ID code: '3LRN' 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' GTP C 0 beta 2016 2022 2019 2044 C1' G C 1 beta 2039 2045 2042 2067 C1' C C 2 beta 2062 2068 2065 2087 C1' G C 3 beta 2082 2088 2085 2110 C1' C C 4 beta 2105 2111 2108 2130 C1' G C 5 beta 2125 2131 2128 2153 C1' C C 6 beta 2148 2154 2151 2173 C1' G C 7 beta 2168 2174 2171 2196 C1' C C 8 beta 2191 2197 2194 2216 C1' G C 9 beta 2211 2217 2214 2239 C1' C C 10 beta 2234 2240 2237 2259 C1' G C 11 beta 2254 2260 2257 2282 C1' C C 12 beta 2277 2283 2280 2302 C1' C C 13 beta 2297 2303 2300 2332 C1' GTP D 0 beta 2327 2333 2330 2355 C1' G D 1 beta 2350 2356 2353 2378 C1' C D 2 beta 2373 2379 2376 2398 C1' G D 3 beta 2393 2399 2396 2421 C1' C D 4 beta 2416 2422 2419 2441 C1' G D 5 beta 2436 2442 2439 2464 C1' C D 6 beta 2459 2465 2462 2484 C1' G D 7 beta 2479 2485 2482 2507 C1' C D 8 beta 2502 2508 2505 2527 C1' G D 9 beta 2522 2528 2525 2550 C1' C D 10 beta 2545 2551 2548 2570 C1' G D 11 beta 2565 2571 2568 2593 C1' C D 12 beta 2588 2594 2591 2613 C1' C D 13 beta 2608 2614 2611 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2019 C2' GTP C 0 OK 2021 2017 2020 2042 C2' G C 1 OK 2044 2040 2043 2065 C2' C C 2 OK 2067 2063 2066 2085 C2' G C 3 OK 2087 2083 2086 2108 C2' C C 4 OK 2110 2106 2109 2128 C2' G C 5 OK 2130 2126 2129 2151 C2' C C 6 OK 2153 2149 2152 2171 C2' G C 7 OK 2173 2169 2172 2194 C2' C C 8 OK 2196 2192 2195 2214 C2' G C 9 OK 2216 2212 2215 2237 C2' C C 10 OK 2239 2235 2238 2257 C2' G C 11 OK 2259 2255 2258 2280 C2' C C 12 OK 2282 2278 2281 2300 C2' C C 13 OK 2302 2298 2301 2330 C2' GTP D 0 OK 2332 2328 2331 2353 C2' G D 1 OK 2355 2351 2354 2376 C2' C D 2 OK 2378 2374 2377 2396 C2' G D 3 OK 2398 2394 2397 2419 C2' C D 4 OK 2421 2417 2420 2439 C2' G D 5 OK 2441 2437 2440 2462 C2' C D 6 OK 2464 2460 2463 2482 C2' G D 7 OK 2484 2480 2483 2505 C2' C D 8 OK 2507 2503 2506 2525 C2' G D 9 OK 2527 2523 2526 2548 C2' C D 10 OK 2550 2546 2549 2568 C2' G D 11 OK 2570 2566 2569 2591 C2' C D 12 OK 2593 2589 2592 2611 C2' C D 13 OK 2613 2609 2612 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2017 C3' GTP C 0 OK 2015 2018 2019 2040 C3' G C 1 OK 2038 2041 2042 2063 C3' C C 2 OK 2061 2064 2065 2083 C3' G C 3 OK 2081 2084 2085 2106 C3' C C 4 OK 2104 2107 2108 2126 C3' G C 5 OK 2124 2127 2128 2149 C3' C C 6 OK 2147 2150 2151 2169 C3' G C 7 OK 2167 2170 2171 2192 C3' C C 8 OK 2190 2193 2194 2212 C3' G C 9 OK 2210 2213 2214 2235 C3' C C 10 OK 2233 2236 2237 2255 C3' G C 11 OK 2253 2256 2257 2278 C3' C C 12 OK 2276 2279 2280 2298 C3' C C 13 OK 2296 2299 2300 2328 C3' GTP D 0 OK 2326 2329 2330 2351 C3' G D 1 OK 2349 2352 2353 2374 C3' C D 2 OK 2372 2375 2376 2394 C3' G D 3 OK 2392 2395 2396 2417 C3' C D 4 OK 2415 2418 2419 2437 C3' G D 5 OK 2435 2438 2439 2460 C3' C D 6 OK 2458 2461 2462 2480 C3' G D 7 OK 2478 2481 2482 2503 C3' C D 8 OK 2501 2504 2505 2523 C3' G D 9 OK 2521 2524 2525 2546 C3' C D 10 OK 2544 2547 2548 2566 C3' G D 11 OK 2564 2567 2568 2589 C3' C D 12 OK 2587 2590 2591 2609 C3' C D 13 OK 2607 2610 2611 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2015 C4' GTP C 0 OK 2017 2014 2016 2038 C4' G C 1 OK 2040 2037 2039 2061 C4' C C 2 OK 2063 2060 2062 2081 C4' G C 3 OK 2083 2080 2082 2104 C4' C C 4 OK 2106 2103 2105 2124 C4' G C 5 OK 2126 2123 2125 2147 C4' C C 6 OK 2149 2146 2148 2167 C4' G C 7 OK 2169 2166 2168 2190 C4' C C 8 OK 2192 2189 2191 2210 C4' G C 9 OK 2212 2209 2211 2233 C4' C C 10 OK 2235 2232 2234 2253 C4' G C 11 OK 2255 2252 2254 2276 C4' C C 12 OK 2278 2275 2277 2296 C4' C C 13 OK 2298 2295 2297 2326 C4' GTP D 0 OK 2328 2325 2327 2349 C4' G D 1 OK 2351 2348 2350 2372 C4' C D 2 OK 2374 2371 2373 2392 C4' G D 3 OK 2394 2391 2393 2415 C4' C D 4 OK 2417 2414 2416 2435 C4' G D 5 OK 2437 2434 2436 2458 C4' C D 6 OK 2460 2457 2459 2478 C4' G D 7 OK 2480 2477 2479 2501 C4' C D 8 OK 2503 2500 2502 2521 C4' G D 9 OK 2523 2520 2522 2544 C4' C D 10 OK 2546 2543 2545 2564 C4' G D 11 OK 2566 2563 2565 2587 C4' C D 12 OK 2589 2586 2588 2607 C4' C D 13 OK 2609 2606 2608 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2014 C5' GTP C 0 2013 2015 2037 C5' G C 1 2036 2038 2060 C5' C C 2 2059 2061 2080 C5' G C 3 2079 2081 2103 C5' C C 4 2102 2104 2123 C5' G C 5 2122 2124 2146 C5' C C 6 2145 2147 2166 C5' G C 7 2165 2167 2189 C5' C C 8 2188 2190 2209 C5' G C 9 2208 2210 2232 C5' C C 10 2231 2233 2252 C5' G C 11 2251 2253 2275 C5' C C 12 2274 2276 2295 C5' C C 13 2294 2296 2325 C5' GTP D 0 2324 2326 2348 C5' G D 1 2347 2349 2371 C5' C D 2 2370 2372 2391 C5' G D 3 2390 2392 2414 C5' C D 4 2413 2415 2434 C5' G D 5 2433 2435 2457 C5' C D 6 2456 2458 2477 C5' G D 7 2476 2478 2500 C5' C D 8 2499 2501 2520 C5' G D 9 2519 2521 2543 C5' C D 10 2542 2544 2563 C5' G D 11 2562 2564 2586 C5' C D 12 2585 2587 2606 C5' C D 13 2605 2607 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2033 P G C 1 distorted distorted 2018 2034 2035 2036 2056 P C C 2 distorted distorted 2041 2057 2058 2059 2076 P G C 3 distorted distorted 2064 2077 2078 2079 2099 P C C 4 distorted distorted 2084 2100 2101 2102 2119 P G C 5 distorted distorted 2107 2120 2121 2122 2142 P C C 6 distorted distorted 2127 2143 2144 2145 2162 P G C 7 distorted distorted 2150 2163 2164 2165 2185 P C C 8 distorted distorted 2170 2186 2187 2188 2205 P G C 9 distorted distorted 2193 2206 2207 2208 2228 P C C 10 distorted distorted 2213 2229 2230 2231 2248 P G C 11 distorted distorted 2236 2249 2250 2251 2271 P C C 12 distorted distorted 2256 2272 2273 2274 2291 P C C 13 distorted distorted 2279 2292 2293 2294 2344 P G D 1 distorted distorted 2329 2345 2346 2347 2367 P C D 2 distorted distorted 2352 2368 2369 2370 2387 P G D 3 distorted distorted 2375 2388 2389 2390 2410 P C D 4 distorted distorted 2395 2411 2412 2413 2430 P G D 5 distorted distorted 2418 2431 2432 2433 2453 P C D 6 distorted distorted 2438 2454 2455 2456 2473 P G D 7 distorted distorted 2461 2474 2475 2476 2496 P C D 8 distorted distorted 2481 2497 2498 2499 2516 P G D 9 distorted distorted 2504 2517 2518 2519 2539 P C D 10 distorted distorted 2524 2540 2541 2542 2559 P G D 11 distorted distorted 2547 2560 2561 2562 2582 P C D 12 distorted distorted 2567 2583 2584 2585 2602 P C D 13 distorted distorted 2590 2603 2604 2605 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