ID code: '4WTA' 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' A T 2 beta 8 14 11 35 C1' A T 3 beta 30 36 33 57 C1' A T 4 beta 52 58 55 79 C1' A T 5 beta 74 80 77 101 C1' U T 6 beta 96 102 99 121 C1' U T 7 beta 116 122 119 141 C1' U T 8 beta 136 142 139 163 C1' A P 2 beta 158 164 161 185 C1' A P 3 beta 180 186 183 207 C1' U P 4 beta 202 208 205 227 C1' U P 5 beta 222 228 225 247 C1' U P 6 beta 242 248 245 4362 C1' UDP A 605 beta 4367 4354 4363 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' A T 2 OK 13 9 12 33 C2' A T 3 OK 35 31 34 55 C2' A T 4 OK 57 53 56 77 C2' A T 5 OK 79 75 78 99 C2' U T 6 OK 101 97 100 119 C2' U T 7 OK 121 117 120 139 C2' U T 8 OK 141 137 140 161 C2' A P 2 OK 163 159 162 183 C2' A P 3 OK 185 181 184 205 C2' U P 4 OK 207 203 206 225 C2' U P 5 OK 227 223 226 245 C2' U P 6 OK 247 243 246 4363 C2' UDP A 605 OK 4362 4365 4364 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' A T 2 OK 7 10 11 31 C3' A T 3 OK 29 32 33 53 C3' A T 4 OK 51 54 55 75 C3' A T 5 OK 73 76 77 97 C3' U T 6 OK 95 98 99 117 C3' U T 7 OK 115 118 119 137 C3' U T 8 OK 135 138 139 159 C3' A P 2 OK 157 160 161 181 C3' A P 3 OK 179 182 183 203 C3' U P 4 OK 201 204 205 223 C3' U P 5 OK 221 224 225 243 C3' U P 6 OK 241 244 245 4365 C3' UDP A 605 OK 4366 4368 4363 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' A T 2 OK 9 6 8 29 C4' A T 3 OK 31 28 30 51 C4' A T 4 OK 53 50 52 73 C4' A T 5 OK 75 72 74 95 C4' U T 6 OK 97 94 96 115 C4' U T 7 OK 117 114 116 135 C4' U T 8 OK 137 134 136 157 C4' A P 2 OK 159 156 158 179 C4' A P 3 OK 181 178 180 201 C4' U P 4 OK 203 200 202 221 C4' U P 5 OK 223 220 222 241 C4' U P 6 OK 243 240 242 4366 C4' UDP A 605 OK 4365 4369 4367 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' A T 2 5 7 28 C5' A T 3 27 29 50 C5' A T 4 49 51 72 C5' A T 5 71 73 94 C5' U T 6 93 95 114 C5' U T 7 113 115 134 C5' U T 8 133 135 156 C5' A P 2 155 157 178 C5' A P 3 177 179 200 C5' U P 4 199 201 220 C5' U P 5 219 221 240 C5' U P 6 239 241 4369 C5' UDP A 605 4370 4366 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P A T 2 distorted distorted 1 3 4 5 24 P A T 3 distorted distorted 10 25 26 27 46 P A T 4 distorted distorted 32 47 48 49 68 P A T 5 distorted distorted 54 69 70 71 90 P U T 6 distorted distorted 76 91 92 93 110 P U T 7 distorted distorted 98 111 112 113 130 P U T 8 distorted distorted 118 131 132 133 152 P A P 2 distorted distorted 151 153 154 155 174 P A P 3 distorted distorted 160 175 176 177 196 P U P 4 distorted distorted 182 197 198 199 216 P U P 5 distorted distorted 204 217 218 219 236 P U P 6 distorted distorted 224 237 238 239 ---------------------------------------------------------------------------------