ID code: '4DWA' 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' --------------------------------------------------------------------------------- 2494 C1' C D 1 beta 2489 2495 2492 2514 C1' U D 2 beta 2509 2515 2512 2534 C1' C D 3 beta 2529 2535 2532 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2492 C2' C D 1 OK 2494 2490 2493 2512 C2' U D 2 OK 2514 2510 2513 2532 C2' C D 3 OK 2534 2530 2533 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2490 C3' C D 1 OK 2488 2491 2492 2510 C3' U D 2 OK 2508 2511 2512 2530 C3' C D 3 OK 2528 2531 2532 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2488 C4' C D 1 OK 2490 2487 2489 2508 C4' U D 2 OK 2510 2507 2509 2528 C4' C D 3 OK 2530 2527 2529 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2487 C5' C D 1 2486 2488 2507 C5' U D 2 2506 2508 2527 C5' C D 3 2526 2528 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2503 P U D 2 distorted distorted 2491 2504 2505 2506 2523 P C D 3 distorted distorted 2511 2524 2525 2526 ---------------------------------------------------------------------------------