ID code: '2R7V' 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 X1102 beta 4 10 7 32 C1' C X1103 beta 27 33 30 52 C1' U X1104 beta 47 53 50 72 C1' U X1105 beta 67 73 70 92 C1' U X1106 beta 87 93 90 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G X1102 OK 9 5 8 30 C2' C X1103 OK 32 28 31 50 C2' U X1104 OK 52 48 51 70 C2' U X1105 OK 72 68 71 90 C2' U X1106 OK 92 88 91 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G X1102 OK 3 6 7 28 C3' C X1103 OK 26 29 30 48 C3' U X1104 OK 46 49 50 68 C3' U X1105 distorted 66 69 70 88 C3' U X1106 OK 86 89 90 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G X1102 OK 5 2 4 26 C4' C X1103 OK 28 25 27 46 C4' U X1104 OK 48 45 47 66 C4' U X1105 OK 68 65 67 86 C4' U X1106 OK 88 85 87 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G X1102 1 3 25 C5' C X1103 24 26 45 C5' U X1104 44 46 65 C5' U X1105 64 66 85 C5' U X1106 84 86 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P C X1103 distorted distorted 6 22 23 24 41 P U X1104 distorted distorted 29 42 43 44 61 P U X1105 distorted distorted 49 62 63 64 81 P U X1106 distorted distorted 69 82 83 84 ---------------------------------------------------------------------------------