ID code: '3GVN' 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' G A 1 beta 4 10 7 32 C1' G A 2 beta 27 33 30 55 C1' U A 3 beta 50 56 53 75 C1' G A 4 beta 70 76 73 98 C1' A A 5 beta 93 99 96 120 C1' G A 6 beta 115 121 118 143 C1' G A 7 beta 138 144 141 164 C1' C B 66 beta 159 165 162 184 C1' C B 67 beta 179 185 182 204 C1' U B 68 beta 199 205 202 224 C1' C B 69 beta 219 225 222 244 C1' A B 70 beta 239 245 242 266 C1' C B 71 beta 261 267 264 286 C1' C B 72 beta 281 287 284 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK 9 5 8 30 C2' G A 2 OK 32 28 31 53 C2' U A 3 OK 55 51 54 73 C2' G A 4 OK 75 71 74 96 C2' A A 5 OK 98 94 97 118 C2' G A 6 OK 120 116 119 141 C2' G A 7 OK 143 139 142 162 C2' C B 66 OK 164 160 163 182 C2' C B 67 OK 184 180 183 202 C2' U B 68 OK 204 200 203 222 C2' C B 69 OK 224 220 223 242 C2' A B 70 OK 244 240 243 264 C2' C B 71 OK 266 262 265 284 C2' C B 72 OK 286 282 285 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 28 C3' G A 2 OK 26 29 30 51 C3' U A 3 OK 49 52 53 71 C3' G A 4 OK 69 72 73 94 C3' A A 5 OK 92 95 96 116 C3' G A 6 OK 114 117 118 139 C3' G A 7 OK 137 140 141 160 C3' C B 66 OK 158 161 162 180 C3' C B 67 OK 178 181 182 200 C3' U B 68 OK 198 201 202 220 C3' C B 69 OK 218 221 222 240 C3' A B 70 OK 238 241 242 262 C3' C B 71 OK 260 263 264 282 C3' C B 72 OK 280 283 284 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 26 C4' G A 2 OK 28 25 27 49 C4' U A 3 OK 51 48 50 69 C4' G A 4 OK 71 68 70 92 C4' A A 5 OK 94 91 93 114 C4' G A 6 OK 116 113 115 137 C4' G A 7 OK 139 136 138 158 C4' C B 66 OK 160 157 159 178 C4' C B 67 OK 180 177 179 198 C4' U B 68 OK 200 197 199 218 C4' C B 69 OK 220 217 219 238 C4' A B 70 OK 240 237 239 260 C4' C B 71 OK 262 259 261 280 C4' C B 72 OK 282 279 281 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 25 C5' G A 2 24 26 48 C5' U A 3 47 49 68 C5' G A 4 67 69 91 C5' A A 5 90 92 113 C5' G A 6 112 114 136 C5' G A 7 135 137 157 C5' C B 66 156 158 177 C5' C B 67 176 178 197 C5' U B 68 196 198 217 C5' C B 69 216 218 237 C5' A B 70 236 238 259 C5' C B 71 258 260 279 C5' C B 72 278 280 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P G A 2 distorted distorted 6 22 23 24 44 P U A 3 distorted distorted 29 45 46 47 64 P G A 4 distorted distorted 52 65 66 67 87 P A A 5 distorted distorted 72 88 89 90 109 P G A 6 distorted distorted 95 110 111 112 132 P G A 7 distorted distorted 117 133 134 135 173 P C B 67 distorted distorted 161 174 175 176 193 P U B 68 distorted distorted 181 194 195 196 213 P C B 69 distorted distorted 201 214 215 216 233 P A B 70 distorted distorted 221 234 235 236 255 P C B 71 distorted distorted 241 256 257 258 275 P C B 72 distorted distorted 263 276 277 278 ---------------------------------------------------------------------------------