ID code: '5UDK' 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' --------------------------------------------------------------------------------- 7712 C1' ATP B 1 alpha beta 7707 7729 7713 7710 7745 C1' A B 2 alpha beta 7740 7762 7746 7743 7778 C1' A B 3 alpha beta 7773 7795 7779 7776 7811 C1' A B 4 alpha beta 7806 7829 7812 7809 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7710 C2' ATP B 1 OK OK 7712 7708 7727 7711 7743 C2' A B 2 OK OK 7745 7741 7760 7744 7776 C2' A B 3 OK OK 7778 7774 7793 7777 7809 C2' A B 4 OK OK 7811 7807 7827 7810 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7708 C3' ATP B 1 OK OK 7706 7726 7709 7710 7741 C3' A B 2 OK OK 7739 7759 7742 7743 7774 C3' A B 3 OK OK 7772 7792 7775 7776 7807 C3' A B 4 OK OK 7805 7825 7808 7809 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7706 C4' ATP B 1 OK OK 7708 7725 7705 7707 7739 C4' A B 2 OK OK 7741 7758 7738 7740 7772 C4' A B 3 OK OK 7774 7791 7771 7773 7805 C4' A B 4 OK OK 7807 7824 7804 7806 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7705 C5' ATP B 1 distorted distorted 7704 7723 7724 7706 7738 C5' A B 2 OK OK 7737 7756 7757 7739 7771 C5' A B 3 OK OK 7770 7789 7790 7772 7804 C5' A B 4 OK OK 7803 7822 7823 7805 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7734 P A B 2 distorted distorted 7709 7735 7736 7737 7767 P A B 3 distorted distorted 7742 7768 7769 7770 7800 P A B 4 distorted distorted 7775 7801 7802 7803 ---------------------------------------------------------------------------------