ID code: '4WTJ' 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 T 1 beta 4 10 7 31 C1' U T 2 beta 26 32 29 51 C1' C T 3 beta 46 52 49 71 C1' C T 4 beta 66 72 69 93 C1' G P 1 beta 88 94 91 116 C1' G P 2 beta 111 117 114 4426 C1' ADP A 604 beta 4421 4427 4424 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' A T 1 OK 9 5 8 29 C2' U T 2 OK 31 27 30 49 C2' C T 3 OK 51 47 50 69 C2' C T 4 OK 71 67 70 91 C2' G P 1 OK 93 89 92 114 C2' G P 2 OK 116 112 115 4424 C2' ADP A 604 OK 4426 4422 4425 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' A T 1 OK 3 6 7 27 C3' U T 2 OK 25 28 29 47 C3' C T 3 OK 45 48 49 67 C3' C T 4 OK 65 68 69 89 C3' G P 1 OK 87 90 91 112 C3' G P 2 OK 110 113 114 4422 C3' ADP A 604 OK 4420 4423 4424 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' A T 1 OK 5 2 4 25 C4' U T 2 OK 27 24 26 45 C4' C T 3 OK 47 44 46 65 C4' C T 4 OK 67 64 66 87 C4' G P 1 OK 89 86 88 110 C4' G P 2 OK 112 109 111 4420 C4' ADP A 604 OK 4422 4419 4421 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' A T 1 1 3 24 C5' U T 2 23 25 44 C5' C T 3 43 45 64 C5' C T 4 63 65 86 C5' G P 1 85 87 109 C5' G P 2 108 110 4419 C5' ADP A 604 4418 4420 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P U T 2 distorted distorted 6 21 22 23 40 P C T 3 distorted distorted 28 41 42 43 60 P C T 4 distorted distorted 48 61 62 63 82 P G P 1 distorted distorted 83 84 85 105 P G P 2 distorted distorted 90 106 107 108 ---------------------------------------------------------------------------------