ID code: '3B0U' 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' --------------------------------------------------------------------------------- 9 C1' G A 18 beta 4 10 7 32 C1' G A 19 beta 27 33 30 53 C1' H2U A 20 beta 50 56 54 75 C1' A A 21 beta 70 76 73 95 C1' G B 18 beta 90 96 93 118 C1' G B 19 beta 113 119 116 139 C1' H2U B 20 beta 136 142 140 161 C1' A B 21 beta 156 162 159 5183 C1' FMN X 400 5184 5214 C1' FMN Y 400 5215 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 18 OK 9 5 8 30 C2' G A 19 OK 32 28 31 54 C2' H2U A 20 OK 53 51 55 73 C2' A A 21 OK 75 71 74 93 C2' G B 18 OK 95 91 94 116 C2' G B 19 OK 118 114 117 140 C2' H2U B 20 OK 139 137 141 159 C2' A B 21 OK 161 157 160 5184 C2' FMN X 400 OK 5183 5186 5185 5215 C2' FMN Y 400 OK 5214 5217 5216 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 18 OK 3 6 7 28 C3' G A 19 OK 26 29 30 51 C3' H2U A 20 OK 49 52 54 71 C3' A A 21 OK 69 72 73 91 C3' G B 18 OK 89 92 93 114 C3' G B 19 OK 112 115 116 137 C3' H2U B 20 OK 135 138 140 157 C3' A B 21 OK 155 158 159 5186 C3' FMN X 400 OK 5188 5187 5184 5217 C3' FMN Y 400 OK 5219 5218 5215 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 18 OK 5 2 4 26 C4' G A 19 OK 28 25 27 49 C4' H2U A 20 OK 51 48 50 69 C4' A A 21 OK 71 68 70 89 C4' G B 18 OK 91 88 90 112 C4' G B 19 OK 114 111 113 135 C4' H2U B 20 OK 137 134 136 155 C4' A B 21 OK 157 154 156 5188 C4' FMN X 400 OK 5186 5190 5189 5219 C4' FMN Y 400 OK 5217 5221 5220 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 18 1 3 25 C5' G A 19 24 26 48 C5' H2U A 20 47 49 68 C5' A A 21 67 69 88 C5' G B 18 87 89 111 C5' G B 19 110 112 134 C5' H2U B 20 133 135 154 C5' A B 21 153 155 5190 C5' FMN X 400 5191 5188 5221 C5' FMN Y 400 5222 5219 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P G A 19 distorted distorted 6 22 23 24 44 P H2U A 20 OK OK 29 45 46 47 64 P A A 21 distorted distorted 52 65 66 67 107 P G B 19 distorted distorted 92 108 109 110 130 P H2U B 20 OK OK 115 131 132 133 150 P A B 21 distorted distorted 138 151 152 153 5192 P FMN X 400 OK OK 5193 5194 5191 5223 P FMN Y 400 OK OK 5224 5225 5222 ---------------------------------------------------------------------------------