ID code: '3KJO' 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' --------------------------------------------------------------------------------- 2318 C1' DT B 3 beta 2314 2319 2317 2339 C1' U B 4 beta 2334 2340 2337 2358 C1' DA B 5 beta 2354 2359 2357 2379 C1' DG B 6 beta 2375 2380 2378 2401 C1' DG B 7 beta 2397 2402 2400 2423 C1' DG B 8 beta 2419 2424 2422 2445 C1' DT B 9 beta 2441 2446 2444 2465 C1' DT B 10 beta 2461 2466 2464 2485 C1' DA B 11 beta 2481 2486 2484 2506 C1' DG B 12 beta 2502 2507 2505 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2317 C2' DT B 3 2318 2315 2337 C2' U B 4 OK 2339 2335 2338 2357 C2' DA B 5 2358 2355 2378 C2' DG B 6 2379 2376 2400 C2' DG B 7 2401 2398 2422 C2' DG B 8 2423 2420 2444 C2' DT B 9 2445 2442 2464 C2' DT B 10 2465 2462 2484 C2' DA B 11 2485 2482 2505 C2' DG B 12 2506 2503 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2315 C3' DT B 3 OK 2313 2316 2317 2335 C3' U B 4 OK 2333 2336 2337 2355 C3' DA B 5 OK 2353 2356 2357 2376 C3' DG B 6 OK 2374 2377 2378 2398 C3' DG B 7 OK 2396 2399 2400 2420 C3' DG B 8 OK 2418 2421 2422 2442 C3' DT B 9 OK 2440 2443 2444 2462 C3' DT B 10 OK 2460 2463 2464 2482 C3' DA B 11 OK 2480 2483 2484 2503 C3' DG B 12 OK 2501 2504 2505 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2313 C4' DT B 3 OK 2315 2312 2314 2333 C4' U B 4 OK 2335 2332 2334 2353 C4' DA B 5 OK 2355 2352 2354 2374 C4' DG B 6 OK 2376 2373 2375 2396 C4' DG B 7 OK 2398 2395 2397 2418 C4' DG B 8 OK 2420 2417 2419 2440 C4' DT B 9 OK 2442 2439 2441 2460 C4' DT B 10 OK 2462 2459 2461 2480 C4' DA B 11 OK 2482 2479 2481 2501 C4' DG B 12 OK 2503 2500 2502 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2312 C5' DT B 3 2311 2313 2332 C5' U B 4 2331 2333 2352 C5' DA B 5 2351 2353 2373 C5' DG B 6 2372 2374 2395 C5' DG B 7 2394 2396 2417 C5' DG B 8 2416 2418 2439 C5' DT B 9 2438 2440 2459 C5' DT B 10 2458 2460 2479 C5' DA B 11 2478 2480 2500 C5' DG B 12 2499 2501 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2328 P U B 4 distorted distorted 2316 2329 2330 2331 2348 P DA B 5 distorted distorted 2336 2349 2350 2351 2369 P DG B 6 distorted distorted 2356 2370 2371 2372 2391 P DG B 7 distorted distorted 2377 2392 2393 2394 2413 P DG B 8 distorted distorted 2399 2414 2415 2416 2435 P DT B 9 distorted distorted 2421 2436 2437 2438 2455 P DT B 10 distorted distorted 2443 2456 2457 2458 2475 P DA B 11 distorted distorted 2463 2476 2477 2478 2496 P DG B 12 distorted distorted 2483 2497 2498 2499 ---------------------------------------------------------------------------------