ID code: '1P26' 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' --------------------------------------------------------------------------------- 8 C1' G B 7 beta 4 9 7 30 C1' G B 8 beta 26 31 29 52 C1' C B 9 beta 48 53 51 71 C1' G B 10 beta 67 72 70 93 C1' C B 11 beta 89 94 92 112 C1' C B 12 beta 108 113 111 129 C1' G C 13 beta 125 130 128 151 C1' G C 14 beta 147 152 150 173 C1' C C 15 beta 169 174 172 192 C1' G C 16 beta 188 193 191 214 C1' C C 17 beta 210 215 213 233 C1' C C 18 beta 229 234 232 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G B 7 8 5 29 C2' G B 8 30 27 51 C2' C B 9 52 49 70 C2' G B 10 71 68 92 C2' C B 11 93 90 111 C2' C B 12 112 109 128 C2' G C 13 129 126 150 C2' G C 14 151 148 172 C2' C C 15 173 170 191 C2' G C 16 192 189 213 C2' C C 17 214 211 232 C2' C C 18 233 230 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G B 7 OK 3 6 7 27 C3' G B 8 OK 25 28 29 49 C3' C B 9 OK 47 50 51 68 C3' G B 10 OK 66 69 70 90 C3' C B 11 OK 88 91 92 109 C3' C B 12 OK 107 110 111 126 C3' G C 13 OK 124 127 128 148 C3' G C 14 OK 146 149 150 170 C3' C C 15 OK 168 171 172 189 C3' G C 16 OK 187 190 191 211 C3' C C 17 OK 209 212 213 230 C3' C C 18 OK 228 231 232 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G B 7 OK 5 2 4 25 C4' G B 8 OK 27 24 26 47 C4' C B 9 OK 49 46 48 66 C4' G B 10 OK 68 65 67 88 C4' C B 11 OK 90 87 89 107 C4' C B 12 OK 109 106 108 124 C4' G C 13 OK 126 123 125 146 C4' G C 14 OK 148 145 147 168 C4' C C 15 OK 170 167 169 187 C4' G C 16 OK 189 186 188 209 C4' C C 17 OK 211 208 210 228 C4' C C 18 OK 230 227 229 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G B 7 1 3 24 C5' G B 8 23 25 46 C5' C B 9 45 47 65 C5' G B 10 64 66 87 C5' C B 11 86 88 106 C5' C B 12 105 107 123 C5' G C 13 122 124 145 C5' G C 14 144 146 167 C5' C C 15 166 168 186 C5' G C 16 185 187 208 C5' C C 17 207 209 227 C5' C C 18 226 228 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P G B 8 distorted distorted 6 21 22 23 42 P C B 9 distorted distorted 28 43 44 45 61 P G B 10 distorted distorted 50 62 63 64 83 P C B 11 distorted distorted 69 84 85 86 102 P C B 12 distorted distorted 91 103 104 105 141 P G C 14 distorted distorted 127 142 143 144 163 P C C 15 distorted distorted 149 164 165 166 182 P G C 16 distorted distorted 171 183 184 185 204 P C C 17 distorted distorted 190 205 206 207 223 P C C 18 distorted distorted 212 224 225 226 ---------------------------------------------------------------------------------