ID code: '2IXZ' 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 alpha beta 4 27 10 7 44 C1' C A 2 alpha beta 39 59 45 42 75 C1' U A 3 alpha beta 70 90 76 73 105 C1' G A 4 alpha beta 100 123 106 103 139 C1' U A 5 alpha beta 134 154 140 137 169 C1' G A 6 alpha beta 164 187 170 167 203 C1' C A 7 alpha beta 198 218 204 201 234 C1' C A 8 alpha beta 229 250 235 232 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 OK 9 5 25 8 42 C2' C A 2 OK OK 44 40 57 43 73 C2' U A 3 OK OK 75 71 88 74 103 C2' G A 4 OK OK 105 101 121 104 137 C2' U A 5 OK OK 139 135 152 138 167 C2' G A 6 OK OK 169 165 185 168 201 C2' C A 7 OK OK 203 199 216 202 232 C2' C A 8 OK OK 234 230 248 233 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' C A 2 OK OK 38 56 41 42 71 C3' U A 3 OK OK 69 87 72 73 101 C3' G A 4 OK OK 99 120 102 103 135 C3' U A 5 OK OK 133 151 136 137 165 C3' G A 6 OK OK 163 184 166 167 199 C3' C A 7 OK OK 197 215 200 201 230 C3' C A 8 OK OK 228 246 231 232 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' C A 2 OK OK 40 55 37 39 69 C4' U A 3 OK OK 71 86 68 70 99 C4' G A 4 OK OK 101 119 98 100 133 C4' U A 5 OK OK 135 150 132 134 163 C4' G A 6 OK OK 165 183 162 164 197 C4' C A 7 OK OK 199 214 196 198 228 C4' C A 8 OK OK 230 245 227 229 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' C A 2 OK OK 36 53 54 38 68 C5' U A 3 OK OK 67 84 85 69 98 C5' G A 4 OK OK 97 117 118 99 132 C5' U A 5 OK OK 131 148 149 133 162 C5' G A 6 OK OK 161 181 182 163 196 C5' C A 7 OK OK 195 212 213 197 227 C5' C A 8 OK OK 226 243 244 228 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P C A 2 distorted distorted 6 34 35 36 64 P U A 3 distorted distorted 41 65 66 67 94 P G A 4 distorted distorted 72 95 96 97 128 P U A 5 distorted distorted 102 129 130 131 158 P G A 6 distorted distorted 136 159 160 161 192 P C A 7 distorted distorted 166 193 194 195 223 P C A 8 distorted distorted 200 224 225 226 ---------------------------------------------------------------------------------