ID code: '2R7W' 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' U X1101 beta 4 10 7 29 C1' G X1102 beta 24 30 27 52 C1' U X1103 beta 47 53 50 72 C1' G X1104 beta 67 73 70 95 C1' A X1105 beta 90 96 93 117 C1' C X1106 beta 112 118 115 137 C1' C X1107 beta 132 138 135 8867 C1' GTP A1201 beta 8862 8868 8865 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U X1101 OK 9 5 8 27 C2' G X1102 OK 29 25 28 50 C2' U X1103 OK 52 48 51 70 C2' G X1104 OK 72 68 71 93 C2' A X1105 OK 95 91 94 115 C2' C X1106 OK 117 113 116 135 C2' C X1107 OK 137 133 136 8865 C2' GTP A1201 OK 8867 8863 8866 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U X1101 OK 3 6 7 25 C3' G X1102 OK 23 26 27 48 C3' U X1103 OK 46 49 50 68 C3' G X1104 OK 66 69 70 91 C3' A X1105 OK 89 92 93 113 C3' C X1106 OK 111 114 115 133 C3' C X1107 OK 131 134 135 8863 C3' GTP A1201 OK 8861 8864 8865 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U X1101 OK 5 2 4 23 C4' G X1102 OK 25 22 24 46 C4' U X1103 OK 48 45 47 66 C4' G X1104 OK 68 65 67 89 C4' A X1105 OK 91 88 90 111 C4' C X1106 OK 113 110 112 131 C4' C X1107 OK 133 130 132 8861 C4' GTP A1201 OK 8863 8860 8862 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U X1101 1 3 22 C5' G X1102 21 23 45 C5' U X1103 44 46 65 C5' G X1104 64 66 88 C5' A X1105 87 89 110 C5' C X1106 109 111 130 C5' C X1107 129 131 8860 C5' GTP A1201 8859 8861 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P G X1102 distorted distorted 6 19 20 21 41 P U X1103 distorted distorted 26 42 43 44 61 P G X1104 distorted distorted 49 62 63 64 84 P A X1105 distorted distorted 69 85 86 87 106 P C X1106 distorted distorted 92 107 108 109 126 P C X1107 distorted distorted 114 127 128 129 ---------------------------------------------------------------------------------