ID code: '1BSU' 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' --------------------------------------------------------------------------------- 3646 C1' A B 902 beta 3642 3647 3645 3667 C1' A B 903 beta 3663 3668 3666 3688 C1' G B 904 beta 3684 3689 3687 3710 C1' A B 905 beta 3706 3711 3709 3738 C1' MCY B 906 beta 3737 3721 3734 3759 C1' INO B 907 beta 3758 3750 3755 3772 C1' T B 908 beta 3768 3773 3771 3792 C1' C B 909 beta 3788 3793 3791 3811 C1' T B 910 beta 3807 3812 3810 3831 C1' T B 911 beta 3827 3832 3830 3869 C1' A C 802 beta 3865 3870 3868 3890 C1' A C 803 beta 3886 3891 3889 3911 C1' G C 804 beta 3907 3912 3910 3933 C1' A C 805 beta 3929 3934 3932 3961 C1' MCY C 806 beta 3960 3944 3957 3982 C1' INO C 807 beta 3981 3973 3978 3995 C1' T C 808 beta 3991 3996 3994 4015 C1' C C 809 beta 4011 4016 4014 4034 C1' T C 810 beta 4030 4035 4033 4054 C1' T C 811 beta 4050 4055 4053 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3645 C2' A B 902 3646 3643 3666 C2' A B 903 3667 3664 3687 C2' G B 904 3688 3685 3709 C2' A B 905 3710 3707 3734 C2' MCY B 906 3738 3739 3755 C2' INO B 907 3759 3760 3771 C2' T B 908 3772 3769 3791 C2' C B 909 3792 3789 3810 C2' T B 910 3811 3808 3830 C2' T B 911 3831 3828 3868 C2' A C 802 3869 3866 3889 C2' A C 803 3890 3887 3910 C2' G C 804 3911 3908 3932 C2' A C 805 3933 3930 3957 C2' MCY C 806 3961 3962 3978 C2' INO C 807 3982 3983 3994 C2' T C 808 3995 3992 4014 C2' C C 809 4015 4012 4033 C2' T C 810 4034 4031 4053 C2' T C 811 4054 4051 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3643 C3' A B 902 OK 3641 3644 3645 3664 C3' A B 903 OK 3662 3665 3666 3685 C3' G B 904 OK 3683 3686 3687 3707 C3' A B 905 OK 3705 3708 3709 3739 C3' MCY B 906 OK 3736 3740 3734 3760 C3' INO B 907 OK 3757 3761 3755 3769 C3' T B 908 OK 3767 3770 3771 3789 C3' C B 909 OK 3787 3790 3791 3808 C3' T B 910 OK 3806 3809 3810 3828 C3' T B 911 OK 3826 3829 3830 3866 C3' A C 802 OK 3864 3867 3868 3887 C3' A C 803 OK 3885 3888 3889 3908 C3' G C 804 OK 3906 3909 3910 3930 C3' A C 805 OK 3928 3931 3932 3962 C3' MCY C 806 OK 3959 3963 3957 3983 C3' INO C 807 OK 3980 3984 3978 3992 C3' T C 808 OK 3990 3993 3994 4012 C3' C C 809 OK 4010 4013 4014 4031 C3' T C 810 OK 4029 4032 4033 4051 C3' T C 811 OK 4049 4052 4053 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3641 C4' A B 902 OK 3643 3640 3642 3662 C4' A B 903 OK 3664 3661 3663 3683 C4' G B 904 OK 3685 3682 3684 3705 C4' A B 905 OK 3707 3704 3706 3736 C4' MCY B 906 OK 3739 3735 3737 3757 C4' INO B 907 OK 3760 3756 3758 3767 C4' T B 908 OK 3769 3766 3768 3787 C4' C B 909 OK 3789 3786 3788 3806 C4' T B 910 OK 3808 3805 3807 3826 C4' T B 911 OK 3828 3825 3827 3864 C4' A C 802 OK 3866 3863 3865 3885 C4' A C 803 OK 3887 3884 3886 3906 C4' G C 804 OK 3908 3905 3907 3928 C4' A C 805 OK 3930 3927 3929 3959 C4' MCY C 806 OK 3962 3958 3960 3980 C4' INO C 807 OK 3983 3979 3981 3990 C4' T C 808 OK 3992 3989 3991 4010 C4' C C 809 OK 4012 4009 4011 4029 C4' T C 810 OK 4031 4028 4030 4049 C4' T C 811 OK 4051 4048 4050 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3640 C5' A B 902 3639 3641 3661 C5' A B 903 3660 3662 3682 C5' G B 904 3681 3683 3704 C5' A B 905 3703 3705 3735 C5' MCY B 906 3733 3736 3756 C5' INO B 907 3749 3757 3766 C5' T B 908 3765 3767 3786 C5' C B 909 3785 3787 3805 C5' T B 910 3804 3806 3825 C5' T B 911 3824 3826 3863 C5' A C 802 3862 3864 3884 C5' A C 803 3883 3885 3905 C5' G C 804 3904 3906 3927 C5' A C 805 3926 3928 3958 C5' MCY C 806 3956 3959 3979 C5' INO C 807 3972 3980 3989 C5' T C 808 3988 3990 4009 C5' C C 809 4008 4010 4028 C5' T C 810 4027 4029 4048 C5' T C 811 4047 4049 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3657 P A B 903 OK OK 3644 3658 3659 3660 3678 P G B 904 OK OK 3665 3679 3680 3681 3700 P A B 905 OK OK 3686 3701 3702 3703 3730 P MCY B 906 OK OK 3708 3731 3732 3733 3746 P INO B 907 OK OK 3740 3747 3748 3749 3762 P T B 908 OK OK 3761 3763 3764 3765 3782 P C B 909 OK OK 3770 3783 3784 3785 3801 P T B 910 OK OK 3790 3802 3803 3804 3821 P T B 911 OK OK 3809 3822 3823 3824 3880 P A C 803 OK OK 3867 3881 3882 3883 3901 P G C 804 OK OK 3888 3902 3903 3904 3923 P A C 805 OK OK 3909 3924 3925 3926 3953 P MCY C 806 OK OK 3931 3954 3955 3956 3969 P INO C 807 OK OK 3963 3970 3971 3972 3985 P T C 808 OK OK 3984 3986 3987 3988 4005 P C C 809 OK OK 3993 4006 4007 4008 4024 P T C 810 OK OK 4013 4025 4026 4027 4044 P T C 811 OK OK 4032 4045 4046 4047 ---------------------------------------------------------------------------------