ID code: '4N48' 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' --------------------------------------------------------------------------------- 6422 C1' G D 1 beta 6417 6423 6420 6445 C1' A D 2 beta 6440 6446 6443 6467 C1' U D 3 beta 6462 6468 6465 6489 C1' G G 1 beta 6484 6490 6487 6512 C1' A G 2 beta 6507 6513 6510 6534 C1' U G 3 beta 6529 6535 6532 6554 C1' C G 4 beta 6549 6555 6552 6580 C1' SAM A 601 beta 6575 6581 6578 6607 C1' SAM B 601 beta 6602 6608 6605 6637 C1' MGT D 101 beta 6632 6638 6635 6669 C1' MGT G 101 beta 6664 6670 6667 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 6420 C2' G D 1 OK 6422 6418 6421 6443 C2' A D 2 OK 6445 6441 6444 6465 C2' U D 3 OK 6467 6463 6466 6487 C2' G G 1 OK 6489 6485 6488 6510 C2' A G 2 OK 6512 6508 6511 6532 C2' U G 3 OK 6534 6530 6533 6552 C2' C G 4 OK 6554 6550 6553 6578 C2' SAM A 601 OK 6580 6576 6579 6605 C2' SAM B 601 OK 6607 6603 6606 6635 C2' MGT D 101 OK 6637 6633 6636 6667 C2' MGT G 101 OK 6669 6665 6668 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 6418 C3' G D 1 OK 6416 6419 6420 6441 C3' A D 2 OK 6439 6442 6443 6463 C3' U D 3 OK 6461 6464 6465 6485 C3' G G 1 OK 6483 6486 6487 6508 C3' A G 2 OK 6506 6509 6510 6530 C3' U G 3 OK 6528 6531 6532 6550 C3' C G 4 OK 6548 6551 6552 6576 C3' SAM A 601 OK 6574 6577 6578 6603 C3' SAM B 601 OK 6601 6604 6605 6633 C3' MGT D 101 OK 6631 6634 6635 6665 C3' MGT G 101 OK 6663 6666 6667 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6416 C4' G D 1 OK 6418 6415 6417 6439 C4' A D 2 OK 6441 6438 6440 6461 C4' U D 3 OK 6463 6460 6462 6483 C4' G G 1 OK 6485 6482 6484 6506 C4' A G 2 OK 6508 6505 6507 6528 C4' U G 3 OK 6530 6527 6529 6548 C4' C G 4 OK 6550 6547 6549 6574 C4' SAM A 601 OK 6576 6573 6575 6601 C4' SAM B 601 OK 6603 6600 6602 6631 C4' MGT D 101 OK 6633 6630 6632 6663 C4' MGT G 101 OK 6665 6662 6664 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6415 C5' G D 1 6414 6416 6438 C5' A D 2 6437 6439 6460 C5' U D 3 6459 6461 6482 C5' G G 1 6481 6483 6505 C5' A G 2 6504 6506 6527 C5' U G 3 6526 6528 6547 C5' C G 4 6546 6548 6573 C5' SAM A 601 6574 6600 C5' SAM B 601 6601 6630 C5' MGT D 101 6629 6631 6662 C5' MGT G 101 6661 6663 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 6434 P A D 2 distorted distorted 6419 6435 6436 6437 6456 P U D 3 distorted distorted 6442 6457 6458 6459 6476 P C D 4 distorted distorted 6464 6477 6478 6479 6501 P A G 2 distorted distorted 6486 6502 6503 6504 6523 P U G 3 distorted distorted 6509 6524 6525 6526 6543 P C G 4 distorted distorted 6531 6544 6545 6546 ---------------------------------------------------------------------------------