ID code: '3MIJ' 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 A 1 beta 4 10 7 29 C1' A A 2 beta 24 30 27 51 C1' G A 3 beta 46 52 49 74 C1' G A 4 beta 69 75 72 97 C1' G A 5 beta 92 98 95 120 C1' U A 6 beta 115 121 118 140 C1' U A 7 beta 135 141 138 160 C1' A A 8 beta 155 161 158 182 C1' G A 9 beta 177 183 180 205 C1' G A 10 beta 200 206 203 228 C1' G A 11 beta 223 229 226 251 C1' U A 12 beta 246 252 249 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U A 1 OK 9 5 8 27 C2' A A 2 OK 29 25 28 49 C2' G A 3 OK 51 47 50 72 C2' G A 4 OK 74 70 73 95 C2' G A 5 OK 97 93 96 118 C2' U A 6 OK 120 116 119 138 C2' U A 7 OK 140 136 139 158 C2' A A 8 OK 160 156 159 180 C2' G A 9 OK 182 178 181 203 C2' G A 10 OK 205 201 204 226 C2' G A 11 OK 228 224 227 249 C2' U A 12 OK 251 247 250 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U A 1 OK 3 6 7 25 C3' A A 2 OK 23 26 27 47 C3' G A 3 OK 45 48 49 70 C3' G A 4 OK 68 71 72 93 C3' G A 5 OK 91 94 95 116 C3' U A 6 OK 114 117 118 136 C3' U A 7 OK 134 137 138 156 C3' A A 8 OK 154 157 158 178 C3' G A 9 OK 176 179 180 201 C3' G A 10 OK 199 202 203 224 C3' G A 11 OK 222 225 226 247 C3' U A 12 OK 245 248 249 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U A 1 OK 5 2 4 23 C4' A A 2 OK 25 22 24 45 C4' G A 3 OK 47 44 46 68 C4' G A 4 OK 70 67 69 91 C4' G A 5 OK 93 90 92 114 C4' U A 6 OK 116 113 115 134 C4' U A 7 OK 136 133 135 154 C4' A A 8 OK 156 153 155 176 C4' G A 9 OK 178 175 177 199 C4' G A 10 OK 201 198 200 222 C4' G A 11 OK 224 221 223 245 C4' U A 12 OK 247 244 246 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U A 1 1 3 22 C5' A A 2 21 23 44 C5' G A 3 43 45 67 C5' G A 4 66 68 90 C5' G A 5 89 91 113 C5' U A 6 112 114 133 C5' U A 7 132 134 153 C5' A A 8 152 154 175 C5' G A 9 174 176 198 C5' G A 10 197 199 221 C5' G A 11 220 222 244 C5' U A 12 243 245 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P A A 2 distorted distorted 6 19 20 21 40 P G A 3 distorted distorted 26 41 42 43 63 P G A 4 distorted distorted 48 64 65 66 86 P G A 5 distorted distorted 71 87 88 89 109 P U A 6 distorted distorted 94 110 111 112 129 P U A 7 distorted distorted 117 130 131 132 149 P A A 8 distorted distorted 137 150 151 152 171 P G A 9 distorted distorted 157 172 173 174 194 P G A 10 distorted distorted 179 195 196 197 217 P G A 11 distorted distorted 202 218 219 220 240 P U A 12 distorted distorted 225 241 242 243 ---------------------------------------------------------------------------------