ID code: '3KMQ' 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' --------------------------------------------------------------------------------- 3771 C1' G B 905 beta 3766 3772 3769 3794 C1' G B 906 beta 3789 3795 3792 3817 C1' G B 907 beta 3812 3818 3815 3840 C1' C B 908 beta 3835 3841 3838 3860 C1' C B 909 beta 3855 3861 3858 3878 C1' G C 916 beta 3873 3879 3876 3901 C1' G C 917 beta 3896 3902 3899 3924 C1' C C 918 beta 3919 3925 3922 3944 C1' C C 919 beta 3939 3945 3942 3964 C1' C C 920 beta 3959 3965 3962 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3769 C2' G B 905 OK 3771 3767 3770 3792 C2' G B 906 OK 3794 3790 3793 3815 C2' G B 907 OK 3817 3813 3816 3838 C2' C B 908 OK 3840 3836 3839 3858 C2' C B 909 OK 3860 3856 3859 3876 C2' G C 916 OK 3878 3874 3877 3899 C2' G C 917 OK 3901 3897 3900 3922 C2' C C 918 OK 3924 3920 3923 3942 C2' C C 919 OK 3944 3940 3943 3962 C2' C C 920 OK 3964 3960 3963 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3767 C3' G B 905 OK 3765 3768 3769 3790 C3' G B 906 OK 3788 3791 3792 3813 C3' G B 907 OK 3811 3814 3815 3836 C3' C B 908 OK 3834 3837 3838 3856 C3' C B 909 OK 3854 3857 3858 3874 C3' G C 916 OK 3872 3875 3876 3897 C3' G C 917 OK 3895 3898 3899 3920 C3' C C 918 OK 3918 3921 3922 3940 C3' C C 919 OK 3938 3941 3942 3960 C3' C C 920 OK 3958 3961 3962 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3765 C4' G B 905 OK 3767 3764 3766 3788 C4' G B 906 OK 3790 3787 3789 3811 C4' G B 907 OK 3813 3810 3812 3834 C4' C B 908 OK 3836 3833 3835 3854 C4' C B 909 OK 3856 3853 3855 3872 C4' G C 916 OK 3874 3871 3873 3895 C4' G C 917 OK 3897 3894 3896 3918 C4' C C 918 OK 3920 3917 3919 3938 C4' C C 919 OK 3940 3937 3939 3958 C4' C C 920 OK 3960 3957 3959 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3764 C5' G B 905 3763 3765 3787 C5' G B 906 3786 3788 3810 C5' G B 907 3809 3811 3833 C5' C B 908 3832 3834 3853 C5' C B 909 3852 3854 3871 C5' G C 916 3870 3872 3894 C5' G C 917 3893 3895 3917 C5' C C 918 3916 3918 3937 C5' C C 919 3936 3938 3957 C5' C C 920 3956 3958 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3760 P G B 905 distorted distorted 3761 3762 3763 3783 P G B 906 distorted distorted 3768 3784 3785 3786 3806 P G B 907 distorted distorted 3791 3807 3808 3809 3829 P C B 908 distorted distorted 3814 3830 3831 3832 3849 P C B 909 distorted distorted 3837 3850 3851 3852 3890 P G C 917 distorted distorted 3875 3891 3892 3893 3913 P C C 918 distorted distorted 3898 3914 3915 3916 3933 P C C 919 distorted distorted 3921 3934 3935 3936 3953 P C C 920 distorted distorted 3941 3954 3955 3956 ---------------------------------------------------------------------------------