ID code: '3KNA' 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' --------------------------------------------------------------------------------- 3766 C1' A B 903 beta 3761 3767 3764 3788 C1' U B 904 beta 3783 3789 3786 3808 C1' G B 905 beta 3803 3809 3806 3831 C1' G B 906 beta 3826 3832 3829 3854 C1' G B 907 beta 3849 3855 3852 3877 C1' C B 908 beta 3872 3878 3875 3897 C1' C B 909 beta 3892 3898 3895 3915 C1' G C 916 beta 3910 3916 3913 3938 C1' G C 917 beta 3933 3939 3936 3961 C1' C C 918 beta 3956 3962 3959 3981 C1' C C 919 beta 3976 3982 3979 4001 C1' C C 920 beta 3996 4002 3999 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3764 C2' A B 903 OK 3766 3762 3765 3786 C2' U B 904 OK 3788 3784 3787 3806 C2' G B 905 OK 3808 3804 3807 3829 C2' G B 906 OK 3831 3827 3830 3852 C2' G B 907 OK 3854 3850 3853 3875 C2' C B 908 OK 3877 3873 3876 3895 C2' C B 909 OK 3897 3893 3896 3913 C2' G C 916 OK 3915 3911 3914 3936 C2' G C 917 OK 3938 3934 3937 3959 C2' C C 918 OK 3961 3957 3960 3979 C2' C C 919 OK 3981 3977 3980 3999 C2' C C 920 OK 4001 3997 4000 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3762 C3' A B 903 OK 3760 3763 3764 3784 C3' U B 904 OK 3782 3785 3786 3804 C3' G B 905 OK 3802 3805 3806 3827 C3' G B 906 OK 3825 3828 3829 3850 C3' G B 907 OK 3848 3851 3852 3873 C3' C B 908 OK 3871 3874 3875 3893 C3' C B 909 OK 3891 3894 3895 3911 C3' G C 916 OK 3909 3912 3913 3934 C3' G C 917 OK 3932 3935 3936 3957 C3' C C 918 OK 3955 3958 3959 3977 C3' C C 919 OK 3975 3978 3979 3997 C3' C C 920 OK 3995 3998 3999 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3760 C4' A B 903 OK 3762 3759 3761 3782 C4' U B 904 OK 3784 3781 3783 3802 C4' G B 905 OK 3804 3801 3803 3825 C4' G B 906 OK 3827 3824 3826 3848 C4' G B 907 OK 3850 3847 3849 3871 C4' C B 908 OK 3873 3870 3872 3891 C4' C B 909 OK 3893 3890 3892 3909 C4' G C 916 OK 3911 3908 3910 3932 C4' G C 917 OK 3934 3931 3933 3955 C4' C C 918 OK 3957 3954 3956 3975 C4' C C 919 OK 3977 3974 3976 3995 C4' C C 920 OK 3997 3994 3996 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3759 C5' A B 903 3758 3760 3781 C5' U B 904 3780 3782 3801 C5' G B 905 3800 3802 3824 C5' G B 906 3823 3825 3847 C5' G B 907 3846 3848 3870 C5' C B 908 3869 3871 3890 C5' C B 909 3889 3891 3908 C5' G C 916 3907 3909 3931 C5' G C 917 3930 3932 3954 C5' C C 918 3953 3955 3974 C5' C C 919 3973 3975 3994 C5' C C 920 3993 3995 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3777 P U B 904 distorted distorted 3763 3778 3779 3780 3797 P G B 905 distorted distorted 3785 3798 3799 3800 3820 P G B 906 distorted distorted 3805 3821 3822 3823 3843 P G B 907 distorted distorted 3828 3844 3845 3846 3866 P C B 908 distorted distorted 3851 3867 3868 3869 3886 P C B 909 distorted distorted 3874 3887 3888 3889 3927 P G C 917 distorted distorted 3912 3928 3929 3930 3950 P C C 918 distorted distorted 3935 3951 3952 3953 3970 P C C 919 distorted distorted 3958 3971 3972 3973 3990 P C C 920 distorted distorted 3978 3991 3992 3993 ---------------------------------------------------------------------------------