ID code: '3NMA' 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' --------------------------------------------------------------------------------- 3714 C1' G B 906 beta 3709 3715 3712 3737 C1' G B 907 beta 3732 3738 3735 3760 C1' C B 908 beta 3755 3761 3758 3781 C1' C C 918 beta 3776 3782 3779 3801 C1' C C 919 beta 3796 3802 3799 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3712 C2' G B 906 OK 3714 3710 3713 3735 C2' G B 907 OK 3737 3733 3736 3758 C2' C B 908 OK 3760 3756 3759 3779 C2' C C 918 OK 3781 3777 3780 3799 C2' C C 919 OK 3801 3797 3800 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3710 C3' G B 906 OK 3708 3711 3712 3733 C3' G B 907 OK 3731 3734 3735 3756 C3' C B 908 OK 3754 3757 3758 3777 C3' C C 918 OK 3775 3778 3779 3797 C3' C C 919 OK 3795 3798 3799 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3708 C4' G B 906 OK 3710 3707 3709 3731 C4' G B 907 OK 3733 3730 3732 3754 C4' C B 908 OK 3756 3753 3755 3775 C4' C C 918 OK 3777 3774 3776 3795 C4' C C 919 OK 3797 3794 3796 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3707 C5' G B 906 3706 3708 3730 C5' G B 907 3729 3731 3753 C5' C B 908 3752 3754 3774 C5' C C 918 3773 3775 3794 C5' C C 919 3793 3795 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3726 P G B 907 distorted distorted 3711 3727 3728 3729 3749 P C B 908 distorted distorted 3734 3750 3751 3752 3770 P C C 918 distorted distorted 3771 3772 3773 3790 P C C 919 distorted distorted 3778 3791 3792 3793 ---------------------------------------------------------------------------------