3 OK 43 46 47 68 C3' A C 4 OK 66 69 70 90 C3' G C 5 OK 88 91 92 113 C3' U C 6 OK 111 114 115 133 C3' U C 7 OK 131 134 135 151 C3' U D 1 OK 149 152 153 171 C3' U D 2 OK 169 172 173 191 C3' G D 3 OK 189 192 193 214 C3' A D 4 OK 212 215 216 236 C3' G D 5 OK 234 237 238 259 C3' U D 6 OK 257 260 261 279 C3' U D 7 OK 277 280 281 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U C 1 OK 5 2 4 23 C4' U C 2 OK 25 22 24 43 C4' G C 3 OK 45 42 44 66 C4' A C 4 OK 68 65 67 88 C4' G C 5 OK 90 87 89 111 C4' U C 6 OK 113 110 112 131 C4' U C 7 OK 133 130 132 149 C4' U D 1 OK 151 148 150 169 C4' U D 2 OK 171 168 170 189 C4' G D 3 OK 191 188 190 212 C4' A D 4 OK 214 211 213 234 C4' G D 5 OK 236 233 235 257 C4' U D 6 OK 259 256 258 277 C4' U D 7 OK 279 276 278 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U C 1 1 3 22 C5' U C 2 21 23 42 C5' G C 3 41 43 65 C5' A C 4 64 66 87 C5' G C 5 86 88 110 C5' U C 6 109 111 130 C5' U C 7 129 131 148 C5' U D 1 147 149 168 C5' U D 2 167 169 188 C5' G D 3 187 189 211 C5' A D 4 210 212 233 C5' G D 5 232 234 256 C5' U D 6 255 257 276 C5' U D 7 275 277 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P U C 2 distorted distorted 6 19 20 21 38 P G C 3 distorted distorted 26 39 40 41 61 P A C 4 distorted distorted 46 62 63 64 83 P G C 5 distorted distorted 69 84 85 86 106 P U C 6 distorted distorted 91 107 108 109 126 P U C 7 distorted distorted 114 127 128 129 164 P U D 2 distorted distorted 152 165 166 167 184 P G D 3 distorted distorted 172 185 186 187 207 P A D 4 distorted distorted 192 208 209 210 229 P G D 5 distorted distorted 215 230 231 232 252 P U D 6 distorted distorted 237 253 254 255 272 P U D 7 distorted distorted 260 273 274 275 ---------------------------------------------------------------------------------