ID code: '4WZQ' 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' --------------------------------------------------------------------------------- 3765 C1' A B 903 beta 3760 3766 3763 3787 C1' U B 904 beta 3782 3788 3785 3807 C1' G B 905 beta 3802 3808 3805 3830 C1' G B 906 beta 3825 3831 3828 3853 C1' G B 907 beta 3848 3854 3851 3876 C1' C B 908 beta 3871 3877 3874 3896 C1' C B 909 beta 3891 3897 3894 3916 C1' C B 910 beta 3911 3917 3914 3934 C1' U C 914 beta 3929 3935 3932 3954 C1' G C 915 beta 3949 3955 3952 3977 C1' G C 916 beta 3972 3978 3975 4000 C1' G C 917 beta 3995 4001 3998 4023 C1' C C 918 beta 4018 4024 4021 4043 C1' C C 919 beta 4038 4044 4041 4063 C1' C C 920 beta 4058 4064 4061 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3763 C2' A B 903 OK 3765 3761 3764 3785 C2' U B 904 OK 3787 3783 3786 3805 C2' G B 905 OK 3807 3803 3806 3828 C2' G B 906 OK 3830 3826 3829 3851 C2' G B 907 OK 3853 3849 3852 3874 C2' C B 908 OK 3876 3872 3875 3894 C2' C B 909 OK 3896 3892 3895 3914 C2' C B 910 OK 3916 3912 3915 3932 C2' U C 914 OK 3934 3930 3933 3952 C2' G C 915 OK 3954 3950 3953 3975 C2' G C 916 OK 3977 3973 3976 3998 C2' G C 917 OK 4000 3996 3999 4021 C2' C C 918 OK 4023 4019 4022 4041 C2' C C 919 OK 4043 4039 4042 4061 C2' C C 920 OK 4063 4059 4062 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3761 C3' A B 903 OK 3759 3762 3763 3783 C3' U B 904 OK 3781 3784 3785 3803 C3' G B 905 OK 3801 3804 3805 3826 C3' G B 906 OK 3824 3827 3828 3849 C3' G B 907 OK 3847 3850 3851 3872 C3' C B 908 OK 3870 3873 3874 3892 C3' C B 909 OK 3890 3893 3894 3912 C3' C B 910 OK 3910 3913 3914 3930 C3' U C 914 OK 3928 3931 3932 3950 C3' G C 915 OK 3948 3951 3952 3973 C3' G C 916 OK 3971 3974 3975 3996 C3' G C 917 OK 3994 3997 3998 4019 C3' C C 918 OK 4017 4020 4021 4039 C3' C C 919 OK 4037 4040 4041 4059 C3' C C 920 OK 4057 4060 4061 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3759 C4' A B 903 OK 3761 3758 3760 3781 C4' U B 904 OK 3783 3780 3782 3801 C4' G B 905 OK 3803 3800 3802 3824 C4' G B 906 OK 3826 3823 3825 3847 C4' G B 907 OK 3849 3846 3848 3870 C4' C B 908 OK 3872 3869 3871 3890 C4' C B 909 OK 3892 3889 3891 3910 C4' C B 910 OK 3912 3909 3911 3928 C4' U C 914 OK 3930 3927 3929 3948 C4' G C 915 OK 3950 3947 3949 3971 C4' G C 916 OK 3973 3970 3972 3994 C4' G C 917 OK 3996 3993 3995 4017 C4' C C 918 OK 4019 4016 4018 4037 C4' C C 919 OK 4039 4036 4038 4057 C4' C C 920 OK 4059 4056 4058 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3758 C5' A B 903 3757 3759 3780 C5' U B 904 3779 3781 3800 C5' G B 905 3799 3801 3823 C5' G B 906 3822 3824 3846 C5' G B 907 3845 3847 3869 C5' C B 908 3868 3870 3889 C5' C B 909 3888 3890 3909 C5' C B 910 3908 3910 3927 C5' U C 914 3926 3928 3947 C5' G C 915 3946 3948 3970 C5' G C 916 3969 3971 3993 C5' G C 917 3992 3994 4016 C5' C C 918 4015 4017 4036 C5' C C 919 4035 4037 4056 C5' C C 920 4055 4057 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3776 P U B 904 distorted distorted 3762 3777 3778 3779 3796 P G B 905 distorted distorted 3784 3797 3798 3799 3819 P G B 906 distorted distorted 3804 3820 3821 3822 3842 P G B 907 distorted distorted 3827 3843 3844 3845 3865 P C B 908 distorted distorted 3850 3866 3867 3868 3885 P C B 909 distorted distorted 3873 3886 3887 3888 3905 P C B 910 distorted distorted 3893 3906 3907 3908 3943 P G C 915 distorted distorted 3931 3944 3945 3946 3966 P G C 916 distorted distorted 3951 3967 3968 3969 3989 P G C 917 distorted distorted 3974 3990 3991 3992 4012 P C C 918 distorted distorted 3997 4013 4014 4015 4032 P C C 919 distorted distorted 4020 4033 4034 4035 4052 P C C 920 distorted distorted 4040 4053 4054 4055 ---------------------------------------------------------------------------------