ID code: '5EMO' 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' --------------------------------------------------------------------------------- 2364 C1' A E 1 beta 2359 2365 2362 2386 C1' U E 2 beta 2381 2387 2384 2406 C1' U E 3 beta 2401 2407 2404 2426 C1' A E 4 beta 2421 2427 2424 2448 C1' A E 5 beta 2443 2449 2446 2470 C1' A E 6 beta 2465 2471 2468 2493 C1' A F 1 beta 2488 2494 2491 2515 C1' U F 2 beta 2510 2516 2513 2535 C1' U F 3 beta 2530 2536 2533 2555 C1' A F 4 beta 2550 2556 2553 2577 C1' A F 5 beta 2572 2578 2575 2599 C1' A F 6 beta 2594 2600 2597 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2362 C2' A E 1 OK 2364 2360 2363 2384 C2' U E 2 OK 2386 2382 2385 2404 C2' U E 3 OK 2406 2402 2405 2424 C2' A E 4 OK 2426 2422 2425 2446 C2' A E 5 OK 2448 2444 2447 2468 C2' A E 6 OK 2470 2466 2469 2491 C2' A F 1 OK 2493 2489 2492 2513 C2' U F 2 OK 2515 2511 2514 2533 C2' U F 3 OK 2535 2531 2534 2553 C2' A F 4 OK 2555 2551 2554 2575 C2' A F 5 OK 2577 2573 2576 2597 C2' A F 6 OK 2599 2595 2598 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2360 C3' A E 1 OK 2358 2361 2362 2382 C3' U E 2 OK 2380 2383 2384 2402 C3' U E 3 OK 2400 2403 2404 2422 C3' A E 4 OK 2420 2423 2424 2444 C3' A E 5 OK 2442 2445 2446 2466 C3' A E 6 OK 2464 2467 2468 2489 C3' A F 1 OK 2487 2490 2491 2511 C3' U F 2 OK 2509 2512 2513 2531 C3' U F 3 OK 2529 2532 2533 2551 C3' A F 4 OK 2549 2552 2553 2573 C3' A F 5 OK 2571 2574 2575 2595 C3' A F 6 OK 2593 2596 2597 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2358 C4' A E 1 OK 2360 2357 2359 2380 C4' U E 2 OK 2382 2379 2381 2400 C4' U E 3 OK 2402 2399 2401 2420 C4' A E 4 OK 2422 2419 2421 2442 C4' A E 5 OK 2444 2441 2443 2464 C4' A E 6 OK 2466 2463 2465 2487 C4' A F 1 OK 2489 2486 2488 2509 C4' U F 2 OK 2511 2508 2510 2529 C4' U F 3 OK 2531 2528 2530 2549 C4' A F 4 OK 2551 2548 2550 2571 C4' A F 5 OK 2573 2570 2572 2593 C4' A F 6 OK 2595 2592 2594 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2357 C5' A E 1 2356 2358 2379 C5' U E 2 2378 2380 2399 C5' U E 3 2398 2400 2419 C5' A E 4 2418 2420 2441 C5' A E 5 2440 2442 2463 C5' A E 6 2462 2464 2486 C5' A F 1 2485 2487 2508 C5' U F 2 2507 2509 2528 C5' U F 3 2527 2529 2548 C5' A F 4 2547 2549 2570 C5' A F 5 2569 2571 2592 C5' A F 6 2591 2593 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2353 P A E 1 distorted distorted 2354 2355 2356 2375 P U E 2 distorted distorted 2361 2376 2377 2378 2395 P U E 3 distorted distorted 2383 2396 2397 2398 2415 P A E 4 distorted distorted 2403 2416 2417 2418 2437 P A E 5 distorted distorted 2423 2438 2439 2440 2459 P A E 6 distorted distorted 2445 2460 2461 2462 2482 P A F 1 distorted distorted 2483 2484 2485 2504 P U F 2 distorted distorted 2490 2505 2506 2507 2524 P U F 3 distorted distorted 2512 2525 2526 2527 2544 P A F 4 distorted distorted 2532 2545 2546 2547 2566 P A F 5 distorted distorted 2552 2567 2568 2569 2588 P A F 6 distorted distorted 2574 2589 2590 2591 ---------------------------------------------------------------------------------