ID code: '5EX7' 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' --------------------------------------------------------------------------------- 2231 C1' U B 2 beta 2226 2232 2229 2251 C1' U B 3 beta 2246 2252 2249 2271 C1' G B 4 beta 2266 2272 2269 2294 C1' U B 5 beta 2289 2295 2292 2314 C1' U B 6 beta 2309 2315 2312 2334 C1' G B 7 beta 2329 2335 2332 2357 C1' U B 8 beta 2352 2358 2355 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2229 C2' U B 2 OK 2231 2227 2230 2249 C2' U B 3 OK 2251 2247 2250 2269 C2' G B 4 OK 2271 2267 2270 2292 C2' U B 5 OK 2294 2290 2293 2312 C2' U B 6 OK 2314 2310 2313 2332 C2' G B 7 OK 2334 2330 2333 2355 C2' U B 8 OK 2357 2353 2356 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2227 C3' U B 2 OK 2225 2228 2229 2247 C3' U B 3 OK 2245 2248 2249 2267 C3' G B 4 OK 2265 2268 2269 2290 C3' U B 5 OK 2288 2291 2292 2310 C3' U B 6 OK 2308 2311 2312 2330 C3' G B 7 OK 2328 2331 2332 2353 C3' U B 8 OK 2351 2354 2355 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2225 C4' U B 2 OK 2227 2224 2226 2245 C4' U B 3 OK 2247 2244 2246 2265 C4' G B 4 OK 2267 2264 2266 2288 C4' U B 5 OK 2290 2287 2289 2308 C4' U B 6 OK 2310 2307 2309 2328 C4' G B 7 OK 2330 2327 2329 2351 C4' U B 8 OK 2353 2350 2352 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2224 C5' U B 2 2223 2225 2244 C5' U B 3 2243 2245 2264 C5' G B 4 2263 2265 2287 C5' U B 5 2286 2288 2307 C5' U B 6 2306 2308 2327 C5' G B 7 2326 2328 2350 C5' U B 8 2349 2351 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2220 P U B 2 OK OK 2221 2222 2223 2240 P U B 3 distorted distorted 2228 2241 2242 2243 2260 P G B 4 distorted distorted 2248 2261 2262 2263 2283 P U B 5 distorted distorted 2268 2284 2285 2286 2303 P U B 6 distorted distorted 2291 2304 2305 2306 2323 P G B 7 distorted distorted 2311 2324 2325 2326 2346 P U B 8 distorted distorted 2331 2347 2348 2349 ---------------------------------------------------------------------------------