ID code: '3NCU' 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' --------------------------------------------------------------------------------- 1997 C1' GDP C 1 beta 1992 1998 1995 2020 C1' A C 2 beta 2015 2021 2018 2042 C1' C C 3 beta 2037 2043 2040 2062 C1' G C 4 beta 2057 2063 2060 2085 C1' C C 5 beta 2080 2086 2083 2105 C1' U C 6 beta 2100 2106 2103 2125 C1' A C 7 beta 2120 2126 2123 2147 C1' G C 8 beta 2142 2148 2145 2170 C1' C C 9 beta 2165 2171 2168 2190 C1' G C 10 beta 2185 2191 2188 2213 C1' U C 11 beta 2208 2214 2211 2233 C1' C C 12 beta 2228 2234 2231 2259 C1' GDP D 1 beta 2254 2260 2257 2282 C1' A D 2 beta 2277 2283 2280 2304 C1' C D 3 beta 2299 2305 2302 2324 C1' G D 4 beta 2319 2325 2322 2347 C1' C D 5 beta 2342 2348 2345 2367 C1' U D 6 beta 2362 2368 2365 2387 C1' A D 7 beta 2382 2388 2385 2409 C1' G D 8 beta 2404 2410 2407 2432 C1' C D 9 beta 2427 2433 2430 2452 C1' G D 10 beta 2447 2453 2450 2475 C1' U D 11 beta 2470 2476 2473 2495 C1' C D 12 beta 2490 2496 2493 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1995 C2' GDP C 1 OK 1997 1993 1996 2018 C2' A C 2 OK 2020 2016 2019 2040 C2' C C 3 OK 2042 2038 2041 2060 C2' G C 4 OK 2062 2058 2061 2083 C2' C C 5 OK 2085 2081 2084 2103 C2' U C 6 OK 2105 2101 2104 2123 C2' A C 7 OK 2125 2121 2124 2145 C2' G C 8 OK 2147 2143 2146 2168 C2' C C 9 OK 2170 2166 2169 2188 C2' G C 10 OK 2190 2186 2189 2211 C2' U C 11 OK 2213 2209 2212 2231 C2' C C 12 OK 2233 2229 2232 2257 C2' GDP D 1 OK 2259 2255 2258 2280 C2' A D 2 OK 2282 2278 2281 2302 C2' C D 3 OK 2304 2300 2303 2322 C2' G D 4 OK 2324 2320 2323 2345 C2' C D 5 OK 2347 2343 2346 2365 C2' U D 6 OK 2367 2363 2366 2385 C2' A D 7 OK 2387 2383 2386 2407 C2' G D 8 OK 2409 2405 2408 2430 C2' C D 9 OK 2432 2428 2431 2450 C2' G D 10 OK 2452 2448 2451 2473 C2' U D 11 OK 2475 2471 2474 2493 C2' C D 12 OK 2495 2491 2494 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1993 C3' GDP C 1 OK 1991 1994 1995 2016 C3' A C 2 OK 2014 2017 2018 2038 C3' C C 3 OK 2036 2039 2040 2058 C3' G C 4 OK 2056 2059 2060 2081 C3' C C 5 OK 2079 2082 2083 2101 C3' U C 6 OK 2099 2102 2103 2121 C3' A C 7 OK 2119 2122 2123 2143 C3' G C 8 OK 2141 2144 2145 2166 C3' C C 9 OK 2164 2167 2168 2186 C3' G C 10 OK 2184 2187 2188 2209 C3' U C 11 OK 2207 2210 2211 2229 C3' C C 12 OK 2227 2230 2231 2255 C3' GDP D 1 OK 2253 2256 2257 2278 C3' A D 2 OK 2276 2279 2280 2300 C3' C D 3 OK 2298 2301 2302 2320 C3' G D 4 OK 2318 2321 2322 2343 C3' C D 5 OK 2341 2344 2345 2363 C3' U D 6 OK 2361 2364 2365 2383 C3' A D 7 OK 2381 2384 2385 2405 C3' G D 8 OK 2403 2406 2407 2428 C3' C D 9 OK 2426 2429 2430 2448 C3' G D 10 OK 2446 2449 2450 2471 C3' U D 11 OK 2469 2472 2473 2491 C3' C D 12 OK 2489 2492 2493 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1991 C4' GDP C 1 OK 1993 1990 1992 2014 C4' A C 2 OK 2016 2013 2015 2036 C4' C C 3 OK 2038 2035 2037 2056 C4' G C 4 OK 2058 2055 2057 2079 C4' C C 5 OK 2081 2078 2080 2099 C4' U C 6 OK 2101 2098 2100 2119 C4' A C 7 OK 2121 2118 2120 2141 C4' G C 8 OK 2143 2140 2142 2164 C4' C C 9 OK 2166 2163 2165 2184 C4' G C 10 OK 2186 2183 2185 2207 C4' U C 11 OK 2209 2206 2208 2227 C4' C C 12 OK 2229 2226 2228 2253 C4' GDP D 1 OK 2255 2252 2254 2276 C4' A D 2 OK 2278 2275 2277 2298 C4' C D 3 OK 2300 2297 2299 2318 C4' G D 4 OK 2320 2317 2319 2341 C4' C D 5 OK 2343 2340 2342 2361 C4' U D 6 OK 2363 2360 2362 2381 C4' A D 7 OK 2383 2380 2382 2403 C4' G D 8 OK 2405 2402 2404 2426 C4' C D 9 OK 2428 2425 2427 2446 C4' G D 10 OK 2448 2445 2447 2469 C4' U D 11 OK 2471 2468 2470 2489 C4' C D 12 OK 2491 2488 2490 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1990 C5' GDP C 1 1989 1991 2013 C5' A C 2 2012 2014 2035 C5' C C 3 2034 2036 2055 C5' G C 4 2054 2056 2078 C5' C C 5 2077 2079 2098 C5' U C 6 2097 2099 2118 C5' A C 7 2117 2119 2140 C5' G C 8 2139 2141 2163 C5' C C 9 2162 2164 2183 C5' G C 10 2182 2184 2206 C5' U C 11 2205 2207 2226 C5' C C 12 2225 2227 2252 C5' GDP D 1 2251 2253 2275 C5' A D 2 2274 2276 2297 C5' C D 3 2296 2298 2317 C5' G D 4 2316 2318 2340 C5' C D 5 2339 2341 2360 C5' U D 6 2359 2361 2380 C5' A D 7 2379 2381 2402 C5' G D 8 2401 2403 2425 C5' C D 9 2424 2426 2445 C5' G D 10 2444 2446 2468 C5' U D 11 2467 2469 2488 C5' C D 12 2487 2489 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2009 P A C 2 distorted distorted 1994 2010 2011 2012 2031 P C C 3 distorted distorted 2017 2032 2033 2034 2051 P G C 4 distorted distorted 2039 2052 2053 2054 2074 P C C 5 distorted distorted 2059 2075 2076 2077 2094 P U C 6 distorted distorted 2082 2095 2096 2097 2114 P A C 7 distorted distorted 2102 2115 2116 2117 2136 P G C 8 distorted distorted 2122 2137 2138 2139 2159 P C C 9 distorted distorted 2144 2160 2161 2162 2179 P G C 10 distorted distorted 2167 2180 2181 2182 2202 P U C 11 distorted distorted 2187 2203 2204 2205 2222 P C C 12 distorted distorted 2210 2223 2224 2225 2271 P A D 2 distorted distorted 2256 2272 2273 2274 2293 P C D 3 distorted distorted 2279 2294 2295 2296 2313 P G D 4 distorted distorted 2301 2314 2315 2316 2336 P C D 5 distorted distorted 2321 2337 2338 2339 2356 P U D 6 distorted distorted 2344 2357 2358 2359 2376 P A D 7 distorted distorted 2364 2377 2378 2379 2398 P G D 8 distorted distorted 2384 2399 2400 2401 2421 P C D 9 distorted distorted 2406 2422 2423 2424 2441 P G D 10 distorted distorted 2429 2442 2443 2444 2464 P U D 11 distorted distorted 2449 2465 2466 2467 2484 P C D 12 distorted distorted 2472 2485 2486 2487 ---------------------------------------------------------------------------------