ID code: '3KMS' 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' --------------------------------------------------------------------------------- 3741 C1' A B 903 beta 3736 3742 3739 3763 C1' U B 904 beta 3758 3764 3761 3783 C1' G B 905 beta 3778 3784 3781 3806 C1' G B 906 beta 3801 3807 3804 3829 C1' G B 907 beta 3824 3830 3827 3852 C1' C B 908 beta 3847 3853 3850 3872 C1' C B 909 beta 3867 3873 3870 3890 C1' G C 916 beta 3885 3891 3888 3913 C1' G C 917 beta 3908 3914 3911 3936 C1' C C 918 beta 3931 3937 3934 3956 C1' C C 919 beta 3951 3957 3954 3976 C1' C C 920 beta 3971 3977 3974 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3739 C2' A B 903 OK 3741 3737 3740 3761 C2' U B 904 OK 3763 3759 3762 3781 C2' G B 905 OK 3783 3779 3782 3804 C2' G B 906 OK 3806 3802 3805 3827 C2' G B 907 OK 3829 3825 3828 3850 C2' C B 908 OK 3852 3848 3851 3870 C2' C B 909 OK 3872 3868 3871 3888 C2' G C 916 OK 3890 3886 3889 3911 C2' G C 917 OK 3913 3909 3912 3934 C2' C C 918 OK 3936 3932 3935 3954 C2' C C 919 OK 3956 3952 3955 3974 C2' C C 920 OK 3976 3972 3975 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3737 C3' A B 903 OK 3735 3738 3739 3759 C3' U B 904 OK 3757 3760 3761 3779 C3' G B 905 OK 3777 3780 3781 3802 C3' G B 906 OK 3800 3803 3804 3825 C3' G B 907 OK 3823 3826 3827 3848 C3' C B 908 OK 3846 3849 3850 3868 C3' C B 909 OK 3866 3869 3870 3886 C3' G C 916 OK 3884 3887 3888 3909 C3' G C 917 OK 3907 3910 3911 3932 C3' C C 918 OK 3930 3933 3934 3952 C3' C C 919 OK 3950 3953 3954 3972 C3' C C 920 OK 3970 3973 3974 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3735 C4' A B 903 OK 3737 3734 3736 3757 C4' U B 904 OK 3759 3756 3758 3777 C4' G B 905 OK 3779 3776 3778 3800 C4' G B 906 OK 3802 3799 3801 3823 C4' G B 907 OK 3825 3822 3824 3846 C4' C B 908 OK 3848 3845 3847 3866 C4' C B 909 OK 3868 3865 3867 3884 C4' G C 916 OK 3886 3883 3885 3907 C4' G C 917 OK 3909 3906 3908 3930 C4' C C 918 OK 3932 3929 3931 3950 C4' C C 919 OK 3952 3949 3951 3970 C4' C C 920 OK 3972 3969 3971 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3734 C5' A B 903 3733 3735 3756 C5' U B 904 3755 3757 3776 C5' G B 905 3775 3777 3799 C5' G B 906 3798 3800 3822 C5' G B 907 3821 3823 3845 C5' C B 908 3844 3846 3865 C5' C B 909 3864 3866 3883 C5' G C 916 3882 3884 3906 C5' G C 917 3905 3907 3929 C5' C C 918 3928 3930 3949 C5' C C 919 3948 3950 3969 C5' C C 920 3968 3970 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3752 P U B 904 distorted distorted 3738 3753 3754 3755 3772 P G B 905 distorted distorted 3760 3773 3774 3775 3795 P G B 906 distorted distorted 3780 3796 3797 3798 3818 P G B 907 distorted distorted 3803 3819 3820 3821 3841 P C B 908 distorted distorted 3826 3842 3843 3844 3861 P C B 909 distorted distorted 3849 3862 3863 3864 3902 P G C 917 distorted distorted 3887 3903 3904 3905 3925 P C C 918 distorted distorted 3910 3926 3927 3928 3945 P C C 919 distorted distorted 3933 3946 3947 3948 3965 P C C 920 distorted distorted 3953 3966 3967 3968 ---------------------------------------------------------------------------------