ID code: '5EMF' 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' --------------------------------------------------------------------------------- 11 C1' G A 1 beta 6 12 9 34 C1' C A 2 beta 29 35 32 54 C1' U A 3 beta 49 55 52 75 C1' G A 4 beta 69 76 73 145 C1' U A 6 146 143 165 C1' G A 7 beta 160 166 163 188 C1' C A 8 beta 183 189 186 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 9 C2' G A 1 OK 11 7 10 32 C2' C A 2 OK 34 30 33 52 C2' U A 3 OK 54 50 53 73 C2' G A 4 OK 75 70 74 143 C2' U A 6 OK 145 141 144 163 C2' G A 7 OK 165 161 164 186 C2' C A 8 OK 188 184 187 206 C2' GPN B 101 205 227 C2' CPN B 102 226 245 C2' APN B 103 244 408 C2' CPN B 108 407 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7 C3' G A 1 OK 5 8 9 30 C3' C A 2 OK 28 31 32 50 C3' U A 3 OK 48 51 52 70 C3' G A 4 68 73 141 C3' U A 6 142 143 161 C3' G A 7 OK 159 162 163 184 C3' C A 8 OK 182 185 186 205 C3' GPN B 101 206 226 C3' CPN B 102 227 244 C3' APN B 103 245 407 C3' CPN B 108 408 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5 C4' G A 1 7 6 28 C4' C A 2 OK 30 27 29 48 C4' U A 3 OK 50 47 49 68 C4' G A 4 OK 70 67 69 159 C4' G A 7 OK 161 158 160 182 C4' C A 8 OK 184 181 183 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 27 C5' C A 2 26 28 47 C5' U A 3 46 48 67 C5' G A 4 66 68 158 C5' G A 7 157 159 181 C5' C A 8 180 182 201 C5' GPN B 101 222 C5' CPN B 102 240 C5' APN B 103 377 C5' GPN B 107 402 C5' CPN B 108 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 23 P C A 2 distorted distorted 8 24 25 26 43 P U A 3 distorted distorted 31 44 45 46 63 P G A 4 distorted distorted 51 64 65 66 87 P C A 5 88 P C A 5 127 P U A 6 128 P U A 6 154 P G A 7 distorted distorted 142 155 156 157 177 P C A 8 distorted distorted 162 178 179 180 ---------------------------------------------------------------------------------