ID code: '5UJ2' 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' --------------------------------------------------------------------------------- 13 C1' U T 2 beta 8 14 11 33 C1' A T 3 beta 28 34 31 55 C1' A T 4 beta 50 56 53 77 C1' A T 5 beta 72 78 75 99 C1' U T 6 beta 94 100 97 119 C1' U T 7 beta 114 120 117 139 C1' U T 8 beta 134 140 137 161 C1' A P 4 beta 156 162 159 183 C1' A P 5 beta 178 184 181 205 C1' U P 6 beta 200 206 203 225 C1' U P 7 beta 220 226 223 245 C1' U P 8 beta 240 246 243 4326 C1' 8B4 P 602 4327 4322 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' U T 2 OK 13 9 12 31 C2' A T 3 OK 33 29 32 53 C2' A T 4 OK 55 51 54 75 C2' A T 5 OK 77 73 76 97 C2' U T 6 OK 99 95 98 117 C2' U T 7 OK 119 115 118 137 C2' U T 8 OK 139 135 138 159 C2' A P 4 OK 161 157 160 181 C2' A P 5 OK 183 179 182 203 C2' U P 6 OK 205 201 204 223 C2' U P 7 OK 225 221 224 243 C2' U P 8 OK 245 241 244 4322 C2' 8B4 P 602 4326 4324 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' U T 2 OK 7 10 11 29 C3' A T 3 OK 27 30 31 51 C3' A T 4 OK 49 52 53 73 C3' A T 5 OK 71 74 75 95 C3' U T 6 OK 93 96 97 115 C3' U T 7 OK 113 116 117 135 C3' U T 8 OK 133 136 137 157 C3' A P 4 OK 155 158 159 179 C3' A P 5 OK 177 180 181 201 C3' U P 6 OK 199 202 203 221 C3' U P 7 OK 219 222 223 241 C3' U P 8 OK 239 242 243 4324 C3' 8B4 P 602 OK 4328 4325 4322 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' U T 2 OK 9 6 8 27 C4' A T 3 OK 29 26 28 49 C4' A T 4 OK 51 48 50 71 C4' A T 5 OK 73 70 72 93 C4' U T 6 OK 95 92 94 113 C4' U T 7 OK 115 112 114 133 C4' U T 8 OK 135 132 134 155 C4' A P 4 OK 157 154 156 177 C4' A P 5 OK 179 176 178 199 C4' U P 6 OK 201 198 200 219 C4' U P 7 OK 221 218 220 239 C4' U P 8 OK 241 238 240 4328 C4' 8B4 P 602 OK 4324 4329 4327 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' U T 2 5 7 26 C5' A T 3 25 27 48 C5' A T 4 47 49 70 C5' A T 5 69 71 92 C5' U T 6 91 93 112 C5' U T 7 111 113 132 C5' U T 8 131 133 154 C5' A P 4 153 155 176 C5' A P 5 175 177 198 C5' U P 6 197 199 218 C5' U P 7 217 219 238 C5' U P 8 237 239 4329 C5' 8B4 P 602 4330 4328 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P U T 2 distorted distorted 1 3 4 5 22 P A T 3 distorted distorted 10 23 24 25 44 P A T 4 distorted distorted 30 45 46 47 66 P A T 5 distorted distorted 52 67 68 69 88 P U T 6 distorted distorted 74 89 90 91 108 P U T 7 distorted distorted 96 109 110 111 128 P U T 8 distorted distorted 116 129 130 131 150 P A P 4 distorted distorted 149 151 152 153 172 P A P 5 distorted distorted 158 173 174 175 194 P U P 6 distorted distorted 180 195 196 197 214 P U P 7 distorted distorted 202 215 216 217 234 P U P 8 distorted distorted 222 235 236 237 ---------------------------------------------------------------------------------