ID code: '5MFX' 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' --------------------------------------------------------------------------------- 3371 C1' A B 1 beta 3366 3372 3369 3393 C1' G B 2 beta 3388 3394 3391 3416 C1' A B 3 beta 3411 3417 3414 3438 C1' C B 4 beta 3433 3439 3436 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3369 C2' A B 1 OK 3371 3367 3370 3391 C2' G B 2 OK 3393 3389 3392 3414 C2' A B 3 OK 3416 3412 3415 3436 C2' C B 4 OK 3438 3434 3437 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3367 C3' A B 1 OK 3365 3368 3369 3389 C3' G B 2 OK 3387 3390 3391 3412 C3' A B 3 OK 3410 3413 3414 3434 C3' C B 4 OK 3432 3435 3436 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3365 C4' A B 1 OK 3367 3364 3366 3387 C4' G B 2 OK 3389 3386 3388 3410 C4' A B 3 OK 3412 3409 3411 3432 C4' C B 4 OK 3434 3431 3433 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3364 C5' A B 1 3363 3365 3386 C5' G B 2 3385 3387 3409 C5' A B 3 3408 3410 3431 C5' C B 4 3430 3432 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3360 P A B 1 distorted distorted 3361 3362 3363 3382 P G B 2 distorted distorted 3368 3383 3384 3385 3405 P A B 3 distorted distorted 3390 3406 3407 3408 3427 P C B 4 distorted distorted 3413 3428 3429 3430 3447 P U B 5 distorted distorted 3435 3448 3449 3450 ---------------------------------------------------------------------------------