ID code: '4QU7' 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' --------------------------------------------------------------------------------- 2565 C1' G U 802 beta 2560 2566 2563 2588 C1' G U 803 beta 2583 2589 2586 2611 C1' G U 804 beta 2606 2612 2609 2635 C1' G V 802 beta 2630 2636 2633 2658 C1' G V 803 beta 2653 2659 2656 2681 C1' G V 804 beta 2676 2682 2679 2704 C1' A V 805 beta 2699 2705 2702 2727 C1' G X 802 beta 2722 2728 2725 2750 C1' G X 803 beta 2745 2751 2748 2773 C1' G X 804 beta 2768 2774 2771 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2563 C2' G U 802 OK 2565 2561 2564 2586 C2' G U 803 OK 2588 2584 2587 2609 C2' G U 804 OK 2611 2607 2610 2633 C2' G V 802 OK 2635 2631 2634 2656 C2' G V 803 OK 2658 2654 2657 2679 C2' G V 804 OK 2681 2677 2680 2702 C2' A V 805 OK 2704 2700 2703 2725 C2' G X 802 OK 2727 2723 2726 2748 C2' G X 803 OK 2750 2746 2749 2771 C2' G X 804 OK 2773 2769 2772 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2561 C3' G U 802 OK 2559 2562 2563 2584 C3' G U 803 OK 2582 2585 2586 2607 C3' G U 804 OK 2605 2608 2609 2631 C3' G V 802 OK 2629 2632 2633 2654 C3' G V 803 OK 2652 2655 2656 2677 C3' G V 804 OK 2675 2678 2679 2700 C3' A V 805 OK 2698 2701 2702 2723 C3' G X 802 OK 2721 2724 2725 2746 C3' G X 803 OK 2744 2747 2748 2769 C3' G X 804 OK 2767 2770 2771 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2559 C4' G U 802 OK 2561 2558 2560 2582 C4' G U 803 OK 2584 2581 2583 2605 C4' G U 804 OK 2607 2604 2606 2629 C4' G V 802 OK 2631 2628 2630 2652 C4' G V 803 OK 2654 2651 2653 2675 C4' G V 804 OK 2677 2674 2676 2698 C4' A V 805 OK 2700 2697 2699 2721 C4' G X 802 OK 2723 2720 2722 2744 C4' G X 803 OK 2746 2743 2745 2767 C4' G X 804 OK 2769 2766 2768 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2558 C5' G U 802 2557 2559 2581 C5' G U 803 2580 2582 2604 C5' G U 804 2603 2605 2628 C5' G V 802 2627 2629 2651 C5' G V 803 2650 2652 2674 C5' G V 804 2673 2675 2697 C5' A V 805 2696 2698 2720 C5' G X 802 2719 2721 2743 C5' G X 803 2742 2744 2766 C5' G X 804 2765 2767 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2554 P G U 802 OK OK 2555 2556 2557 2577 P G U 803 distorted distorted 2562 2578 2579 2580 2600 P G U 804 distorted distorted 2585 2601 2602 2603 2624 P G V 802 distorted distorted 2625 2626 2627 2647 P G V 803 distorted distorted 2632 2648 2649 2650 2670 P G V 804 distorted distorted 2655 2671 2672 2673 2693 P A V 805 distorted distorted 2678 2694 2695 2696 2716 P G X 802 OK OK 2717 2718 2719 2739 P G X 803 distorted distorted 2724 2740 2741 2742 2762 P G X 804 distorted distorted 2747 2763 2764 2765 ---------------------------------------------------------------------------------