ID code: '1XZS' 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' --------------------------------------------------------------------------------- 2223 C1' G X 1 beta 2219 2224 2222 2245 C1' C X 2 beta 2241 2246 2244 2264 C1' G X 3 beta 2260 2265 2263 2286 C1' T X 4 beta 2282 2287 2285 2306 C1' C X 5 beta 2302 2307 2305 2325 C1' C X 6 beta 2321 2326 2324 2342 C1' 3DR X 7 2341 2338 2364 C1' C X 8 beta 2360 2365 2363 2383 C1' G X 9 beta 2379 2384 2382 2405 C1' A X 10 beta 2401 2406 2404 2426 C1' C X 11 beta 2422 2427 2425 2445 C1' G X 12 beta 2441 2446 2444 2467 C1' A X 13 beta 2463 2468 2466 2488 C1' C X 14 beta 2484 2489 2487 2507 C1' G X 15 beta 2503 2508 2506 2527 C1' G Y 17 beta 2523 2528 2526 2549 C1' T Y 18 beta 2545 2550 2548 2569 C1' C Y 19 beta 2565 2570 2568 2588 C1' G Y 20 beta 2584 2589 2587 2610 C1' T Y 21 beta 2606 2611 2609 2630 C1' C Y 22 beta 2626 2631 2629 2649 C1' G Y 23 beta 2645 2650 2648 2671 C1' G Y 24 beta 2667 2672 2670 2693 C1' G Y 25 beta 2689 2694 2692 2715 C1' G Y 26 beta 2711 2716 2714 2737 C1' A Y 27 beta 2733 2738 2736 2758 C1' C Y 28 beta 2754 2759 2757 2777 C1' G Y 29 beta 2773 2778 2776 2799 C1' C Y 30 beta 2795 2800 2798 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2222 C2' G X 1 2223 2220 2244 C2' C X 2 2245 2242 2263 C2' G X 3 2264 2261 2285 C2' T X 4 2286 2283 2305 C2' C X 5 2306 2303 2324 C2' C X 6 2325 2322 2338 C2' 3DR X 7 OK OK 2342 2343 2346 2347 2363 C2' C X 8 2364 2361 2382 C2' G X 9 2383 2380 2404 C2' A X 10 2405 2402 2425 C2' C X 11 2426 2423 2444 C2' G X 12 2445 2442 2466 C2' A X 13 2467 2464 2487 C2' C X 14 2488 2485 2506 C2' G X 15 2507 2504 2526 C2' G Y 17 2527 2524 2548 C2' T Y 18 2549 2546 2568 C2' C Y 19 2569 2566 2587 C2' G Y 20 2588 2585 2609 C2' T Y 21 2610 2607 2629 C2' C Y 22 2630 2627 2648 C2' G Y 23 2649 2646 2670 C2' G Y 24 2671 2668 2692 C2' G Y 25 2693 2690 2714 C2' G Y 26 2715 2712 2736 C2' A Y 27 2737 2734 2757 C2' C Y 28 2758 2755 2776 C2' G Y 29 2777 2774 2798 C2' C Y 30 2799 2796 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2220 C3' G X 1 OK 2218 2221 2222 2242 C3' C X 2 OK 2240 2243 2244 2261 C3' G X 3 OK 2259 2262 2263 2283 C3' T X 4 OK 2281 2284 2285 2303 C3' C X 5 OK 2301 2304 2305 2322 C3' C X 6 OK 2320 2323 2324 2343 C3' 3DR X 7 OK OK 2340 2353 2344 2338 2361 C3' C X 8 OK 2359 2362 2363 2380 C3' G X 9 OK 2378 2381 2382 2402 C3' A X 10 OK 2400 2403 2404 2423 C3' C X 11 OK 2421 2424 2425 2442 C3' G X 12 OK 2440 2443 2444 2464 C3' A X 13 OK 2462 2465 2466 2485 C3' C X 14 OK 2483 2486 2487 2504 C3' G X 15 OK 2502 2505 2506 2524 C3' G Y 17 OK 2522 2525 2526 2546 C3' T Y 18 OK 2544 2547 2548 2566 C3' C Y 19 OK 2564 2567 2568 2585 C3' G Y 20 OK 2583 2586 2587 2607 C3' T Y 21 OK 2605 2608 2609 2627 C3' C Y 22 OK 2625 2628 2629 2646 C3' G Y 23 OK 2644 2647 2648 2668 C3' G Y 24 OK 2666 2669 2670 2690 C3' G Y 25 OK 2688 2691 2692 2712 C3' G Y 26 OK 2710 2713 2714 2734 C3' A Y 27 OK 2732 2735 2736 2755 C3' C Y 28 OK 2753 2756 2757 2774 C3' G Y 29 OK 2772 2775 2776 2796 C3' C Y 30 OK 2794 2797 2798 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2218 C4' G X 1 OK 2220 2217 2219 2240 C4' C X 2 OK 2242 2239 2241 2259 C4' G X 3 OK 2261 2258 2260 2281 C4' T X 4 OK 2283 2280 2282 2301 C4' C X 5 OK 2303 2300 2302 2320 C4' C X 6 OK 2322 2319 2321 2340 C4' 3DR X 7 OK 2343 2339 2341 2359 C4' C X 8 OK 2361 2358 2360 2378 C4' G X 9 OK 2380 2377 2379 2400 C4' A X 10 OK 2402 2399 2401 2421 C4' C X 11 OK 2423 2420 2422 2440 C4' G X 12 OK 2442 2439 2441 2462 C4' A X 13 OK 2464 2461 2463 2483 C4' C X 14 OK 2485 2482 2484 2502 C4' G X 15 OK 2504 2501 2503 2522 C4' G Y 17 OK 2524 2521 2523 2544 C4' T Y 18 OK 2546 2543 2545 2564 C4' C Y 19 OK 2566 2563 2565 2583 C4' G Y 20 OK 2585 2582 2584 2605 C4' T Y 21 OK 2607 2604 2606 2625 C4' C Y 22 OK 2627 2624 2626 2644 C4' G Y 23 OK 2646 2643 2645 2666 C4' G Y 24 OK 2668 2665 2667 2688 C4' G Y 25 OK 2690 2687 2689 2710 C4' G Y 26 OK 2712 2709 2711 2732 C4' A Y 27 OK 2734 2731 2733 2753 C4' C Y 28 OK 2755 2752 2754 2772 C4' G Y 29 OK 2774 2771 2773 2794 C4' C Y 30 OK 2796 2793 2795 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2217 C5' G X 1 2216 2218 2239 C5' C X 2 2238 2240 2258 C5' G X 3 2257 2259 2280 C5' T X 4 2279 2281 2300 C5' C X 5 2299 2301 2319 C5' C X 6 2318 2320 2339 C5' 3DR X 7 OK OK 2334 2348 2349 2340 2358 C5' C X 8 2357 2359 2377 C5' G X 9 2376 2378 2399 C5' A X 10 2398 2400 2420 C5' C X 11 2419 2421 2439 C5' G X 12 2438 2440 2461 C5' A X 13 2460 2462 2482 C5' C X 14 2481 2483 2501 C5' G X 15 2500 2502 2521 C5' G Y 17 2520 2522 2543 C5' T Y 18 2542 2544 2563 C5' C Y 19 2562 2564 2582 C5' G Y 20 2581 2583 2604 C5' T Y 21 2603 2605 2624 C5' C Y 22 2623 2625 2643 C5' G Y 23 2642 2644 2665 C5' G Y 24 2664 2666 2687 C5' G Y 25 2686 2688 2709 C5' G Y 26 2708 2710 2731 C5' A Y 27 2730 2732 2752 C5' C Y 28 2751 2753 2771 C5' G Y 29 2770 2772 2793 C5' C Y 30 2792 2794 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2235 P C X 2 distorted distorted 2221 2236 2237 2238 2254 P G X 3 distorted distorted 2243 2255 2256 2257 2276 P T X 4 distorted distorted 2262 2277 2278 2279 2296 P C X 5 distorted distorted 2284 2297 2298 2299 2315 P C X 6 distorted distorted 2304 2316 2317 2318 2335 P 3DR X 7 distorted distorted 2323 2336 2337 2334 2354 P C X 8 distorted distorted 2344 2355 2356 2357 2373 P G X 9 distorted distorted 2362 2374 2375 2376 2395 P A X 10 distorted distorted 2381 2396 2397 2398 2416 P C X 11 distorted distorted 2403 2417 2418 2419 2435 P G X 12 distorted distorted 2424 2436 2437 2438 2457 P A X 13 distorted distorted 2443 2458 2459 2460 2478 P C X 14 distorted distorted 2465 2479 2480 2481 2497 P G X 15 distorted distorted 2486 2498 2499 2500 2539 P T Y 18 distorted distorted 2525 2540 2541 2542 2559 P C Y 19 distorted distorted 2547 2560 2561 2562 2578 P G Y 20 distorted distorted 2567 2579 2580 2581 2600 P T Y 21 distorted distorted 2586 2601 2602 2603 2620 P C Y 22 distorted distorted 2608 2621 2622 2623 2639 P G Y 23 distorted distorted 2628 2640 2641 2642 2661 P G Y 24 distorted distorted 2647 2662 2663 2664 2683 P G Y 25 distorted distorted 2669 2684 2685 2686 2705 P G Y 26 distorted distorted 2691 2706 2707 2708 2727 P A Y 27 distorted distorted 2713 2728 2729 2730 2748 P C Y 28 distorted distorted 2735 2749 2750 2751 2767 P G Y 29 distorted distorted 2756 2768 2769 2770 2789 P C Y 30 distorted distorted 2775 2790 2791 2792 ---------------------------------------------------------------------------------