ID code: '3UQ2' 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' --------------------------------------------------------------------------------- 2404 C1' DC T 1 beta 2400 2405 2403 2423 C1' DG T 2 beta 2419 2424 2422 2445 C1' DG T 3 beta 2441 2446 2444 2467 C1' DC T 4 beta 2463 2468 2466 2486 C1' DT T 5 beta 2482 2487 2485 2506 C1' DG T 6 beta 2502 2507 2505 2528 C1' DT T 7 beta 2524 2529 2527 2548 C1' DA T 8 beta 2544 2549 2547 2569 C1' DC T 9 beta 2565 2570 2568 2588 C1' DT T 10 beta 2584 2589 2587 2608 C1' DG T 11 beta 2604 2609 2607 2628 C1' DC P 1 beta 2624 2629 2627 2647 C1' DA P 2 beta 2643 2648 2646 2668 C1' DG P 3 beta 2664 2669 2667 2690 C1' DT P 4 beta 2686 2691 2689 2710 C1' DA P 5 beta 2706 2711 2709 2732 C1' C P 6 beta 2727 2733 2730 2751 C1' DA P 7 beta 2747 2752 2750 2774 C1' DG D 1 beta 2770 2775 2773 2796 C1' DC D 2 beta 2792 2797 2795 2815 C1' DC D 3 beta 2811 2816 2814 2834 C1' DG D 4 beta 2830 2835 2833 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2403 C2' DC T 1 2404 2401 2422 C2' DG T 2 2423 2420 2444 C2' DG T 3 2445 2442 2466 C2' DC T 4 2467 2464 2485 C2' DT T 5 2486 2483 2505 C2' DG T 6 2506 2503 2527 C2' DT T 7 2528 2525 2547 C2' DA T 8 2548 2545 2568 C2' DC T 9 2569 2566 2587 C2' DT T 10 2588 2585 2607 C2' DG T 11 2608 2605 2627 C2' DC P 1 2628 2625 2646 C2' DA P 2 2647 2644 2667 C2' DG P 3 2668 2665 2689 C2' DT P 4 2690 2687 2709 C2' DA P 5 2710 2707 2730 C2' C P 6 OK 2732 2728 2731 2750 C2' DA P 7 2751 2748 2773 C2' DG D 1 2774 2771 2795 C2' DC D 2 2796 2793 2814 C2' DC D 3 2815 2812 2833 C2' DG D 4 2834 2831 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2401 C3' DC T 1 OK 2399 2402 2403 2420 C3' DG T 2 OK 2418 2421 2422 2442 C3' DG T 3 OK 2440 2443 2444 2464 C3' DC T 4 OK 2462 2465 2466 2483 C3' DT T 5 OK 2481 2484 2485 2503 C3' DG T 6 OK 2501 2504 2505 2525 C3' DT T 7 OK 2523 2526 2527 2545 C3' DA T 8 OK 2543 2546 2547 2566 C3' DC T 9 OK 2564 2567 2568 2585 C3' DT T 10 OK 2583 2586 2587 2605 C3' DG T 11 OK 2603 2606 2607 2625 C3' DC P 1 OK 2623 2626 2627 2644 C3' DA P 2 OK 2642 2645 2646 2665 C3' DG P 3 OK 2663 2666 2667 2687 C3' DT P 4 OK 2685 2688 2689 2707 C3' DA P 5 OK 2705 2708 2709 2728 C3' C P 6 OK 2726 2729 2730 2748 C3' DA P 7 OK 2746 2749 2750 2771 C3' DG D 1 OK 2769 2772 2773 2793 C3' DC D 2 OK 2791 2794 2795 2812 C3' DC D 3 OK 2810 2813 2814 2831 C3' DG D 4 OK 2829 2832 2833 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2399 C4' DC T 1 OK 2401 2398 2400 2418 C4' DG T 2 OK 2420 2417 2419 2440 C4' DG T 3 OK 2442 2439 2441 2462 C4' DC T 4 OK 2464 2461 2463 2481 C4' DT T 5 OK 2483 2480 2482 2501 C4' DG T 6 OK 2503 2500 2502 2523 C4' DT T 7 OK 2525 2522 2524 2543 C4' DA T 8 OK 2545 2542 2544 2564 C4' DC T 9 OK 2566 2563 2565 2583 C4' DT T 10 OK 2585 2582 2584 2603 C4' DG T 11 OK 2605 2602 2604 2623 C4' DC P 1 OK 2625 2622 2624 2642 C4' DA P 2 OK 2644 2641 2643 2663 C4' DG P 3 OK 2665 2662 2664 2685 C4' DT P 4 OK 2687 2684 2686 2705 C4' DA P 5 OK 2707 2704 2706 2726 C4' C P 6 OK 2728 2725 2727 2746 C4' DA P 7 OK 2748 2745 2747 2769 C4' DG D 1 OK 2771 2768 2770 2791 C4' DC D 2 OK 2793 2790 2792 2810 C4' DC D 3 OK 2812 2809 2811 2829 C4' DG D 4 OK 2831 2828 2830 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2398 C5' DC T 1 2397 2399 2417 C5' DG T 2 2416 2418 2439 C5' DG T 3 2438 2440 2461 C5' DC T 4 2460 2462 2480 C5' DT T 5 2479 2481 2500 C5' DG T 6 2499 2501 2522 C5' DT T 7 2521 2523 2542 C5' DA T 8 2541 2543 2563 C5' DC T 9 2562 2564 2582 C5' DT T 10 2581 2583 2602 C5' DG T 11 2601 2603 2622 C5' DC P 1 2621 2623 2641 C5' DA P 2 2640 2642 2662 C5' DG P 3 2661 2663 2684 C5' DT P 4 2683 2685 2704 C5' DA P 5 2703 2705 2725 C5' C P 6 2724 2726 2745 C5' DA P 7 2744 2746 2768 C5' DG D 1 2767 2769 2790 C5' DC D 2 2789 2791 2809 C5' DC D 3 2808 2810 2828 C5' DG D 4 2827 2829 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2413 P DG T 2 distorted distorted 2402 2414 2415 2416 2435 P DG T 3 distorted distorted 2421 2436 2437 2438 2457 P DC T 4 distorted distorted 2443 2458 2459 2460 2476 P DT T 5 distorted distorted 2465 2477 2478 2479 2496 P DG T 6 distorted distorted 2484 2497 2498 2499 2518 P DT T 7 distorted distorted 2504 2519 2520 2521 2538 P DA T 8 distorted distorted 2526 2539 2540 2541 2559 P DC T 9 distorted distorted 2546 2560 2561 2562 2578 P DT T 10 distorted distorted 2567 2579 2580 2581 2598 P DG T 11 distorted distorted 2586 2599 2600 2601 2637 P DA P 2 distorted distorted 2626 2638 2639 2640 2658 P DG P 3 distorted distorted 2645 2659 2660 2661 2680 P DT P 4 distorted distorted 2666 2681 2682 2683 2700 P DA P 5 distorted distorted 2688 2701 2702 2703 2721 P C P 6 distorted distorted 2708 2722 2723 2724 2741 P DA P 7 distorted distorted 2729 2742 2743 2744 2764 P DG D 1 OK OK 2765 2766 2767 2786 P DC D 2 distorted distorted 2772 2787 2788 2789 2805 P DC D 3 distorted distorted 2794 2806 2807 2808 2824 P DG D 4 distorted distorted 2813 2825 2826 2827 ---------------------------------------------------------------------------------