ID code: '3OG8' 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' --------------------------------------------------------------------------------- 2109 C1' G C 1 beta 2104 2110 2107 2132 C1' G C 2 beta 2127 2133 2130 2155 C1' C C 3 beta 2150 2156 2153 2175 C1' G C 4 beta 2170 2176 2173 2198 C1' C C 5 beta 2193 2199 2196 2218 C1' G C 6 beta 2213 2219 2216 2241 C1' C C 7 beta 2236 2242 2239 2261 C1' G C 8 beta 2256 2262 2259 2284 C1' C C 9 beta 2279 2285 2282 2304 C1' G C 10 beta 2299 2305 2302 2327 C1' C C 11 beta 2322 2328 2325 2347 C1' G C 12 beta 2342 2348 2345 2370 C1' C C 13 beta 2365 2371 2368 2390 C1' C C 14 beta 2385 2391 2388 2408 C1' G D 1 beta 2403 2409 2406 2431 C1' G D 2 beta 2426 2432 2429 2454 C1' C D 3 beta 2449 2455 2452 2474 C1' G D 4 beta 2469 2475 2472 2497 C1' C D 5 beta 2492 2498 2495 2517 C1' G D 6 beta 2512 2518 2515 2540 C1' C D 7 beta 2535 2541 2538 2560 C1' G D 8 beta 2555 2561 2558 2583 C1' C D 9 beta 2578 2584 2581 2603 C1' G D 10 beta 2598 2604 2601 2626 C1' C D 11 beta 2621 2627 2624 2646 C1' G D 12 beta 2641 2647 2644 2669 C1' C D 13 beta 2664 2670 2667 2689 C1' C D 14 beta 2684 2690 2687 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2107 C2' G C 1 OK 2109 2105 2108 2130 C2' G C 2 OK 2132 2128 2131 2153 C2' C C 3 OK 2155 2151 2154 2173 C2' G C 4 OK 2175 2171 2174 2196 C2' C C 5 OK 2198 2194 2197 2216 C2' G C 6 OK 2218 2214 2217 2239 C2' C C 7 OK 2241 2237 2240 2259 C2' G C 8 OK 2261 2257 2260 2282 C2' C C 9 OK 2284 2280 2283 2302 C2' G C 10 OK 2304 2300 2303 2325 C2' C C 11 OK 2327 2323 2326 2345 C2' G C 12 OK 2347 2343 2346 2368 C2' C C 13 OK 2370 2366 2369 2388 C2' C C 14 OK 2390 2386 2389 2406 C2' G D 1 OK 2408 2404 2407 2429 C2' G D 2 OK 2431 2427 2430 2452 C2' C D 3 OK 2454 2450 2453 2472 C2' G D 4 OK 2474 2470 2473 2495 C2' C D 5 OK 2497 2493 2496 2515 C2' G D 6 OK 2517 2513 2516 2538 C2' C D 7 OK 2540 2536 2539 2558 C2' G D 8 OK 2560 2556 2559 2581 C2' C D 9 OK 2583 2579 2582 2601 C2' G D 10 OK 2603 2599 2602 2624 C2' C D 11 OK 2626 2622 2625 2644 C2' G D 12 OK 2646 2642 2645 2667 C2' C D 13 OK 2669 2665 2668 2687 C2' C D 14 OK 2689 2685 2688 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2105 C3' G C 1 OK 2103 2106 2107 2128 C3' G C 2 OK 2126 2129 2130 2151 C3' C C 3 OK 2149 2152 2153 2171 C3' G C 4 OK 2169 2172 2173 2194 C3' C C 5 OK 2192 2195 2196 2214 C3' G C 6 OK 2212 2215 2216 2237 C3' C C 7 OK 2235 2238 2239 2257 C3' G C 8 OK 2255 2258 2259 2280 C3' C C 9 OK 2278 2281 2282 2300 C3' G C 10 OK 2298 2301 2302 2323 C3' C C 11 OK 2321 2324 2325 2343 C3' G C 12 OK 2341 2344 2345 2366 C3' C C 13 OK 2364 2367 2368 2386 C3' C C 14 OK 2384 2387 2388 2404 C3' G D 1 OK 2402 2405 2406 2427 C3' G D 2 OK 2425 2428 2429 2450 C3' C D 3 OK 2448 2451 2452 2470 C3' G D 4 OK 2468 2471 2472 2493 C3' C D 5 OK 2491 2494 2495 2513 C3' G D 6 OK 2511 2514 2515 2536 C3' C D 7 OK 2534 2537 2538 2556 C3' G D 8 OK 2554 2557 2558 2579 C3' C D 9 OK 2577 2580 2581 2599 C3' G D 10 OK 2597 2600 2601 2622 C3' C D 11 OK 2620 2623 2624 2642 C3' G D 12 OK 2640 2643 2644 2665 C3' C D 13 OK 2663 2666 2667 2685 C3' C D 14 OK 2683 2686 2687 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2103 C4' G C 1 OK 2105 2102 2104 2126 C4' G C 2 OK 2128 2125 2127 2149 C4' C C 3 OK 2151 2148 2150 2169 C4' G C 4 OK 2171 2168 2170 2192 C4' C C 5 OK 2194 2191 2193 2212 C4' G C 6 OK 2214 2211 2213 2235 C4' C C 7 OK 2237 2234 2236 2255 C4' G C 8 OK 2257 2254 2256 2278 C4' C C 9 OK 2280 2277 2279 2298 C4' G C 10 OK 2300 2297 2299 2321 C4' C C 11 OK 2323 2320 2322 2341 C4' G C 12 OK 2343 2340 2342 2364 C4' C C 13 OK 2366 2363 2365 2384 C4' C C 14 OK 2386 2383 2385 2402 C4' G D 1 OK 2404 2401 2403 2425 C4' G D 2 OK 2427 2424 2426 2448 C4' C D 3 OK 2450 2447 2449 2468 C4' G D 4 OK 2470 2467 2469 2491 C4' C D 5 OK 2493 2490 2492 2511 C4' G D 6 OK 2513 2510 2512 2534 C4' C D 7 OK 2536 2533 2535 2554 C4' G D 8 OK 2556 2553 2555 2577 C4' C D 9 OK 2579 2576 2578 2597 C4' G D 10 OK 2599 2596 2598 2620 C4' C D 11 OK 2622 2619 2621 2640 C4' G D 12 OK 2642 2639 2641 2663 C4' C D 13 OK 2665 2662 2664 2683 C4' C D 14 OK 2685 2682 2684 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2102 C5' G C 1 2101 2103 2125 C5' G C 2 2124 2126 2148 C5' C C 3 2147 2149 2168 C5' G C 4 2167 2169 2191 C5' C C 5 2190 2192 2211 C5' G C 6 2210 2212 2234 C5' C C 7 2233 2235 2254 C5' G C 8 2253 2255 2277 C5' C C 9 2276 2278 2297 C5' G C 10 2296 2298 2320 C5' C C 11 2319 2321 2340 C5' G C 12 2339 2341 2363 C5' C C 13 2362 2364 2383 C5' C C 14 2382 2384 2401 C5' G D 1 2400 2402 2424 C5' G D 2 2423 2425 2447 C5' C D 3 2446 2448 2467 C5' G D 4 2466 2468 2490 C5' C D 5 2489 2491 2510 C5' G D 6 2509 2511 2533 C5' C D 7 2532 2534 2553 C5' G D 8 2552 2554 2576 C5' C D 9 2575 2577 2596 C5' G D 10 2595 2597 2619 C5' C D 11 2618 2620 2639 C5' G D 12 2638 2640 2662 C5' C D 13 2661 2663 2682 C5' C D 14 2681 2683 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2121 P G C 2 distorted distorted 2106 2122 2123 2124 2144 P C C 3 distorted distorted 2129 2145 2146 2147 2164 P G C 4 distorted distorted 2152 2165 2166 2167 2187 P C C 5 distorted distorted 2172 2188 2189 2190 2207 P G C 6 distorted distorted 2195 2208 2209 2210 2230 P C C 7 distorted distorted 2215 2231 2232 2233 2250 P G C 8 distorted distorted 2238 2251 2252 2253 2273 P C C 9 distorted distorted 2258 2274 2275 2276 2293 P G C 10 distorted distorted 2281 2294 2295 2296 2316 P C C 11 distorted distorted 2301 2317 2318 2319 2336 P G C 12 distorted distorted 2324 2337 2338 2339 2359 P C C 13 distorted distorted 2344 2360 2361 2362 2379 P C C 14 distorted distorted 2367 2380 2381 2382 2420 P G D 2 distorted distorted 2405 2421 2422 2423 2443 P C D 3 distorted distorted 2428 2444 2445 2446 2463 P G D 4 distorted distorted 2451 2464 2465 2466 2486 P C D 5 distorted distorted 2471 2487 2488 2489 2506 P G D 6 distorted distorted 2494 2507 2508 2509 2529 P C D 7 distorted distorted 2514 2530 2531 2532 2549 P G D 8 distorted distorted 2537 2550 2551 2552 2572 P C D 9 distorted distorted 2557 2573 2574 2575 2592 P G D 10 distorted distorted 2580 2593 2594 2595 2615 P C D 11 distorted distorted 2600 2616 2617 2618 2635 P G D 12 distorted distorted 2623 2636 2637 2638 2658 P C D 13 distorted distorted 2643 2659 2660 2661 2678 P C D 14 distorted distorted 2666 2679 2680 2681 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