ID code: '3MQK' 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' --------------------------------------------------------------------------------- 3671 C1' G D 5 beta 3666 3672 3669 3694 C1' U D 6 beta 3689 3695 3692 3714 C1' U D 7 beta 3709 3715 3712 3734 C1' C D 8 beta 3729 3735 3732 3754 C1' G D 9 beta 3749 3755 3752 3777 C1' A D 10 beta 3772 3778 3775 3799 C1' U D 11 beta 3794 3800 3797 3819 C1' C D 12 beta 3814 3820 3817 3839 C1' C D 13 beta 3834 3840 3837 3859 C1' A D 14 beta 3854 3860 3857 3881 C1' C D 15 beta 3876 3882 3879 3901 C1' A D 16 beta 3896 3902 3899 3923 C1' G D 17 beta 3918 3924 3921 3947 C1' C E 8 beta 3942 3948 3945 3967 C1' G E 9 beta 3962 3968 3965 3990 C1' A E 10 beta 3985 3991 3988 4012 C1' U E 11 beta 4007 4013 4010 4032 C1' C E 12 beta 4027 4033 4030 4052 C1' C E 13 beta 4047 4053 4050 4072 C1' A E 14 beta 4067 4073 4070 4094 C1' C E 15 beta 4089 4095 4092 4114 C1' A E 16 beta 4109 4115 4112 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3669 C2' G D 5 OK 3671 3667 3670 3692 C2' U D 6 OK 3694 3690 3693 3712 C2' U D 7 OK 3714 3710 3713 3732 C2' C D 8 OK 3734 3730 3733 3752 C2' G D 9 OK 3754 3750 3753 3775 C2' A D 10 OK 3777 3773 3776 3797 C2' U D 11 OK 3799 3795 3798 3817 C2' C D 12 OK 3819 3815 3818 3837 C2' C D 13 OK 3839 3835 3838 3857 C2' A D 14 OK 3859 3855 3858 3879 C2' C D 15 OK 3881 3877 3880 3899 C2' A D 16 OK 3901 3897 3900 3921 C2' G D 17 OK 3923 3919 3922 3945 C2' C E 8 OK 3947 3943 3946 3965 C2' G E 9 OK 3967 3963 3966 3988 C2' A E 10 OK 3990 3986 3989 4010 C2' U E 11 OK 4012 4008 4011 4030 C2' C E 12 OK 4032 4028 4031 4050 C2' C E 13 OK 4052 4048 4051 4070 C2' A E 14 OK 4072 4068 4071 4092 C2' C E 15 OK 4094 4090 4093 4112 C2' A E 16 OK 4114 4110 4113 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3667 C3' G D 5 OK 3665 3668 3669 3690 C3' U D 6 OK 3688 3691 3692 3710 C3' U D 7 OK 3708 3711 3712 3730 C3' C D 8 OK 3728 3731 3732 3750 C3' G D 9 OK 3748 3751 3752 3773 C3' A D 10 OK 3771 3774 3775 3795 C3' U D 11 OK 3793 3796 3797 3815 C3' C D 12 OK 3813 3816 3817 3835 C3' C D 13 OK 3833 3836 3837 3855 C3' A D 14 OK 3853 3856 3857 3877 C3' C D 15 OK 3875 3878 3879 3897 C3' A D 16 OK 3895 3898 3899 3919 C3' G D 17 OK 3917 3920 3921 3943 C3' C E 8 OK 3941 3944 3945 3963 C3' G E 9 OK 3961 3964 3965 3986 C3' A E 10 OK 3984 3987 3988 4008 C3' U E 11 OK 4006 4009 4010 4028 C3' C E 12 OK 4026 4029 4030 4048 C3' C E 13 OK 4046 4049 4050 4068 C3' A E 14 OK 4066 4069 4070 4090 C3' C E 15 OK 4088 4091 4092 4110 C3' A E 16 OK 4108 4111 4112 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3665 C4' G D 5 OK 3667 3664 3666 3688 C4' U D 6 OK 3690 3687 3689 3708 C4' U D 7 OK 3710 3707 3709 3728 C4' C D 8 OK 3730 3727 3729 3748 C4' G D 9 OK 3750 3747 3749 3771 C4' A D 10 OK 3773 3770 3772 3793 C4' U D 11 OK 3795 3792 3794 3813 C4' C D 12 OK 3815 3812 3814 3833 C4' C D 13 OK 3835 3832 3834 3853 C4' A D 14 OK 3855 3852 3854 3875 C4' C D 15 OK 3877 3874 3876 3895 C4' A D 16 OK 3897 3894 3896 3917 C4' G D 17 OK 3919 3916 3918 3941 C4' C E 8 OK 3943 3940 3942 3961 C4' G E 9 OK 3963 3960 3962 3984 C4' A E 10 OK 3986 3983 3985 4006 C4' U E 11 OK 4008 4005 4007 4026 C4' C E 12 OK 4028 4025 4027 4046 C4' C E 13 OK 4048 4045 4047 4066 C4' A E 14 OK 4068 4065 4067 4088 C4' C E 15 OK 4090 4087 4089 4108 C4' A E 16 OK 4110 4107 4109 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3664 C5' G D 5 3663 3665 3687 C5' U D 6 3686 3688 3707 C5' U D 7 3706 3708 3727 C5' C D 8 3726 3728 3747 C5' G D 9 3746 3748 3770 C5' A D 10 3769 3771 3792 C5' U D 11 3791 3793 3812 C5' C D 12 3811 3813 3832 C5' C D 13 3831 3833 3852 C5' A D 14 3851 3853 3874 C5' C D 15 3873 3875 3894 C5' A D 16 3893 3895 3916 C5' G D 17 3915 3917 3940 C5' C E 8 3939 3941 3960 C5' G E 9 3959 3961 3983 C5' A E 10 3982 3984 4005 C5' U E 11 4004 4006 4025 C5' C E 12 4024 4026 4045 C5' C E 13 4044 4046 4065 C5' A E 14 4064 4066 4087 C5' C E 15 4086 4088 4107 C5' A E 16 4106 4108 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3660 P G D 5 OK OK 3661 3662 3663 3683 P U D 6 distorted distorted 3668 3684 3685 3686 3703 P U D 7 distorted distorted 3691 3704 3705 3706 3723 P C D 8 distorted distorted 3711 3724 3725 3726 3743 P G D 9 distorted distorted 3731 3744 3745 3746 3766 P A D 10 distorted distorted 3751 3767 3768 3769 3788 P U D 11 distorted distorted 3774 3789 3790 3791 3808 P C D 12 distorted distorted 3796 3809 3810 3811 3828 P C D 13 distorted distorted 3816 3829 3830 3831 3848 P A D 14 distorted distorted 3836 3849 3850 3851 3870 P C D 15 distorted distorted 3856 3871 3872 3873 3890 P A D 16 distorted distorted 3878 3891 3892 3893 3912 P G D 17 distorted distorted 3898 3913 3914 3915 3936 P C E 8 OK OK 3937 3938 3939 3956 P G E 9 distorted distorted 3944 3957 3958 3959 3979 P A E 10 distorted distorted 3964 3980 3981 3982 4001 P U E 11 distorted distorted 3987 4002 4003 4004 4021 P C E 12 distorted distorted 4009 4022 4023 4024 4041 P C E 13 distorted distorted 4029 4042 4043 4044 4061 P A E 14 distorted distorted 4049 4062 4063 4064 4083 P C E 15 distorted distorted 4069 4084 4085 4086 4103 P A E 16 distorted distorted 4091 4104 4105 4106 ---------------------------------------------------------------------------------