ID code: '4NGB' 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' --------------------------------------------------------------------------------- 2244 C1' G B 1 beta 2239 2245 2242 2267 C1' C B 2 beta 2262 2268 2265 2287 C1' G B 3 beta 2282 2288 2285 2310 C1' A B 4 beta 2305 2311 2308 2332 C1' A B 5 beta 2327 2333 2330 2354 C1' U B 6 beta 2349 2355 2352 2374 C1' U B 7 beta 2369 2375 2372 2394 C1' C B 8 beta 2389 2395 2392 2414 C1' G B 9 beta 2409 2415 2412 2437 C1' C B 10 beta 2432 2438 2435 2457 C1' U B 11 beta 2452 2458 2455 2477 C1' U B 12 beta 2472 2478 2475 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2242 C2' G B 1 OK 2244 2240 2243 2265 C2' C B 2 OK 2267 2263 2266 2285 C2' G B 3 OK 2287 2283 2286 2308 C2' A B 4 OK 2310 2306 2309 2330 C2' A B 5 OK 2332 2328 2331 2352 C2' U B 6 OK 2354 2350 2353 2372 C2' U B 7 OK 2374 2370 2373 2392 C2' C B 8 OK 2394 2390 2393 2412 C2' G B 9 OK 2414 2410 2413 2435 C2' C B 10 OK 2437 2433 2436 2455 C2' U B 11 OK 2457 2453 2456 2475 C2' U B 12 OK 2477 2473 2476 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2240 C3' G B 1 OK 2238 2241 2242 2263 C3' C B 2 OK 2261 2264 2265 2283 C3' G B 3 OK 2281 2284 2285 2306 C3' A B 4 OK 2304 2307 2308 2328 C3' A B 5 OK 2326 2329 2330 2350 C3' U B 6 OK 2348 2351 2352 2370 C3' U B 7 OK 2368 2371 2372 2390 C3' C B 8 OK 2388 2391 2392 2410 C3' G B 9 OK 2408 2411 2412 2433 C3' C B 10 OK 2431 2434 2435 2453 C3' U B 11 OK 2451 2454 2455 2473 C3' U B 12 OK 2471 2474 2475 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2238 C4' G B 1 OK 2240 2237 2239 2261 C4' C B 2 OK 2263 2260 2262 2281 C4' G B 3 OK 2283 2280 2282 2304 C4' A B 4 OK 2306 2303 2305 2326 C4' A B 5 OK 2328 2325 2327 2348 C4' U B 6 OK 2350 2347 2349 2368 C4' U B 7 OK 2370 2367 2369 2388 C4' C B 8 OK 2390 2387 2389 2408 C4' G B 9 OK 2410 2407 2409 2431 C4' C B 10 OK 2433 2430 2432 2451 C4' U B 11 OK 2453 2450 2452 2471 C4' U B 12 OK 2473 2470 2472 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2237 C5' G B 1 2236 2238 2260 C5' C B 2 2259 2261 2280 C5' G B 3 2279 2281 2303 C5' A B 4 2302 2304 2325 C5' A B 5 2324 2326 2347 C5' U B 6 2346 2348 2367 C5' U B 7 2366 2368 2387 C5' C B 8 2386 2388 2407 C5' G B 9 2406 2408 2430 C5' C B 10 2429 2431 2450 C5' U B 11 2449 2451 2470 C5' U B 12 2469 2471 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2256 P C B 2 distorted distorted 2241 2257 2258 2259 2276 P G B 3 distorted distorted 2264 2277 2278 2279 2299 P A B 4 distorted distorted 2284 2300 2301 2302 2321 P A B 5 distorted distorted 2307 2322 2323 2324 2343 P U B 6 distorted distorted 2329 2344 2345 2346 2363 P U B 7 distorted distorted 2351 2364 2365 2366 2383 P C B 8 distorted distorted 2371 2384 2385 2386 2403 P G B 9 distorted distorted 2391 2404 2405 2406 2426 P C B 10 distorted distorted 2411 2427 2428 2429 2446 P U B 11 distorted distorted 2434 2447 2448 2449 2466 P U B 12 distorted distorted 2454 2467 2468 2469 ---------------------------------------------------------------------------------