ID code: '2Q66' 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' --------------------------------------------------------------------------------- 12 C1' A X 1 beta 7 13 10 34 C1' A X 2 beta 29 35 32 56 C1' A X 3 beta 51 57 54 78 C1' A X 4 beta 73 79 76 100 C1' A X 5 beta 95 101 98 4472 C1' ATP A 605 beta 4467 4473 4470 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' A X 1 OK 12 8 11 32 C2' A X 2 OK 34 30 33 54 C2' A X 3 OK 56 52 55 76 C2' A X 4 OK 78 74 77 98 C2' A X 5 OK 100 96 99 4470 C2' ATP A 605 OK 4472 4468 4471 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' A X 1 OK 6 9 10 30 C3' A X 2 OK 28 31 32 52 C3' A X 3 OK 50 53 54 74 C3' A X 4 OK 72 75 76 96 C3' A X 5 OK 94 97 98 4468 C3' ATP A 605 OK 4466 4469 4470 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' A X 1 OK 8 5 7 28 C4' A X 2 OK 30 27 29 50 C4' A X 3 OK 52 49 51 72 C4' A X 4 OK 74 71 73 94 C4' A X 5 OK 96 93 95 4466 C4' ATP A 605 OK 4468 4465 4467 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' A X 1 4 6 27 C5' A X 2 26 28 49 C5' A X 3 48 50 71 C5' A X 4 70 72 93 C5' A X 5 92 94 4465 C5' ATP A 605 4464 4466 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A X 1 OK OK 2 3 4 23 P A X 2 distorted distorted 9 24 25 26 45 P A X 3 distorted distorted 31 46 47 48 67 P A X 4 distorted distorted 53 68 69 70 89 P A X 5 distorted distorted 75 90 91 92 ---------------------------------------------------------------------------------