ID code: '3BDP' 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' --------------------------------------------------------------------------------- 4665 C1' G P 7 beta 4661 4666 4664 4687 C1' C P 8 beta 4683 4688 4686 4706 C1' A P 9 beta 4702 4707 4705 4727 C1' T P 10 beta 4723 4728 4726 4747 C1' G P 11 beta 4743 4748 4746 4769 C1' A P 12 beta 4765 4770 4768 4790 C1' T P 13 beta 4786 4791 4789 4810 C1' G P 14 beta 4806 4811 4809 4832 C1' C P 15 beta 4828 4833 4831 4858 C1' 2DT P 16 beta 4857 4845 4854 4868 C1' A T 18 beta 4864 4869 4867 4889 C1' G T 19 beta 4885 4890 4888 4911 C1' C T 20 beta 4907 4912 4910 4930 C1' A T 21 beta 4926 4931 4929 4951 C1' T T 22 beta 4947 4952 4950 4971 C1' C T 23 beta 4967 4972 4970 4990 C1' A T 24 beta 4986 4991 4989 5011 C1' T T 25 beta 5007 5012 5010 5031 C1' G T 26 beta 5027 5032 5030 5053 C1' C T 27 beta 5049 5054 5052 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4664 C2' G P 7 4665 4662 4686 C2' C P 8 4687 4684 4705 C2' A P 9 4706 4703 4726 C2' T P 10 4727 4724 4746 C2' G P 11 4747 4744 4768 C2' A P 12 4769 4766 4789 C2' T P 13 4790 4787 4809 C2' G P 14 4810 4807 4831 C2' C P 15 4832 4829 4854 C2' 2DT P 16 4858 4859 4867 C2' A T 18 4868 4865 4888 C2' G T 19 4889 4886 4910 C2' C T 20 4911 4908 4929 C2' A T 21 4930 4927 4950 C2' T T 22 4951 4948 4970 C2' C T 23 4971 4968 4989 C2' A T 24 4990 4987 5010 C2' T T 25 5011 5008 5030 C2' G T 26 5031 5028 5052 C2' C T 27 5053 5050 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4662 C3' G P 7 OK 4660 4663 4664 4684 C3' C P 8 OK 4682 4685 4686 4703 C3' A P 9 OK 4701 4704 4705 4724 C3' T P 10 OK 4722 4725 4726 4744 C3' G P 11 OK 4742 4745 4746 4766 C3' A P 12 OK 4764 4767 4768 4787 C3' T P 13 OK 4785 4788 4789 4807 C3' G P 14 OK 4805 4808 4809 4829 C3' C P 15 OK 4827 4830 4831 4859 C3' 2DT P 16 4856 4854 4865 C3' A T 18 OK 4863 4866 4867 4886 C3' G T 19 OK 4884 4887 4888 4908 C3' C T 20 OK 4906 4909 4910 4927 C3' A T 21 OK 4925 4928 4929 4948 C3' T T 22 OK 4946 4949 4950 4968 C3' C T 23 OK 4966 4969 4970 4987 C3' A T 24 OK 4985 4988 4989 5008 C3' T T 25 OK 5006 5009 5010 5028 C3' G T 26 OK 5026 5029 5030 5050 C3' C T 27 OK 5048 5051 5052 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4660 C4' G P 7 OK 4662 4659 4661 4682 C4' C P 8 OK 4684 4681 4683 4701 C4' A P 9 OK 4703 4700 4702 4722 C4' T P 10 OK 4724 4721 4723 4742 C4' G P 11 OK 4744 4741 4743 4764 C4' A P 12 OK 4766 4763 4765 4785 C4' T P 13 OK 4787 4784 4786 4805 C4' G P 14 OK 4807 4804 4806 4827 C4' C P 15 OK 4829 4826 4828 4856 C4' 2DT P 16 OK 4859 4855 4857 4863 C4' A T 18 OK 4865 4862 4864 4884 C4' G T 19 OK 4886 4883 4885 4906 C4' C T 20 OK 4908 4905 4907 4925 C4' A T 21 OK 4927 4924 4926 4946 C4' T T 22 OK 4948 4945 4947 4966 C4' C T 23 OK 4968 4965 4967 4985 C4' A T 24 OK 4987 4984 4986 5006 C4' T T 25 OK 5008 5005 5007 5026 C4' G T 26 OK 5028 5025 5027 5048 C4' C T 27 OK 5050 5047 5049 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4659 C5' G P 7 4658 4660 4681 C5' C P 8 4680 4682 4700 C5' A P 9 4699 4701 4721 C5' T P 10 4720 4722 4741 C5' G P 11 4740 4742 4763 C5' A P 12 4762 4764 4784 C5' T P 13 4783 4785 4804 C5' G P 14 4803 4805 4826 C5' C P 15 4825 4827 4855 C5' 2DT P 16 4844 4856 4862 C5' A T 18 4861 4863 4883 C5' G T 19 4882 4884 4905 C5' C T 20 4904 4906 4924 C5' A T 21 4923 4925 4945 C5' T T 22 4944 4946 4965 C5' C T 23 4964 4966 4984 C5' A T 24 4983 4985 5005 C5' T T 25 5004 5006 5025 C5' G T 26 5024 5026 5047 C5' C T 27 5046 5048 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4677 P C P 8 OK OK 4663 4678 4679 4680 4696 P A P 9 OK OK 4685 4697 4698 4699 4717 P T P 10 OK OK 4704 4718 4719 4720 4737 P G P 11 OK OK 4725 4738 4739 4740 4759 P A P 12 OK OK 4745 4760 4761 4762 4780 P T P 13 OK OK 4767 4781 4782 4783 4800 P G P 14 OK OK 4788 4801 4802 4803 4822 P C P 15 OK OK 4808 4823 4824 4825 4841 P 2DT P 16 OK OK 4830 4842 4843 4844 4879 P G T 19 OK OK 4866 4880 4881 4882 4901 P C T 20 OK OK 4887 4902 4903 4904 4920 P A T 21 OK OK 4909 4921 4922 4923 4941 P T T 22 OK OK 4928 4942 4943 4944 4961 P C T 23 OK OK 4949 4962 4963 4964 4980 P A T 24 OK OK 4969 4981 4982 4983 5001 P T T 25 OK OK 4988 5002 5003 5004 5021 P G T 26 OK OK 5009 5022 5023 5024 5043 P C T 27 OK OK 5029 5044 5045 5046 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