ID code: '4P5B' 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' --------------------------------------------------------------------------------- 7467 C1' FAD A 301 7468 7489 C1' BRU A 302 beta 7494 7480 7490 7515 C1' BRU B 301 beta 7520 7506 7516 7567 C1' FAD B 302 7568 7620 C1' FAD C 301 7621 7642 C1' BRU C 302 beta 7647 7633 7643 7663 C1' BRU D 301 beta 7668 7654 7664 7715 C1' FAD D 302 7716 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7468 C2' FAD A 301 OK 7467 7470 7469 7490 C2' BRU A 302 7489 7491 7516 C2' BRU B 301 7515 7517 7568 C2' FAD B 302 OK 7567 7570 7569 7621 C2' FAD C 301 OK 7620 7623 7622 7643 C2' BRU C 302 7642 7644 7664 C2' BRU D 301 7663 7665 7716 C2' FAD D 302 OK 7715 7718 7717 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7470 C3' FAD A 301 OK 7472 7471 7468 7491 C3' BRU A 302 OK 7492 7493 7490 7517 C3' BRU B 301 OK 7518 7519 7516 7570 C3' FAD B 302 OK 7572 7571 7568 7623 C3' FAD C 301 OK 7625 7624 7621 7644 C3' BRU C 302 OK 7645 7646 7643 7665 C3' BRU D 301 OK 7666 7667 7664 7718 C3' FAD D 302 OK 7720 7719 7716 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7472 C4' FAD A 301 OK 7470 7474 7473 7492 C4' BRU A 302 OK 7491 7495 7494 7518 C4' BRU B 301 OK 7517 7521 7520 7572 C4' FAD B 302 OK 7570 7574 7573 7625 C4' FAD C 301 OK 7623 7627 7626 7645 C4' BRU C 302 OK 7644 7648 7647 7666 C4' BRU D 301 OK 7665 7669 7668 7720 C4' FAD D 302 OK 7718 7722 7721 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7474 C5' FAD A 301 7475 7472 7495 C5' BRU A 302 7496 7492 7521 C5' BRU B 301 7522 7518 7574 C5' FAD B 302 7575 7572 7627 C5' FAD C 301 7628 7625 7648 C5' BRU C 302 7649 7645 7669 C5' BRU D 301 7670 7666 7722 C5' FAD D 302 7723 7720 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7476 P FAD A 301 distorted distorted 7477 7478 7475 7497 P BRU A 302 distorted distorted 7498 7499 7496 7523 P BRU B 301 OK OK 7524 7525 7522 7576 P FAD B 302 distorted distorted 7577 7578 7575 7629 P FAD C 301 distorted distorted 7630 7631 7628 7650 P BRU C 302 OK OK 7651 7652 7649 7671 P BRU D 301 distorted distorted 7672 7673 7670 7724 P FAD D 302 distorted distorted 7725 7726 7723 ---------------------------------------------------------------------------------