ID code: '2R7U' 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' A X1103 beta 4 10 7 31 C1' A X1104 beta 26 32 29 53 C1' G X1105 beta 48 54 51 76 C1' C X1106 beta 71 77 74 96 C1' C X1107 beta 91 97 94 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' A X1103 OK 9 5 8 29 C2' A X1104 OK 31 27 30 51 C2' G X1105 OK 53 49 52 74 C2' C X1106 OK 76 72 75 94 C2' C X1107 OK 96 92 95 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' A X1103 OK 3 6 7 27 C3' A X1104 OK 25 28 29 49 C3' G X1105 distorted 47 50 51 72 C3' C X1106 distorted 70 73 74 92 C3' C X1107 OK 90 93 94 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' A X1103 OK 5 2 4 25 C4' A X1104 OK 27 24 26 47 C4' G X1105 OK 49 46 48 70 C4' C X1106 OK 72 69 71 90 C4' C X1107 OK 92 89 91 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' A X1103 1 3 24 C5' A X1104 23 25 46 C5' G X1105 45 47 69 C5' C X1106 68 70 89 C5' C X1107 88 90 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P A X1104 distorted distorted 6 21 22 23 42 P G X1105 distorted distorted 28 43 44 45 65 P C X1106 distorted distorted 50 66 67 68 85 P C X1107 distorted distorted 73 86 87 88 ---------------------------------------------------------------------------------