ID code: '1Q2R' 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' G E 26 beta 7 13 10 35 C1' C E 27 beta 30 36 33 55 C1' A E 28 beta 50 56 53 77 C1' C E 29 beta 72 78 75 97 C1' G E 30 beta 92 98 95 120 C1' G E 31 beta 115 121 118 143 C1' C E 39 beta 138 144 141 163 C1' C E 40 beta 158 164 161 183 C1' G E 41 beta 178 184 181 206 C1' U E 42 beta 201 207 204 226 C1' G E 43 beta 221 227 224 249 C1' C E 44 beta 244 250 247 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G E 26 OK 12 8 11 33 C2' C E 27 OK 35 31 34 53 C2' A E 28 OK 55 51 54 75 C2' C E 29 OK 77 73 76 95 C2' G E 30 OK 97 93 96 118 C2' G E 31 OK 120 116 119 141 C2' C E 39 OK 143 139 142 161 C2' C E 40 OK 163 159 162 181 C2' G E 41 OK 183 179 182 204 C2' U E 42 OK 206 202 205 224 C2' G E 43 OK 226 222 225 247 C2' C E 44 OK 249 245 248 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G E 26 OK 6 9 10 31 C3' C E 27 OK 29 32 33 51 C3' A E 28 OK 49 52 53 73 C3' C E 29 OK 71 74 75 93 C3' G E 30 OK 91 94 95 116 C3' G E 31 OK 114 117 118 139 C3' C E 39 OK 137 140 141 159 C3' C E 40 OK 157 160 161 179 C3' G E 41 OK 177 180 181 202 C3' U E 42 OK 200 203 204 222 C3' G E 43 OK 220 223 224 245 C3' C E 44 OK 243 246 247 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G E 26 OK 8 5 7 29 C4' C E 27 OK 31 28 30 49 C4' A E 28 OK 51 48 50 71 C4' C E 29 OK 73 70 72 91 C4' G E 30 OK 93 90 92 114 C4' G E 31 OK 116 113 115 137 C4' C E 39 OK 139 136 138 157 C4' C E 40 OK 159 156 158 177 C4' G E 41 OK 179 176 178 200 C4' U E 42 OK 202 199 201 220 C4' G E 43 OK 222 219 221 243 C4' C E 44 OK 245 242 244 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G E 26 4 6 28 C5' C E 27 27 29 48 C5' A E 28 47 49 70 C5' C E 29 69 71 90 C5' G E 30 89 91 113 C5' G E 31 112 114 136 C5' C E 39 135 137 156 C5' C E 40 155 157 176 C5' G E 41 175 177 199 C5' U E 42 198 200 219 C5' G E 43 218 220 242 C5' C E 44 241 243 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G E 26 distorted distorted 2 3 4 24 P C E 27 distorted distorted 9 25 26 27 44 P A E 28 distorted distorted 32 45 46 47 66 P C E 29 distorted distorted 52 67 68 69 86 P G E 30 distorted distorted 74 87 88 89 109 P G E 31 distorted distorted 94 110 111 112 132 P C E 39 distorted distorted 133 134 135 152 P C E 40 distorted distorted 140 153 154 155 172 P G E 41 distorted distorted 160 173 174 175 195 P U E 42 distorted distorted 180 196 197 198 215 P G E 43 distorted distorted 203 216 217 218 238 P C E 44 distorted distorted 223 239 240 241 ---------------------------------------------------------------------------------