ID code: '3KOA' 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' --------------------------------------------------------------------------------- 3748 C1' A B 903 beta 3743 3749 3746 3770 C1' U B 904 beta 3765 3771 3768 3790 C1' G B 905 beta 3785 3791 3788 3813 C1' G B 906 beta 3808 3814 3811 3836 C1' G B 907 beta 3831 3837 3834 3861 C1' C C 918 beta 3856 3862 3859 3881 C1' C C 919 beta 3876 3882 3879 3901 C1' C C 920 beta 3896 3902 3899 3921 C1' G C 921 beta 3916 3922 3919 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3746 C2' A B 903 OK 3748 3744 3747 3768 C2' U B 904 OK 3770 3766 3769 3788 C2' G B 905 OK 3790 3786 3789 3811 C2' G B 906 OK 3813 3809 3812 3834 C2' G B 907 OK 3836 3832 3835 3859 C2' C C 918 OK 3861 3857 3860 3879 C2' C C 919 OK 3881 3877 3880 3899 C2' C C 920 OK 3901 3897 3900 3919 C2' G C 921 OK 3921 3917 3920 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3744 C3' A B 903 OK 3742 3745 3746 3766 C3' U B 904 OK 3764 3767 3768 3786 C3' G B 905 OK 3784 3787 3788 3809 C3' G B 906 OK 3807 3810 3811 3832 C3' G B 907 OK 3830 3833 3834 3857 C3' C C 918 OK 3855 3858 3859 3877 C3' C C 919 OK 3875 3878 3879 3897 C3' C C 920 OK 3895 3898 3899 3917 C3' G C 921 OK 3915 3918 3919 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3742 C4' A B 903 OK 3744 3741 3743 3764 C4' U B 904 OK 3766 3763 3765 3784 C4' G B 905 OK 3786 3783 3785 3807 C4' G B 906 OK 3809 3806 3808 3830 C4' G B 907 OK 3832 3829 3831 3855 C4' C C 918 OK 3857 3854 3856 3875 C4' C C 919 OK 3877 3874 3876 3895 C4' C C 920 OK 3897 3894 3896 3915 C4' G C 921 OK 3917 3914 3916 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3741 C5' A B 903 3740 3742 3763 C5' U B 904 3762 3764 3783 C5' G B 905 3782 3784 3806 C5' G B 906 3805 3807 3829 C5' G B 907 3828 3830 3854 C5' C C 918 3853 3855 3874 C5' C C 919 3873 3875 3894 C5' C C 920 3893 3895 3914 C5' G C 921 3913 3915 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3737 P A B 903 distorted distorted 3738 3739 3740 3759 P U B 904 distorted distorted 3745 3760 3761 3762 3779 P G B 905 distorted distorted 3767 3780 3781 3782 3802 P G B 906 distorted distorted 3787 3803 3804 3805 3825 P G B 907 distorted distorted 3810 3826 3827 3828 3848 P C B 908 3833 3850 P C C 918 distorted distorted 3851 3852 3853 3870 P C C 919 distorted distorted 3858 3871 3872 3873 3890 P C C 920 distorted distorted 3878 3891 3892 3893 3910 P G C 921 distorted distorted 3898 3911 3912 3913 ---------------------------------------------------------------------------------