ID code: '2BX2' 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' --------------------------------------------------------------------------------- 3797 C1' U R 1 beta 3792 3798 3795 3817 C1' U R 2 beta 3812 3818 3815 3837 C1' U R 3 beta 3832 3838 3835 3857 C1' A R 4 beta 3852 3858 3855 3879 C1' C R 5 beta 3874 3880 3877 3899 C1' A R 6 beta 3894 3900 3897 3921 C1' G R 7 beta 3916 3922 3919 3944 C1' U R 8 beta 3939 3945 3942 3964 C1' A R 9 beta 3959 3965 3962 3986 C1' U R 10 beta 3981 3987 3984 4006 C1' U R 11 beta 4001 4007 4004 4026 C1' U R 12 beta 4021 4027 4024 4046 C1' G R 13 beta 4041 4047 4044 4069 C1' U R 14 beta 4064 4070 4067 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3795 C2' U R 1 OK 3797 3793 3796 3815 C2' U R 2 OK 3817 3813 3816 3835 C2' U R 3 OK 3837 3833 3836 3855 C2' A R 4 OK 3857 3853 3856 3877 C2' C R 5 OK 3879 3875 3878 3897 C2' A R 6 OK 3899 3895 3898 3919 C2' G R 7 OK 3921 3917 3920 3942 C2' U R 8 OK 3944 3940 3943 3962 C2' A R 9 OK 3964 3960 3963 3984 C2' U R 10 OK 3986 3982 3985 4004 C2' U R 11 OK 4006 4002 4005 4024 C2' U R 12 OK 4026 4022 4025 4044 C2' G R 13 OK 4046 4042 4045 4067 C2' U R 14 OK 4069 4065 4068 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3793 C3' U R 1 OK 3791 3794 3795 3813 C3' U R 2 OK 3811 3814 3815 3833 C3' U R 3 OK 3831 3834 3835 3853 C3' A R 4 OK 3851 3854 3855 3875 C3' C R 5 OK 3873 3876 3877 3895 C3' A R 6 OK 3893 3896 3897 3917 C3' G R 7 OK 3915 3918 3919 3940 C3' U R 8 OK 3938 3941 3942 3960 C3' A R 9 OK 3958 3961 3962 3982 C3' U R 10 OK 3980 3983 3984 4002 C3' U R 11 OK 4000 4003 4004 4022 C3' U R 12 OK 4020 4023 4024 4042 C3' G R 13 OK 4040 4043 4044 4065 C3' U R 14 OK 4063 4066 4067 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3791 C4' U R 1 OK 3793 3790 3792 3811 C4' U R 2 OK 3813 3810 3812 3831 C4' U R 3 OK 3833 3830 3832 3851 C4' A R 4 OK 3853 3850 3852 3873 C4' C R 5 OK 3875 3872 3874 3893 C4' A R 6 OK 3895 3892 3894 3915 C4' G R 7 OK 3917 3914 3916 3938 C4' U R 8 OK 3940 3937 3939 3958 C4' A R 9 OK 3960 3957 3959 3980 C4' U R 10 OK 3982 3979 3981 4000 C4' U R 11 OK 4002 3999 4001 4020 C4' U R 12 OK 4022 4019 4021 4040 C4' G R 13 OK 4042 4039 4041 4063 C4' U R 14 OK 4065 4062 4064 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3790 C5' U R 1 3789 3791 3810 C5' U R 2 3809 3811 3830 C5' U R 3 3829 3831 3850 C5' A R 4 3849 3851 3872 C5' C R 5 3871 3873 3892 C5' A R 6 3891 3893 3914 C5' G R 7 3913 3915 3937 C5' U R 8 3936 3938 3957 C5' A R 9 3956 3958 3979 C5' U R 10 3978 3980 3999 C5' U R 11 3998 4000 4019 C5' U R 12 4018 4020 4039 C5' G R 13 4038 4040 4062 C5' U R 14 4061 4063 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3786 P U R 1 distorted distorted 3787 3788 3789 3806 P U R 2 distorted distorted 3794 3807 3808 3809 3826 P U R 3 distorted distorted 3814 3827 3828 3829 3846 P A R 4 distorted distorted 3834 3847 3848 3849 3868 P C R 5 distorted distorted 3854 3869 3870 3871 3888 P A R 6 distorted distorted 3876 3889 3890 3891 3910 P G R 7 distorted distorted 3896 3911 3912 3913 3933 P U R 8 distorted distorted 3918 3934 3935 3936 3953 P A R 9 distorted distorted 3941 3954 3955 3956 3975 P U R 10 distorted distorted 3961 3976 3977 3978 3995 P U R 11 distorted distorted 3983 3996 3997 3998 4015 P U R 12 distorted distorted 4003 4016 4017 4018 4035 P G R 13 distorted distorted 4023 4036 4037 4038 4058 P U R 14 distorted distorted 4043 4059 4060 4061 ---------------------------------------------------------------------------------