ID code: '3LRR' 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' --------------------------------------------------------------------------------- 2021 C1' ATP C 1 beta 2016 2022 2019 2043 C1' U C 2 beta 2038 2044 2041 2063 C1' A C 3 beta 2058 2064 2061 2085 C1' U C 4 beta 2080 2086 2083 2105 C1' A C 5 beta 2100 2106 2103 2127 C1' U C 6 beta 2122 2128 2125 2147 C1' A C 7 beta 2142 2148 2145 2169 C1' U C 8 beta 2164 2170 2167 2189 C1' A C 9 beta 2184 2190 2187 2211 C1' U C 10 beta 2206 2212 2209 2231 C1' A C 11 beta 2226 2232 2229 2253 C1' U C 12 beta 2248 2254 2251 2283 C1' ATP D 1 beta 2278 2284 2281 2305 C1' U D 2 beta 2300 2306 2303 2325 C1' A D 3 beta 2320 2326 2323 2347 C1' U D 4 beta 2342 2348 2345 2367 C1' A D 5 beta 2362 2368 2365 2389 C1' U D 6 beta 2384 2390 2387 2409 C1' A D 7 beta 2404 2410 2407 2431 C1' U D 8 beta 2426 2432 2429 2451 C1' A D 9 beta 2446 2452 2449 2473 C1' U D 10 beta 2468 2474 2471 2493 C1' A D 11 beta 2488 2494 2491 2515 C1' U D 12 beta 2510 2516 2513 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2019 C2' ATP C 1 OK 2021 2017 2020 2041 C2' U C 2 OK 2043 2039 2042 2061 C2' A C 3 OK 2063 2059 2062 2083 C2' U C 4 OK 2085 2081 2084 2103 C2' A C 5 OK 2105 2101 2104 2125 C2' U C 6 OK 2127 2123 2126 2145 C2' A C 7 OK 2147 2143 2146 2167 C2' U C 8 OK 2169 2165 2168 2187 C2' A C 9 OK 2189 2185 2188 2209 C2' U C 10 OK 2211 2207 2210 2229 C2' A C 11 OK 2231 2227 2230 2251 C2' U C 12 OK 2253 2249 2252 2281 C2' ATP D 1 OK 2283 2279 2282 2303 C2' U D 2 OK 2305 2301 2304 2323 C2' A D 3 OK 2325 2321 2324 2345 C2' U D 4 OK 2347 2343 2346 2365 C2' A D 5 OK 2367 2363 2366 2387 C2' U D 6 OK 2389 2385 2388 2407 C2' A D 7 OK 2409 2405 2408 2429 C2' U D 8 OK 2431 2427 2430 2449 C2' A D 9 OK 2451 2447 2450 2471 C2' U D 10 OK 2473 2469 2472 2491 C2' A D 11 OK 2493 2489 2492 2513 C2' U D 12 OK 2515 2511 2514 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2017 C3' ATP C 1 OK 2015 2018 2019 2039 C3' U C 2 OK 2037 2040 2041 2059 C3' A C 3 OK 2057 2060 2061 2081 C3' U C 4 OK 2079 2082 2083 2101 C3' A C 5 OK 2099 2102 2103 2123 C3' U C 6 OK 2121 2124 2125 2143 C3' A C 7 OK 2141 2144 2145 2165 C3' U C 8 OK 2163 2166 2167 2185 C3' A C 9 OK 2183 2186 2187 2207 C3' U C 10 OK 2205 2208 2209 2227 C3' A C 11 OK 2225 2228 2229 2249 C3' U C 12 OK 2247 2250 2251 2279 C3' ATP D 1 OK 2277 2280 2281 2301 C3' U D 2 OK 2299 2302 2303 2321 C3' A D 3 OK 2319 2322 2323 2343 C3' U D 4 OK 2341 2344 2345 2363 C3' A D 5 OK 2361 2364 2365 2385 C3' U D 6 OK 2383 2386 2387 2405 C3' A D 7 OK 2403 2406 2407 2427 C3' U D 8 OK 2425 2428 2429 2447 C3' A D 9 OK 2445 2448 2449 2469 C3' U D 10 OK 2467 2470 2471 2489 C3' A D 11 OK 2487 2490 2491 2511 C3' U D 12 OK 2509 2512 2513 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2015 C4' ATP C 1 OK 2017 2014 2016 2037 C4' U C 2 OK 2039 2036 2038 2057 C4' A C 3 OK 2059 2056 2058 2079 C4' U C 4 OK 2081 2078 2080 2099 C4' A C 5 OK 2101 2098 2100 2121 C4' U C 6 OK 2123 2120 2122 2141 C4' A C 7 OK 2143 2140 2142 2163 C4' U C 8 OK 2165 2162 2164 2183 C4' A C 9 OK 2185 2182 2184 2205 C4' U C 10 OK 2207 2204 2206 2225 C4' A C 11 OK 2227 2224 2226 2247 C4' U C 12 OK 2249 2246 2248 2277 C4' ATP D 1 OK 2279 2276 2278 2299 C4' U D 2 OK 2301 2298 2300 2319 C4' A D 3 OK 2321 2318 2320 2341 C4' U D 4 OK 2343 2340 2342 2361 C4' A D 5 OK 2363 2360 2362 2383 C4' U D 6 OK 2385 2382 2384 2403 C4' A D 7 OK 2405 2402 2404 2425 C4' U D 8 OK 2427 2424 2426 2445 C4' A D 9 OK 2447 2444 2446 2467 C4' U D 10 OK 2469 2466 2468 2487 C4' A D 11 OK 2489 2486 2488 2509 C4' U D 12 OK 2511 2508 2510 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2014 C5' ATP C 1 2013 2015 2036 C5' U C 2 2035 2037 2056 C5' A C 3 2055 2057 2078 C5' U C 4 2077 2079 2098 C5' A C 5 2097 2099 2120 C5' U C 6 2119 2121 2140 C5' A C 7 2139 2141 2162 C5' U C 8 2161 2163 2182 C5' A C 9 2181 2183 2204 C5' U C 10 2203 2205 2224 C5' A C 11 2223 2225 2246 C5' U C 12 2245 2247 2276 C5' ATP D 1 2275 2277 2298 C5' U D 2 2297 2299 2318 C5' A D 3 2317 2319 2340 C5' U D 4 2339 2341 2360 C5' A D 5 2359 2361 2382 C5' U D 6 2381 2383 2402 C5' A D 7 2401 2403 2424 C5' U D 8 2423 2425 2444 C5' A D 9 2443 2445 2466 C5' U D 10 2465 2467 2486 C5' A D 11 2485 2487 2508 C5' U D 12 2507 2509 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2032 P U C 2 distorted distorted 2018 2033 2034 2035 2052 P A C 3 distorted distorted 2040 2053 2054 2055 2074 P U C 4 distorted distorted 2060 2075 2076 2077 2094 P A C 5 distorted distorted 2082 2095 2096 2097 2116 P U C 6 distorted distorted 2102 2117 2118 2119 2136 P A C 7 distorted distorted 2124 2137 2138 2139 2158 P U C 8 distorted distorted 2144 2159 2160 2161 2178 P A C 9 distorted distorted 2166 2179 2180 2181 2200 P U C 10 distorted distorted 2186 2201 2202 2203 2220 P A C 11 distorted distorted 2208 2221 2222 2223 2242 P U C 12 distorted distorted 2228 2243 2244 2245 2294 P U D 2 distorted distorted 2280 2295 2296 2297 2314 P A D 3 distorted distorted 2302 2315 2316 2317 2336 P U D 4 distorted distorted 2322 2337 2338 2339 2356 P A D 5 distorted distorted 2344 2357 2358 2359 2378 P U D 6 distorted distorted 2364 2379 2380 2381 2398 P A D 7 distorted distorted 2386 2399 2400 2401 2420 P U D 8 distorted distorted 2406 2421 2422 2423 2440 P A D 9 distorted distorted 2428 2441 2442 2443 2462 P U D 10 distorted distorted 2448 2463 2464 2465 2482 P A D 11 distorted distorted 2470 2483 2484 2485 2504 P U D 12 distorted distorted 2490 2505 2506 2507 ---------------------------------------------------------------------------------