ID code: '4XW1' 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 C 1 beta 4 10 7 32 C1' C C 2 beta 27 33 30 52 C1' C C 3 beta 47 53 50 72 C1' U C 4 beta 67 73 70 96 C1' LCG C 5 beta 99 87 93 116 C1' C C 6 beta 111 117 114 136 C1' C C 7 beta 131 137 134 156 C1' U C 8 beta 151 157 154 176 C1' G C 9 beta 171 177 174 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G C 1 OK 9 5 8 30 C2' C C 2 OK 32 28 31 50 C2' C C 3 OK 52 48 51 70 C2' U C 4 OK 72 68 71 93 C2' LCG C 5 OK 96 85 103 114 C2' C C 6 OK 116 112 115 134 C2' C C 7 OK 136 132 135 154 C2' U C 8 OK 156 152 155 174 C2' G C 9 OK 176 172 175 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G C 1 OK 3 6 7 28 C3' C C 2 OK 26 29 30 48 C3' C C 3 OK 46 49 50 68 C3' U C 4 OK 66 69 70 85 C3' LCG C 5 OK 95 104 93 112 C3' C C 6 OK 110 113 114 132 C3' C C 7 OK 130 133 134 152 C3' U C 8 OK 150 153 154 172 C3' G C 9 OK 170 173 174 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G C 1 OK 5 2 4 26 C4' C C 2 OK 28 25 27 46 C4' C C 3 OK 48 45 47 66 C4' U C 4 OK 68 65 67 95 C4' LCG C 5 OK 85 84 99 110 C4' C C 6 OK 112 109 111 130 C4' C C 7 OK 132 129 131 150 C4' U C 8 OK 152 149 151 170 C4' G C 9 OK 172 169 171 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G C 1 1 3 25 C5' C C 2 24 26 45 C5' C C 3 44 46 65 C5' U C 4 64 66 84 C5' LCG C 5 83 95 109 C5' C C 6 108 110 129 C5' C C 7 128 130 149 C5' U C 8 148 150 169 C5' G C 9 168 170 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P C C 2 distorted distorted 6 22 23 24 41 P C C 3 distorted distorted 29 42 43 44 61 P U C 4 distorted distorted 49 62 63 64 81 P LCG C 5 distorted distorted 69 82 100 83 105 P C C 6 distorted distorted 104 106 107 108 125 P C C 7 distorted distorted 113 126 127 128 145 P U C 8 distorted distorted 133 146 147 148 165 P G C 9 distorted distorted 153 166 167 168 ---------------------------------------------------------------------------------