ID code: '5MJV' 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' --------------------------------------------------------------------------------- 5378 C1' G D 1 beta 5373 5379 5376 5401 C1' U D 2 beta 5396 5402 5399 5421 C1' U D 3 beta 5416 5422 5419 5441 C1' U D 4 beta 5436 5442 5439 5461 C1' U D 5 beta 5456 5462 5459 5481 C1' U D 6 beta 5476 5482 5479 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5376 C2' G D 1 OK 5378 5374 5377 5399 C2' U D 2 OK 5401 5397 5400 5419 C2' U D 3 OK 5421 5417 5420 5439 C2' U D 4 OK 5441 5437 5440 5459 C2' U D 5 OK 5461 5457 5460 5479 C2' U D 6 OK 5481 5477 5480 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5374 C3' G D 1 OK 5372 5375 5376 5397 C3' U D 2 OK 5395 5398 5399 5417 C3' U D 3 OK 5415 5418 5419 5437 C3' U D 4 OK 5435 5438 5439 5457 C3' U D 5 OK 5455 5458 5459 5477 C3' U D 6 OK 5475 5478 5479 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5372 C4' G D 1 OK 5374 5371 5373 5395 C4' U D 2 OK 5397 5394 5396 5415 C4' U D 3 OK 5417 5414 5416 5435 C4' U D 4 OK 5437 5434 5436 5455 C4' U D 5 OK 5457 5454 5456 5475 C4' U D 6 OK 5477 5474 5476 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5371 C5' G D 1 5370 5372 5394 C5' U D 2 5393 5395 5414 C5' U D 3 5413 5415 5434 C5' U D 4 5433 5435 5454 C5' U D 5 5453 5455 5474 C5' U D 6 5473 5475 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5390 P U D 2 distorted distorted 5375 5391 5392 5393 5410 P U D 3 distorted distorted 5398 5411 5412 5413 5430 P U D 4 distorted distorted 5418 5431 5432 5433 5450 P U D 5 distorted distorted 5438 5451 5452 5453 5470 P U D 6 distorted distorted 5458 5471 5472 5473 ---------------------------------------------------------------------------------