ID code: '2XNR' 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' --------------------------------------------------------------------------------- 618 C1' U C 1 beta 613 619 616 638 C1' C C 2 beta 633 639 636 658 C1' U C 3 beta 653 659 656 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 616 C2' U C 1 OK 618 614 617 636 C2' C C 2 OK 638 634 637 656 C2' U C 3 OK 658 654 657 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 614 C3' U C 1 OK 612 615 616 634 C3' C C 2 OK 632 635 636 654 C3' U C 3 OK 652 655 656 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 612 C4' U C 1 OK 614 611 613 632 C4' C C 2 OK 634 631 633 652 C4' U C 3 OK 654 651 653 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 611 C5' U C 1 610 612 631 C5' C C 2 630 632 651 C5' U C 3 650 652 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 607 P U C 1 distorted distorted 606 608 609 610 627 P C C 2 distorted distorted 615 628 629 630 647 P U C 3 OK OK 635 648 649 650 667 P U C 4 distorted distorted 655 668 669 670 ---------------------------------------------------------------------------------