ID code: '4WKR' 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' --------------------------------------------------------------------------------- 2550 C1' U C -3 beta 2545 2551 2548 2570 C1' U C -2 beta 2565 2571 2568 2590 C1' U C -1 beta 2585 2591 2588 2611 C1' C D -5 beta 2606 2612 2609 2631 C1' U D -4 beta 2626 2632 2629 2651 C1' U D -3 beta 2646 2652 2649 2671 C1' U D -2 beta 2666 2672 2669 2691 C1' U D -1 beta 2686 2692 2689 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2548 C2' U C -3 OK 2550 2546 2549 2568 C2' U C -2 OK 2570 2566 2569 2588 C2' U C -1 OK 2590 2586 2589 2609 C2' C D -5 OK 2611 2607 2610 2629 C2' U D -4 OK 2631 2627 2630 2649 C2' U D -3 OK 2651 2647 2650 2669 C2' U D -2 OK 2671 2667 2670 2689 C2' U D -1 OK 2691 2687 2690 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2546 C3' U C -3 OK 2544 2547 2548 2566 C3' U C -2 OK 2564 2567 2568 2586 C3' U C -1 OK 2584 2587 2588 2607 C3' C D -5 OK 2605 2608 2609 2627 C3' U D -4 OK 2625 2628 2629 2647 C3' U D -3 OK 2645 2648 2649 2667 C3' U D -2 OK 2665 2668 2669 2687 C3' U D -1 OK 2685 2688 2689 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2544 C4' U C -3 OK 2546 2543 2545 2564 C4' U C -2 OK 2566 2563 2565 2584 C4' U C -1 OK 2586 2583 2585 2605 C4' C D -5 OK 2607 2604 2606 2625 C4' U D -4 OK 2627 2624 2626 2645 C4' U D -3 OK 2647 2644 2646 2665 C4' U D -2 OK 2667 2664 2666 2685 C4' U D -1 OK 2687 2684 2686 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2543 C5' U C -3 2542 2544 2563 C5' U C -2 2562 2564 2583 C5' U C -1 2582 2584 2604 C5' C D -5 2603 2605 2624 C5' U D -4 2623 2625 2644 C5' U D -3 2643 2645 2664 C5' U D -2 2663 2665 2684 C5' U D -1 2683 2685 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2531 P C C -5 distorted distorted 2532 2533 2534 2535 P U C -4 distorted distorted 2536 2537 2538 2539 P U C -3 distorted distorted 2540 2541 2542 2559 P U C -2 distorted distorted 2547 2560 2561 2562 2579 P U C -1 distorted distorted 2567 2580 2581 2582 2600 P C D -5 OK OK 2601 2602 2603 2620 P U D -4 distorted distorted 2608 2621 2622 2623 2640 P U D -3 distorted distorted 2628 2641 2642 2643 2660 P U D -2 distorted distorted 2648 2661 2662 2663 2680 P U D -1 distorted distorted 2668 2681 2682 2683 ---------------------------------------------------------------------------------