ID code: '3UQ0' 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' --------------------------------------------------------------------------------- 2358 C1' DC T 1 beta 2354 2359 2357 2377 C1' DG T 2 beta 2373 2378 2376 2399 C1' DG T 3 beta 2395 2400 2398 2421 C1' DC T 4 beta 2417 2422 2420 2440 C1' DT T 5 beta 2436 2441 2439 2460 C1' DG T 6 beta 2456 2461 2459 2482 C1' DT T 7 beta 2478 2483 2481 2502 C1' DA T 8 beta 2498 2503 2501 2523 C1' DC T 9 beta 2519 2524 2522 2542 C1' DT T 10 beta 2538 2543 2541 2562 C1' DG T 11 beta 2558 2563 2561 2582 C1' DC P 1 beta 2578 2583 2581 2601 C1' DA P 2 beta 2597 2602 2600 2622 C1' DG P 3 beta 2618 2623 2621 2644 C1' DT P 4 beta 2640 2645 2643 2664 C1' DA P 5 beta 2660 2665 2663 2685 C1' DC P 6 beta 2681 2686 2684 2705 C1' A P 7 beta 2700 2706 2703 2728 C1' DG D 1 beta 2724 2729 2727 2750 C1' DC D 2 beta 2746 2751 2749 2769 C1' DC D 3 beta 2765 2770 2768 2788 C1' DG D 4 beta 2784 2789 2787 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2357 C2' DC T 1 2358 2355 2376 C2' DG T 2 2377 2374 2398 C2' DG T 3 2399 2396 2420 C2' DC T 4 2421 2418 2439 C2' DT T 5 2440 2437 2459 C2' DG T 6 2460 2457 2481 C2' DT T 7 2482 2479 2501 C2' DA T 8 2502 2499 2522 C2' DC T 9 2523 2520 2541 C2' DT T 10 2542 2539 2561 C2' DG T 11 2562 2559 2581 C2' DC P 1 2582 2579 2600 C2' DA P 2 2601 2598 2621 C2' DG P 3 2622 2619 2643 C2' DT P 4 2644 2641 2663 C2' DA P 5 2664 2661 2684 C2' DC P 6 2685 2682 2703 C2' A P 7 OK 2705 2701 2704 2727 C2' DG D 1 2728 2725 2749 C2' DC D 2 2750 2747 2768 C2' DC D 3 2769 2766 2787 C2' DG D 4 2788 2785 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2355 C3' DC T 1 OK 2353 2356 2357 2374 C3' DG T 2 OK 2372 2375 2376 2396 C3' DG T 3 OK 2394 2397 2398 2418 C3' DC T 4 OK 2416 2419 2420 2437 C3' DT T 5 OK 2435 2438 2439 2457 C3' DG T 6 OK 2455 2458 2459 2479 C3' DT T 7 OK 2477 2480 2481 2499 C3' DA T 8 OK 2497 2500 2501 2520 C3' DC T 9 OK 2518 2521 2522 2539 C3' DT T 10 OK 2537 2540 2541 2559 C3' DG T 11 OK 2557 2560 2561 2579 C3' DC P 1 OK 2577 2580 2581 2598 C3' DA P 2 OK 2596 2599 2600 2619 C3' DG P 3 OK 2617 2620 2621 2641 C3' DT P 4 OK 2639 2642 2643 2661 C3' DA P 5 OK 2659 2662 2663 2682 C3' DC P 6 OK 2680 2683 2684 2701 C3' A P 7 OK 2699 2702 2703 2725 C3' DG D 1 OK 2723 2726 2727 2747 C3' DC D 2 OK 2745 2748 2749 2766 C3' DC D 3 OK 2764 2767 2768 2785 C3' DG D 4 OK 2783 2786 2787 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2353 C4' DC T 1 OK 2355 2352 2354 2372 C4' DG T 2 OK 2374 2371 2373 2394 C4' DG T 3 OK 2396 2393 2395 2416 C4' DC T 4 OK 2418 2415 2417 2435 C4' DT T 5 OK 2437 2434 2436 2455 C4' DG T 6 OK 2457 2454 2456 2477 C4' DT T 7 OK 2479 2476 2478 2497 C4' DA T 8 OK 2499 2496 2498 2518 C4' DC T 9 OK 2520 2517 2519 2537 C4' DT T 10 OK 2539 2536 2538 2557 C4' DG T 11 OK 2559 2556 2558 2577 C4' DC P 1 OK 2579 2576 2578 2596 C4' DA P 2 OK 2598 2595 2597 2617 C4' DG P 3 OK 2619 2616 2618 2639 C4' DT P 4 OK 2641 2638 2640 2659 C4' DA P 5 OK 2661 2658 2660 2680 C4' DC P 6 OK 2682 2679 2681 2699 C4' A P 7 OK 2701 2698 2700 2723 C4' DG D 1 OK 2725 2722 2724 2745 C4' DC D 2 OK 2747 2744 2746 2764 C4' DC D 3 OK 2766 2763 2765 2783 C4' DG D 4 OK 2785 2782 2784 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2352 C5' DC T 1 2351 2353 2371 C5' DG T 2 2370 2372 2393 C5' DG T 3 2392 2394 2415 C5' DC T 4 2414 2416 2434 C5' DT T 5 2433 2435 2454 C5' DG T 6 2453 2455 2476 C5' DT T 7 2475 2477 2496 C5' DA T 8 2495 2497 2517 C5' DC T 9 2516 2518 2536 C5' DT T 10 2535 2537 2556 C5' DG T 11 2555 2557 2576 C5' DC P 1 2575 2577 2595 C5' DA P 2 2594 2596 2616 C5' DG P 3 2615 2617 2638 C5' DT P 4 2637 2639 2658 C5' DA P 5 2657 2659 2679 C5' DC P 6 2678 2680 2698 C5' A P 7 2697 2699 2722 C5' DG D 1 2721 2723 2744 C5' DC D 2 2743 2745 2763 C5' DC D 3 2762 2764 2782 C5' DG D 4 2781 2783 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2367 P DG T 2 distorted distorted 2356 2368 2369 2370 2389 P DG T 3 distorted distorted 2375 2390 2391 2392 2411 P DC T 4 distorted distorted 2397 2412 2413 2414 2430 P DT T 5 distorted distorted 2419 2431 2432 2433 2450 P DG T 6 distorted distorted 2438 2451 2452 2453 2472 P DT T 7 distorted distorted 2458 2473 2474 2475 2492 P DA T 8 distorted distorted 2480 2493 2494 2495 2513 P DC T 9 distorted distorted 2500 2514 2515 2516 2532 P DT T 10 distorted distorted 2521 2533 2534 2535 2552 P DG T 11 distorted distorted 2540 2553 2554 2555 2591 P DA P 2 distorted distorted 2580 2592 2593 2594 2612 P DG P 3 distorted distorted 2599 2613 2614 2615 2634 P DT P 4 distorted distorted 2620 2635 2636 2637 2654 P DA P 5 distorted distorted 2642 2655 2656 2657 2675 P DC P 6 distorted distorted 2662 2676 2677 2678 2694 P A P 7 distorted distorted 2683 2695 2696 2697 2718 P DG D 1 OK OK 2719 2720 2721 2740 P DC D 2 distorted distorted 2726 2741 2742 2743 2759 P DC D 3 distorted distorted 2748 2760 2761 2762 2778 P DG D 4 distorted distorted 2767 2779 2780 2781 ---------------------------------------------------------------------------------