ID code: '3OGD' 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' --------------------------------------------------------------------------------- 2267 C1' DG B 15 beta 2263 2268 2266 2289 C1' DC B 16 beta 2285 2290 2288 2308 C1' DA B 17 beta 2304 2309 2307 2329 C1' DG B 18 beta 2325 2330 2328 2351 C1' DT B 19 beta 2347 2352 2350 2371 C1' DC B 20 beta 2367 2372 2370 2390 C1' DA B 21 beta 2386 2391 2389 2411 C1' DT B 22 beta 2407 2412 2410 2431 C1' DG B 23 beta 2427 2432 2430 2451 C1' DC C 3 beta 2447 2452 2450 2470 C1' DA C 4 beta 2466 2471 2469 2490 C1' BRU C 5 beta 2495 2481 2491 2511 C1' DG C 6 beta 2507 2512 2510 2533 C1' DA C 7 beta 2529 2534 2532 2554 C1' DC C 8 beta 2550 2555 2553 2572 C1' BRU C 9 beta 2577 2563 2573 2593 C1' DG C 10 beta 2589 2594 2592 2615 C1' DC C 11 beta 2611 2616 2614 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2266 C2' DG B 15 2267 2264 2288 C2' DC B 16 2289 2286 2307 C2' DA B 17 2308 2305 2328 C2' DG B 18 2329 2326 2350 C2' DT B 19 2351 2348 2370 C2' DC B 20 2371 2368 2389 C2' DA B 21 2390 2387 2410 C2' DT B 22 2411 2408 2430 C2' DG B 23 2431 2428 2450 C2' DC C 3 2451 2448 2469 C2' DA C 4 2470 2467 2491 C2' BRU C 5 2490 2492 2510 C2' DG C 6 2511 2508 2532 C2' DA C 7 2533 2530 2553 C2' DC C 8 2554 2551 2573 C2' BRU C 9 2572 2574 2592 C2' DG C 10 2593 2590 2614 C2' DC C 11 2615 2612 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2264 C3' DG B 15 OK 2262 2265 2266 2286 C3' DC B 16 OK 2284 2287 2288 2305 C3' DA B 17 OK 2303 2306 2307 2326 C3' DG B 18 OK 2324 2327 2328 2348 C3' DT B 19 OK 2346 2349 2350 2368 C3' DC B 20 OK 2366 2369 2370 2387 C3' DA B 21 OK 2385 2388 2389 2408 C3' DT B 22 OK 2406 2409 2410 2428 C3' DG B 23 OK 2426 2429 2430 2448 C3' DC C 3 OK 2446 2449 2450 2467 C3' DA C 4 OK 2465 2468 2469 2492 C3' BRU C 5 OK 2493 2494 2491 2508 C3' DG C 6 OK 2506 2509 2510 2530 C3' DA C 7 OK 2528 2531 2532 2551 C3' DC C 8 OK 2549 2552 2553 2574 C3' BRU C 9 OK 2575 2576 2573 2590 C3' DG C 10 OK 2588 2591 2592 2612 C3' DC C 11 OK 2610 2613 2614 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2262 C4' DG B 15 OK 2264 2261 2263 2284 C4' DC B 16 OK 2286 2283 2285 2303 C4' DA B 17 OK 2305 2302 2304 2324 C4' DG B 18 OK 2326 2323 2325 2346 C4' DT B 19 OK 2348 2345 2347 2366 C4' DC B 20 OK 2368 2365 2367 2385 C4' DA B 21 OK 2387 2384 2386 2406 C4' DT B 22 OK 2408 2405 2407 2426 C4' DG B 23 OK 2428 2425 2427 2446 C4' DC C 3 OK 2448 2445 2447 2465 C4' DA C 4 OK 2467 2464 2466 2493 C4' BRU C 5 OK 2492 2496 2495 2506 C4' DG C 6 OK 2508 2505 2507 2528 C4' DA C 7 OK 2530 2527 2529 2549 C4' DC C 8 OK 2551 2548 2550 2575 C4' BRU C 9 OK 2574 2578 2577 2588 C4' DG C 10 OK 2590 2587 2589 2610 C4' DC C 11 OK 2612 2609 2611 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2261 C5' DG B 15 2260 2262 2283 C5' DC B 16 2282 2284 2302 C5' DA B 17 2301 2303 2323 C5' DG B 18 2322 2324 2345 C5' DT B 19 2344 2346 2365 C5' DC B 20 2364 2366 2384 C5' DA B 21 2383 2385 2405 C5' DT B 22 2404 2406 2425 C5' DG B 23 2424 2426 2445 C5' DC C 3 2444 2446 2464 C5' DA C 4 2463 2465 2496 C5' BRU C 5 2497 2493 2505 C5' DG C 6 2504 2506 2527 C5' DA C 7 2526 2528 2548 C5' DC C 8 2547 2549 2578 C5' BRU C 9 2579 2575 2587 C5' DG C 10 2586 2588 2609 C5' DC C 11 2608 2610 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2279 P DC B 16 distorted distorted 2265 2280 2281 2282 2298 P DA B 17 distorted distorted 2287 2299 2300 2301 2319 P DG B 18 distorted distorted 2306 2320 2321 2322 2341 P DT B 19 distorted distorted 2327 2342 2343 2344 2361 P DC B 20 distorted distorted 2349 2362 2363 2364 2380 P DA B 21 distorted distorted 2369 2381 2382 2383 2401 P DT B 22 distorted distorted 2388 2402 2403 2404 2421 P DG B 23 distorted distorted 2409 2422 2423 2424 2460 P DA C 4 distorted distorted 2449 2461 2462 2463 2498 P BRU C 5 distorted distorted 2468 2499 2500 2497 2501 P DG C 6 distorted distorted 2494 2502 2503 2504 2523 P DA C 7 distorted distorted 2509 2524 2525 2526 2544 P DC C 8 distorted distorted 2531 2545 2546 2547 2580 P BRU C 9 distorted distorted 2552 2581 2582 2579 2583 P DG C 10 distorted distorted 2576 2584 2585 2586 2605 P DC C 11 distorted distorted 2591 2606 2607 2608 ---------------------------------------------------------------------------------