ID code: '4GV9' 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' --------------------------------------------------------------------------------- 21 C1' GTP E 8 beta 16 22 19 44 C1' G E 9 beta 39 45 42 67 C1' G E 10 beta 62 68 65 90 C1' C E 11 beta 85 91 88 111 C1' C F 1 beta 106 112 109 131 C1' G F 2 beta 126 132 129 154 C1' C F 3 beta 149 155 152 174 C1' C F 4 beta 169 175 172 194 C1' C F 5 beta 189 195 192 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 19 C2' GTP E 8 OK 21 17 20 42 C2' G E 9 OK 44 40 43 65 C2' G E 10 OK 67 63 66 88 C2' C E 11 OK 90 86 89 109 C2' C F 1 OK 111 107 110 129 C2' G F 2 OK 131 127 130 152 C2' C F 3 OK 154 150 153 172 C2' C F 4 OK 174 170 173 192 C2' C F 5 OK 194 190 193 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 17 C3' GTP E 8 OK 15 18 19 40 C3' G E 9 OK 38 41 42 63 C3' G E 10 OK 61 64 65 86 C3' C E 11 OK 84 87 88 107 C3' C F 1 OK 105 108 109 127 C3' G F 2 OK 125 128 129 150 C3' C F 3 OK 148 151 152 170 C3' C F 4 OK 168 171 172 190 C3' C F 5 OK 188 191 192 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 15 C4' GTP E 8 OK 17 14 16 38 C4' G E 9 OK 40 37 39 61 C4' G E 10 OK 63 60 62 84 C4' C E 11 OK 86 83 85 105 C4' C F 1 OK 107 104 106 125 C4' G F 2 OK 127 124 126 148 C4' C F 3 OK 150 147 149 168 C4' C F 4 OK 170 167 169 188 C4' C F 5 OK 190 187 189 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 14 C5' GTP E 8 13 15 37 C5' G E 9 36 38 60 C5' G E 10 59 61 83 C5' C E 11 82 84 104 C5' C F 1 103 105 124 C5' G F 2 123 125 147 C5' C F 3 146 148 167 C5' C F 4 166 168 187 C5' C F 5 186 188 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G E 9 distorted distorted 18 34 35 36 56 P G E 10 distorted distorted 41 57 58 59 79 P C E 11 distorted distorted 64 80 81 82 100 P C F 1 distorted distorted 101 102 103 120 P G F 2 distorted distorted 108 121 122 123 143 P C F 3 distorted distorted 128 144 145 146 163 P C F 4 distorted distorted 151 164 165 166 183 P C F 5 distorted distorted 171 184 185 186 ---------------------------------------------------------------------------------