ID code: '3MDG' 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' --------------------------------------------------------------------------------- 3417 C1' U C 1 beta 3412 3418 3415 3437 C1' U C 2 beta 3432 3438 3435 3457 C1' G C 3 beta 3452 3458 3455 3480 C1' U C 4 beta 3475 3481 3478 3500 C1' A C 5 beta 3495 3501 3498 3522 C1' U C 6 beta 3517 3523 3520 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3415 C2' U C 1 OK 3417 3413 3416 3435 C2' U C 2 OK 3437 3433 3436 3455 C2' G C 3 OK 3457 3453 3456 3478 C2' U C 4 OK 3480 3476 3479 3498 C2' A C 5 OK 3500 3496 3499 3520 C2' U C 6 OK 3522 3518 3521 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3413 C3' U C 1 OK 3411 3414 3415 3433 C3' U C 2 OK 3431 3434 3435 3453 C3' G C 3 OK 3451 3454 3455 3476 C3' U C 4 OK 3474 3477 3478 3496 C3' A C 5 OK 3494 3497 3498 3518 C3' U C 6 OK 3516 3519 3520 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3411 C4' U C 1 OK 3413 3410 3412 3431 C4' U C 2 OK 3433 3430 3432 3451 C4' G C 3 OK 3453 3450 3452 3474 C4' U C 4 OK 3476 3473 3475 3494 C4' A C 5 OK 3496 3493 3495 3516 C4' U C 6 OK 3518 3515 3517 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3410 C5' U C 1 3409 3411 3430 C5' U C 2 3429 3431 3450 C5' G C 3 3449 3451 3473 C5' U C 4 3472 3474 3493 C5' A C 5 3492 3494 3515 C5' U C 6 3514 3516 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3426 P U C 2 distorted distorted 3414 3427 3428 3429 3446 P G C 3 distorted distorted 3434 3447 3448 3449 3469 P U C 4 distorted distorted 3454 3470 3471 3472 3489 P A C 5 distorted distorted 3477 3490 3491 3492 3511 P U C 6 distorted distorted 3497 3512 3513 3514 ---------------------------------------------------------------------------------