ID code: '1XZR' 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' --------------------------------------------------------------------------------- 2220 C1' G X 1 beta 2216 2221 2219 2242 C1' C X 2 beta 2238 2243 2241 2261 C1' G X 3 beta 2257 2262 2260 2283 C1' T X 4 beta 2279 2284 2282 2303 C1' C X 5 beta 2299 2304 2302 2322 C1' C X 6 beta 2318 2323 2321 2339 C1' 3DR X 7 2338 2335 2361 C1' C X 8 beta 2357 2362 2360 2380 C1' G X 9 beta 2376 2381 2379 2402 C1' A X 10 beta 2398 2403 2401 2423 C1' C X 11 beta 2419 2424 2422 2442 C1' G X 12 beta 2438 2443 2441 2464 C1' A X 13 beta 2460 2465 2463 2485 C1' C X 14 beta 2481 2486 2484 2504 C1' G X 15 beta 2500 2505 2503 2524 C1' G Y 17 beta 2520 2525 2523 2546 C1' T Y 18 beta 2542 2547 2545 2566 C1' C Y 19 beta 2562 2567 2565 2585 C1' G Y 20 beta 2581 2586 2584 2607 C1' T Y 21 beta 2603 2608 2606 2627 C1' C Y 22 beta 2623 2628 2626 2646 C1' G Y 23 beta 2642 2647 2645 2668 C1' G Y 24 beta 2664 2669 2667 2690 C1' G Y 25 beta 2686 2691 2689 2712 C1' G Y 26 beta 2708 2713 2711 2734 C1' A Y 27 beta 2730 2735 2733 2755 C1' C Y 28 beta 2751 2756 2754 2774 C1' G Y 29 beta 2770 2775 2773 2796 C1' C Y 30 beta 2792 2797 2795 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2219 C2' G X 1 2220 2217 2241 C2' C X 2 2242 2239 2260 C2' G X 3 2261 2258 2282 C2' T X 4 2283 2280 2302 C2' C X 5 2303 2300 2321 C2' C X 6 2322 2319 2335 C2' 3DR X 7 OK OK 2339 2340 2343 2344 2360 C2' C X 8 2361 2358 2379 C2' G X 9 2380 2377 2401 C2' A X 10 2402 2399 2422 C2' C X 11 2423 2420 2441 C2' G X 12 2442 2439 2463 C2' A X 13 2464 2461 2484 C2' C X 14 2485 2482 2503 C2' G X 15 2504 2501 2523 C2' G Y 17 2524 2521 2545 C2' T Y 18 2546 2543 2565 C2' C Y 19 2566 2563 2584 C2' G Y 20 2585 2582 2606 C2' T Y 21 2607 2604 2626 C2' C Y 22 2627 2624 2645 C2' G Y 23 2646 2643 2667 C2' G Y 24 2668 2665 2689 C2' G Y 25 2690 2687 2711 C2' G Y 26 2712 2709 2733 C2' A Y 27 2734 2731 2754 C2' C Y 28 2755 2752 2773 C2' G Y 29 2774 2771 2795 C2' C Y 30 2796 2793 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2217 C3' G X 1 OK 2215 2218 2219 2239 C3' C X 2 OK 2237 2240 2241 2258 C3' G X 3 OK 2256 2259 2260 2280 C3' T X 4 OK 2278 2281 2282 2300 C3' C X 5 OK 2298 2301 2302 2319 C3' C X 6 OK 2317 2320 2321 2340 C3' 3DR X 7 OK OK 2337 2350 2341 2335 2358 C3' C X 8 OK 2356 2359 2360 2377 C3' G X 9 OK 2375 2378 2379 2399 C3' A X 10 OK 2397 2400 2401 2420 C3' C X 11 OK 2418 2421 2422 2439 C3' G X 12 OK 2437 2440 2441 2461 C3' A X 13 OK 2459 2462 2463 2482 C3' C X 14 OK 2480 2483 2484 2501 C3' G X 15 OK 2499 2502 2503 2521 C3' G Y 17 OK 2519 2522 2523 2543 C3' T Y 18 OK 2541 2544 2545 2563 C3' C Y 19 OK 2561 2564 2565 2582 C3' G Y 20 OK 2580 2583 2584 2604 C3' T Y 21 OK 2602 2605 2606 2624 C3' C Y 22 OK 2622 2625 2626 2643 C3' G Y 23 OK 2641 2644 2645 2665 C3' G Y 24 OK 2663 2666 2667 2687 C3' G Y 25 OK 2685 2688 2689 2709 C3' G Y 26 OK 2707 2710 2711 2731 C3' A Y 27 OK 2729 2732 2733 2752 C3' C Y 28 OK 2750 2753 2754 2771 C3' G Y 29 OK 2769 2772 2773 2793 C3' C Y 30 OK 2791 2794 2795 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2215 C4' G X 1 OK 2217 2214 2216 2237 C4' C X 2 OK 2239 2236 2238 2256 C4' G X 3 OK 2258 2255 2257 2278 C4' T X 4 OK 2280 2277 2279 2298 C4' C X 5 OK 2300 2297 2299 2317 C4' C X 6 OK 2319 2316 2318 2337 C4' 3DR X 7 OK 2340 2336 2338 2356 C4' C X 8 OK 2358 2355 2357 2375 C4' G X 9 OK 2377 2374 2376 2397 C4' A X 10 OK 2399 2396 2398 2418 C4' C X 11 OK 2420 2417 2419 2437 C4' G X 12 OK 2439 2436 2438 2459 C4' A X 13 OK 2461 2458 2460 2480 C4' C X 14 OK 2482 2479 2481 2499 C4' G X 15 OK 2501 2498 2500 2519 C4' G Y 17 OK 2521 2518 2520 2541 C4' T Y 18 OK 2543 2540 2542 2561 C4' C Y 19 OK 2563 2560 2562 2580 C4' G Y 20 OK 2582 2579 2581 2602 C4' T Y 21 OK 2604 2601 2603 2622 C4' C Y 22 OK 2624 2621 2623 2641 C4' G Y 23 OK 2643 2640 2642 2663 C4' G Y 24 OK 2665 2662 2664 2685 C4' G Y 25 OK 2687 2684 2686 2707 C4' G Y 26 OK 2709 2706 2708 2729 C4' A Y 27 OK 2731 2728 2730 2750 C4' C Y 28 OK 2752 2749 2751 2769 C4' G Y 29 OK 2771 2768 2770 2791 C4' C Y 30 OK 2793 2790 2792 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2214 C5' G X 1 2213 2215 2236 C5' C X 2 2235 2237 2255 C5' G X 3 2254 2256 2277 C5' T X 4 2276 2278 2297 C5' C X 5 2296 2298 2316 C5' C X 6 2315 2317 2336 C5' 3DR X 7 OK OK 2331 2345 2346 2337 2355 C5' C X 8 2354 2356 2374 C5' G X 9 2373 2375 2396 C5' A X 10 2395 2397 2417 C5' C X 11 2416 2418 2436 C5' G X 12 2435 2437 2458 C5' A X 13 2457 2459 2479 C5' C X 14 2478 2480 2498 C5' G X 15 2497 2499 2518 C5' G Y 17 2517 2519 2540 C5' T Y 18 2539 2541 2560 C5' C Y 19 2559 2561 2579 C5' G Y 20 2578 2580 2601 C5' T Y 21 2600 2602 2621 C5' C Y 22 2620 2622 2640 C5' G Y 23 2639 2641 2662 C5' G Y 24 2661 2663 2684 C5' G Y 25 2683 2685 2706 C5' G Y 26 2705 2707 2728 C5' A Y 27 2727 2729 2749 C5' C Y 28 2748 2750 2768 C5' G Y 29 2767 2769 2790 C5' C Y 30 2789 2791 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2232 P C X 2 distorted distorted 2218 2233 2234 2235 2251 P G X 3 distorted distorted 2240 2252 2253 2254 2273 P T X 4 distorted distorted 2259 2274 2275 2276 2293 P C X 5 distorted distorted 2281 2294 2295 2296 2312 P C X 6 distorted distorted 2301 2313 2314 2315 2332 P 3DR X 7 distorted distorted 2320 2333 2334 2331 2351 P C X 8 distorted distorted 2341 2352 2353 2354 2370 P G X 9 distorted distorted 2359 2371 2372 2373 2392 P A X 10 distorted distorted 2378 2393 2394 2395 2413 P C X 11 distorted distorted 2400 2414 2415 2416 2432 P G X 12 distorted distorted 2421 2433 2434 2435 2454 P A X 13 distorted distorted 2440 2455 2456 2457 2475 P C X 14 distorted distorted 2462 2476 2477 2478 2494 P G X 15 distorted distorted 2483 2495 2496 2497 2536 P T Y 18 distorted distorted 2522 2537 2538 2539 2556 P C Y 19 distorted distorted 2544 2557 2558 2559 2575 P G Y 20 distorted distorted 2564 2576 2577 2578 2597 P T Y 21 distorted distorted 2583 2598 2599 2600 2617 P C Y 22 distorted distorted 2605 2618 2619 2620 2636 P G Y 23 distorted distorted 2625 2637 2638 2639 2658 P G Y 24 distorted distorted 2644 2659 2660 2661 2680 P G Y 25 distorted distorted 2666 2681 2682 2683 2702 P G Y 26 distorted distorted 2688 2703 2704 2705 2724 P A Y 27 distorted distorted 2710 2725 2726 2727 2745 P C Y 28 distorted distorted 2732 2746 2747 2748 2764 P G Y 29 distorted distorted 2753 2765 2766 2767 2786 P C Y 30 distorted distorted 2772 2787 2788 2789 ---------------------------------------------------------------------------------