ID code: '3MDI' 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' --------------------------------------------------------------------------------- 3377 C1' U C 1 beta 3372 3378 3375 3397 C1' G C 2 beta 3392 3398 3395 3420 C1' U C 3 beta 3415 3421 3418 3440 C1' A C 4 beta 3435 3441 3438 3462 C1' A C 5 beta 3457 3463 3460 3484 C1' A C 6 beta 3479 3485 3482 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3375 C2' U C 1 OK 3377 3373 3376 3395 C2' G C 2 OK 3397 3393 3396 3418 C2' U C 3 OK 3420 3416 3419 3438 C2' A C 4 OK 3440 3436 3439 3460 C2' A C 5 OK 3462 3458 3461 3482 C2' A C 6 OK 3484 3480 3483 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3373 C3' U C 1 OK 3371 3374 3375 3393 C3' G C 2 OK 3391 3394 3395 3416 C3' U C 3 OK 3414 3417 3418 3436 C3' A C 4 OK 3434 3437 3438 3458 C3' A C 5 OK 3456 3459 3460 3480 C3' A C 6 OK 3478 3481 3482 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3371 C4' U C 1 OK 3373 3370 3372 3391 C4' G C 2 OK 3393 3390 3392 3414 C4' U C 3 OK 3416 3413 3415 3434 C4' A C 4 OK 3436 3433 3435 3456 C4' A C 5 OK 3458 3455 3457 3478 C4' A C 6 OK 3480 3477 3479 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3370 C5' U C 1 3369 3371 3390 C5' G C 2 3389 3391 3413 C5' U C 3 3412 3414 3433 C5' A C 4 3432 3434 3455 C5' A C 5 3454 3456 3477 C5' A C 6 3476 3478 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3386 P G C 2 distorted distorted 3374 3387 3388 3389 3409 P U C 3 distorted distorted 3394 3410 3411 3412 3429 P A C 4 distorted distorted 3417 3430 3431 3432 3451 P A C 5 distorted distorted 3437 3452 3453 3454 3473 P A C 6 distorted distorted 3459 3474 3475 3476 ---------------------------------------------------------------------------------