ID code: '2XZL' 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' --------------------------------------------------------------------------------- 5662 C1' U B 1 beta 5657 5663 5660 5682 C1' U B 2 beta 5677 5683 5680 5702 C1' U B 3 beta 5697 5703 5700 5722 C1' U B 4 beta 5717 5723 5720 5742 C1' U B 5 beta 5737 5743 5740 5762 C1' U B 6 beta 5757 5763 5760 5782 C1' U B 7 beta 5777 5783 5780 5802 C1' U B 8 beta 5797 5803 5800 5835 C1' ADP A1854 beta 5830 5836 5833 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5660 C2' U B 1 OK 5662 5658 5661 5680 C2' U B 2 OK 5682 5678 5681 5700 C2' U B 3 OK 5702 5698 5701 5720 C2' U B 4 OK 5722 5718 5721 5740 C2' U B 5 OK 5742 5738 5741 5760 C2' U B 6 OK 5762 5758 5761 5780 C2' U B 7 OK 5782 5778 5781 5800 C2' U B 8 OK 5802 5798 5801 5833 C2' ADP A1854 OK 5835 5831 5834 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5658 C3' U B 1 OK 5656 5659 5660 5678 C3' U B 2 OK 5676 5679 5680 5698 C3' U B 3 OK 5696 5699 5700 5718 C3' U B 4 OK 5716 5719 5720 5738 C3' U B 5 OK 5736 5739 5740 5758 C3' U B 6 OK 5756 5759 5760 5778 C3' U B 7 OK 5776 5779 5780 5798 C3' U B 8 OK 5796 5799 5800 5831 C3' ADP A1854 OK 5829 5832 5833 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5656 C4' U B 1 OK 5658 5655 5657 5676 C4' U B 2 OK 5678 5675 5677 5696 C4' U B 3 OK 5698 5695 5697 5716 C4' U B 4 OK 5718 5715 5717 5736 C4' U B 5 OK 5738 5735 5737 5756 C4' U B 6 OK 5758 5755 5757 5776 C4' U B 7 OK 5778 5775 5777 5796 C4' U B 8 OK 5798 5795 5797 5829 C4' ADP A1854 OK 5831 5828 5830 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5655 C5' U B 1 5654 5656 5675 C5' U B 2 5674 5676 5695 C5' U B 3 5694 5696 5715 C5' U B 4 5714 5716 5735 C5' U B 5 5734 5736 5755 C5' U B 6 5754 5756 5775 C5' U B 7 5774 5776 5795 C5' U B 8 5794 5796 5828 C5' ADP A1854 5827 5829 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5651 P U B 1 distorted distorted 5652 5653 5654 5671 P U B 2 distorted distorted 5659 5672 5673 5674 5691 P U B 3 distorted distorted 5679 5692 5693 5694 5711 P U B 4 OK OK 5699 5712 5713 5714 5731 P U B 5 distorted distorted 5719 5732 5733 5734 5751 P U B 6 distorted distorted 5739 5752 5753 5754 5771 P U B 7 distorted distorted 5759 5772 5773 5774 5791 P U B 8 distorted distorted 5779 5792 5793 5794 5811 P U B 9 distorted distorted 5799 5812 5813 5814 ---------------------------------------------------------------------------------