ID code: '2XBM' 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' --------------------------------------------------------------------------------- 8317 C1' G E 1 beta 8312 8318 8315 8340 C1' A E 2 beta 8335 8341 8338 8362 C1' A E 3 beta 8357 8363 8360 8384 C1' C E 4 beta 8379 8385 8382 8404 C1' C E 5 beta 8399 8405 8402 8424 C1' U E 6 beta 8419 8425 8422 8444 C1' G E 7 beta 8439 8445 8442 8522 C1' G F 1 beta 8517 8523 8520 8545 C1' A F 2 beta 8540 8546 8543 8567 C1' A F 3 beta 8562 8568 8565 8589 C1' C F 4 beta 8584 8590 8587 8609 C1' C F 5 beta 8604 8610 8607 8629 C1' U F 6 beta 8624 8630 8627 8649 C1' G F 7 beta 8644 8650 8647 8701 C1' SAH A 268 beta 8696 8702 8699 8753 C1' SAH B 268 beta 8748 8754 8751 8795 C1' SAH C 266 beta 8790 8796 8793 8831 C1' SAH D 266 beta 8826 8832 8829 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 8315 C2' G E 1 OK 8317 8313 8316 8338 C2' A E 2 OK 8340 8336 8339 8360 C2' A E 3 OK 8362 8358 8361 8382 C2' C E 4 OK 8384 8380 8383 8402 C2' C E 5 OK 8404 8400 8403 8422 C2' U E 6 OK 8424 8420 8423 8442 C2' G E 7 OK 8444 8440 8443 8520 C2' G F 1 OK 8522 8518 8521 8543 C2' A F 2 OK 8545 8541 8544 8565 C2' A F 3 OK 8567 8563 8566 8587 C2' C F 4 OK 8589 8585 8588 8607 C2' C F 5 OK 8609 8605 8608 8627 C2' U F 6 OK 8629 8625 8628 8647 C2' G F 7 OK 8649 8645 8648 8699 C2' SAH A 268 OK 8701 8697 8700 8751 C2' SAH B 268 OK 8753 8749 8752 8793 C2' SAH C 266 OK 8795 8791 8794 8829 C2' SAH D 266 OK 8831 8827 8830 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8313 C3' G E 1 OK 8311 8314 8315 8336 C3' A E 2 OK 8334 8337 8338 8358 C3' A E 3 OK 8356 8359 8360 8380 C3' C E 4 OK 8378 8381 8382 8400 C3' C E 5 OK 8398 8401 8402 8420 C3' U E 6 OK 8418 8421 8422 8440 C3' G E 7 OK 8438 8441 8442 8518 C3' G F 1 OK 8516 8519 8520 8541 C3' A F 2 OK 8539 8542 8543 8563 C3' A F 3 OK 8561 8564 8565 8585 C3' C F 4 OK 8583 8586 8587 8605 C3' C F 5 OK 8603 8606 8607 8625 C3' U F 6 OK 8623 8626 8627 8645 C3' G F 7 OK 8643 8646 8647 8697 C3' SAH A 268 OK 8695 8698 8699 8749 C3' SAH B 268 OK 8747 8750 8751 8791 C3' SAH C 266 OK 8789 8792 8793 8827 C3' SAH D 266 OK 8825 8828 8829 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 8311 C4' G E 1 OK 8313 8310 8312 8334 C4' A E 2 OK 8336 8333 8335 8356 C4' A E 3 OK 8358 8355 8357 8378 C4' C E 4 OK 8380 8377 8379 8398 C4' C E 5 OK 8400 8397 8399 8418 C4' U E 6 OK 8420 8417 8419 8438 C4' G E 7 OK 8440 8437 8439 8516 C4' G F 1 OK 8518 8515 8517 8539 C4' A F 2 OK 8541 8538 8540 8561 C4' A F 3 OK 8563 8560 8562 8583 C4' C F 4 OK 8585 8582 8584 8603 C4' C F 5 OK 8605 8602 8604 8623 C4' U F 6 OK 8625 8622 8624 8643 C4' G F 7 OK 8645 8642 8644 8695 C4' SAH A 268 OK 8697 8694 8696 8747 C4' SAH B 268 OK 8749 8746 8748 8789 C4' SAH C 266 OK 8791 8788 8790 8825 C4' SAH D 266 OK 8827 8824 8826 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 8310 C5' G E 1 8309 8311 8333 C5' A E 2 8332 8334 8355 C5' A E 3 8354 8356 8377 C5' C E 4 8376 8378 8397 C5' C E 5 8396 8398 8417 C5' U E 6 8416 8418 8437 C5' G E 7 8436 8438 8515 C5' G F 1 8514 8516 8538 C5' A F 2 8537 8539 8560 C5' A F 3 8559 8561 8582 C5' C F 4 8581 8583 8602 C5' C F 5 8601 8603 8622 C5' U F 6 8621 8623 8642 C5' G F 7 8641 8643 8694 C5' SAH A 268 8695 8746 C5' SAH B 268 8747 8788 C5' SAH C 266 8789 8824 C5' SAH D 266 8825 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 8306 P G E 1 OK OK 8307 8308 8309 8329 P A E 2 distorted distorted 8314 8330 8331 8332 8351 P A E 3 distorted distorted 8337 8352 8353 8354 8373 P C E 4 distorted distorted 8359 8374 8375 8376 8393 P C E 5 distorted distorted 8381 8394 8395 8396 8413 P U E 6 distorted distorted 8401 8414 8415 8416 8433 P G E 7 distorted distorted 8421 8434 8435 8436 8456 P A E 8 distorted distorted 8441 8457 8458 8459 8511 P G F 1 OK OK 8512 8513 8514 8534 P A F 2 distorted distorted 8519 8535 8536 8537 8556 P A F 3 distorted distorted 8542 8557 8558 8559 8578 P C F 4 distorted distorted 8564 8579 8580 8581 8598 P C F 5 distorted distorted 8586 8599 8600 8601 8618 P U F 6 distorted distorted 8606 8619 8620 8621 8638 P G F 7 distorted distorted 8626 8639 8640 8641 8661 P A F 8 distorted distorted 8646 8662 8663 8664 ---------------------------------------------------------------------------------