ID code: '3OH9' 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' --------------------------------------------------------------------------------- 2263 C1' DG B 14 beta 2259 2264 2262 2285 C1' DG B 15 beta 2281 2286 2284 2307 C1' DC B 16 beta 2303 2308 2306 2326 C1' DA B 17 beta 2322 2327 2325 2347 C1' DT B 18 beta 2343 2348 2346 2367 C1' DT B 19 beta 2363 2368 2366 2387 C1' DC B 20 beta 2383 2388 2386 2406 C1' DA B 21 beta 2402 2407 2405 2427 C1' DT B 22 beta 2423 2428 2426 2447 C1' DG B 23 beta 2443 2448 2446 2469 C1' DT B 24 beta 2465 2470 2468 2487 C1' DA C 2 beta 2483 2488 2486 2508 C1' DC C 3 beta 2504 2509 2507 2527 C1' DA C 4 beta 2523 2528 2526 2547 C1' BRU C 5 beta 2552 2538 2548 2568 C1' DG C 6 beta 2564 2569 2567 2590 C1' DA C 7 beta 2586 2591 2589 2611 C1' DA C 8 beta 2607 2612 2610 2631 C1' BRU C 9 beta 2636 2622 2632 2652 C1' DG C 10 beta 2648 2653 2651 2674 C1' DC C 11 beta 2670 2675 2673 2693 C1' DC C 12 beta 2689 2694 2692 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2262 C2' DG B 14 2263 2260 2284 C2' DG B 15 2285 2282 2306 C2' DC B 16 2307 2304 2325 C2' DA B 17 2326 2323 2346 C2' DT B 18 2347 2344 2366 C2' DT B 19 2367 2364 2386 C2' DC B 20 2387 2384 2405 C2' DA B 21 2406 2403 2426 C2' DT B 22 2427 2424 2446 C2' DG B 23 2447 2444 2468 C2' DT B 24 2469 2466 2486 C2' DA C 2 2487 2484 2507 C2' DC C 3 2508 2505 2526 C2' DA C 4 2527 2524 2548 C2' BRU C 5 2547 2549 2567 C2' DG C 6 2568 2565 2589 C2' DA C 7 2590 2587 2610 C2' DA C 8 2611 2608 2632 C2' BRU C 9 2631 2633 2651 C2' DG C 10 2652 2649 2673 C2' DC C 11 2674 2671 2692 C2' DC C 12 2693 2690 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2260 C3' DG B 14 OK 2258 2261 2262 2282 C3' DG B 15 OK 2280 2283 2284 2304 C3' DC B 16 OK 2302 2305 2306 2323 C3' DA B 17 OK 2321 2324 2325 2344 C3' DT B 18 OK 2342 2345 2346 2364 C3' DT B 19 OK 2362 2365 2366 2384 C3' DC B 20 OK 2382 2385 2386 2403 C3' DA B 21 OK 2401 2404 2405 2424 C3' DT B 22 OK 2422 2425 2426 2444 C3' DG B 23 OK 2442 2445 2446 2466 C3' DT B 24 OK 2464 2467 2468 2484 C3' DA C 2 OK 2482 2485 2486 2505 C3' DC C 3 OK 2503 2506 2507 2524 C3' DA C 4 OK 2522 2525 2526 2549 C3' BRU C 5 OK 2550 2551 2548 2565 C3' DG C 6 OK 2563 2566 2567 2587 C3' DA C 7 OK 2585 2588 2589 2608 C3' DA C 8 OK 2606 2609 2610 2633 C3' BRU C 9 OK 2634 2635 2632 2649 C3' DG C 10 OK 2647 2650 2651 2671 C3' DC C 11 OK 2669 2672 2673 2690 C3' DC C 12 OK 2688 2691 2692 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2258 C4' DG B 14 OK 2260 2257 2259 2280 C4' DG B 15 OK 2282 2279 2281 2302 C4' DC B 16 OK 2304 2301 2303 2321 C4' DA B 17 OK 2323 2320 2322 2342 C4' DT B 18 OK 2344 2341 2343 2362 C4' DT B 19 OK 2364 2361 2363 2382 C4' DC B 20 OK 2384 2381 2383 2401 C4' DA B 21 OK 2403 2400 2402 2422 C4' DT B 22 OK 2424 2421 2423 2442 C4' DG B 23 OK 2444 2441 2443 2464 C4' DT B 24 OK 2466 2463 2465 2482 C4' DA C 2 OK 2484 2481 2483 2503 C4' DC C 3 OK 2505 2502 2504 2522 C4' DA C 4 OK 2524 2521 2523 2550 C4' BRU C 5 OK 2549 2553 2552 2563 C4' DG C 6 OK 2565 2562 2564 2585 C4' DA C 7 OK 2587 2584 2586 2606 C4' DA C 8 OK 2608 2605 2607 2634 C4' BRU C 9 OK 2633 2637 2636 2647 C4' DG C 10 OK 2649 2646 2648 2669 C4' DC C 11 OK 2671 2668 2670 2688 C4' DC C 12 OK 2690 2687 2689 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2257 C5' DG B 14 2256 2258 2279 C5' DG B 15 2278 2280 2301 C5' DC B 16 2300 2302 2320 C5' DA B 17 2319 2321 2341 C5' DT B 18 2340 2342 2361 C5' DT B 19 2360 2362 2381 C5' DC B 20 2380 2382 2400 C5' DA B 21 2399 2401 2421 C5' DT B 22 2420 2422 2441 C5' DG B 23 2440 2442 2463 C5' DT B 24 2462 2464 2481 C5' DA C 2 2480 2482 2502 C5' DC C 3 2501 2503 2521 C5' DA C 4 2520 2522 2553 C5' BRU C 5 2554 2550 2562 C5' DG C 6 2561 2563 2584 C5' DA C 7 2583 2585 2605 C5' DA C 8 2604 2606 2637 C5' BRU C 9 2638 2634 2646 C5' DG C 10 2645 2647 2668 C5' DC C 11 2667 2669 2687 C5' DC C 12 2686 2688 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2275 P DG B 15 distorted distorted 2261 2276 2277 2278 2297 P DC B 16 distorted distorted 2283 2298 2299 2300 2316 P DA B 17 distorted distorted 2305 2317 2318 2319 2337 P DT B 18 distorted distorted 2324 2338 2339 2340 2357 P DT B 19 distorted distorted 2345 2358 2359 2360 2377 P DC B 20 distorted distorted 2365 2378 2379 2380 2396 P DA B 21 distorted distorted 2385 2397 2398 2399 2417 P DT B 22 distorted distorted 2404 2418 2419 2420 2437 P DG B 23 distorted distorted 2425 2438 2439 2440 2459 P DT B 24 distorted distorted 2445 2460 2461 2462 2498 P DC C 3 distorted distorted 2485 2499 2500 2501 2517 P DA C 4 distorted distorted 2506 2518 2519 2520 2555 P BRU C 5 distorted distorted 2525 2556 2557 2554 2558 P DG C 6 distorted distorted 2551 2559 2560 2561 2580 P DA C 7 distorted distorted 2566 2581 2582 2583 2601 P DA C 8 distorted distorted 2588 2602 2603 2604 2639 P BRU C 9 distorted distorted 2609 2640 2641 2638 2642 P DG C 10 distorted distorted 2635 2643 2644 2645 2664 P DC C 11 distorted distorted 2650 2665 2666 2667 2683 P DC C 12 distorted distorted 2672 2684 2685 2686 ---------------------------------------------------------------------------------