ID code: '1WMQ' 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 C 1 beta 7 13 10 32 C1' U C 2 beta 27 33 30 52 C1' U C 3 beta 47 53 50 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 132 138 135 158 C1' U D 1 beta 153 159 156 178 C1' U D 2 beta 173 179 176 198 C1' U D 3 beta 193 199 196 218 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' --------------------------------------------------------------------------------------------------------------------- 10 C2' U C 1 OK 12 8 11 30 C2' U C 2 OK 32 28 31 50 C2' U C 3 OK 52 48 51 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 137 133 136 156 C2' U D 1 OK 158 154 157 176 C2' U D 2 OK 178 174 177 196 C2' U D 3 OK 198 194 197 216 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' --------------------------------------------------------------------------------- 8 C3' U C 1 OK 6 9 10 28 C3' U C 2 OK 26 29 30 48 C3' U C 3 OK 46 49 50 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 131 134 135 154 C3' U D 1 OK 152 155 156 174 C3' U D 2 OK 172 175 176 194 C3' U D 3 OK 192 195 196 214 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' --------------------------------------------------------------------------------- 6 C4' U C 1 OK 8 5 7 26 C4' U C 2 OK 28 25 27 46 C4' U C 3 OK 48 45 47 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 133 130 132 152 C4' U D 1 OK 154 151 153 172 C4' U D 2 OK 174 171 173 192 C4' U D 3 OK 194 191 193 212 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' --------------------------------------------------------------------------------- 5 C5' U C 1 4 6 25 C5' U C 2 24 26 45 C5' U C 3 44 46 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 7 129 131 151 C5' U D 1 150 152 171 C5' U D 2 170 172 191 C5' U D 3 190 192 211 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' --------------------------------------------------------------------------------- 1 P U C 1 distorted distorted 2 3 4 21 P U C 2 distorted distorted 9 22 23 24 41 P U C 3 distorted distorted 29 42 43 44 61 P A C 4 distorted distorted 49 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 114 127 128 129 147 P U D 1 distorted distorted 148 149 150 167 P U D 2 distorted distorted 155 168 169 170 187 P U D 3 distorted distorted 175 188 189 190 207 P A D 4 distorted distorted 195 208 209 210 229 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 ---------------------------------------------------------------------------------