ID code: '4WTI' 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' --------------------------------------------------------------------------------- 13 C1' C T 2 beta 8 14 11 33 C1' G T 3 beta 28 34 31 56 C1' G T 4 beta 51 57 54 81 C1' C P 1 beta 76 82 79 101 C1' C P 2 beta 96 102 99 4364 C1' GDP A 605 beta 4359 4365 4362 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' C T 2 OK 13 9 12 31 C2' G T 3 OK 33 29 32 54 C2' G T 4 OK 56 52 55 79 C2' C P 1 OK 81 77 80 99 C2' C P 2 OK 101 97 100 4362 C2' GDP A 605 OK 4364 4360 4363 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' C T 2 OK 7 10 11 29 C3' G T 3 OK 27 30 31 52 C3' G T 4 OK 50 53 54 77 C3' C P 1 OK 75 78 79 97 C3' C P 2 OK 95 98 99 4360 C3' GDP A 605 OK 4358 4361 4362 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' C T 2 OK 9 6 8 27 C4' G T 3 OK 29 26 28 50 C4' G T 4 OK 52 49 51 75 C4' C P 1 OK 77 74 76 95 C4' C P 2 OK 97 94 96 4358 C4' GDP A 605 OK 4360 4357 4359 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' C T 2 5 7 26 C5' G T 3 25 27 49 C5' G T 4 48 50 74 C5' C P 1 73 75 94 C5' C P 2 93 95 4357 C5' GDP A 605 4356 4358 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P C T 2 distorted distorted 1 3 4 5 22 P G T 3 distorted distorted 10 23 24 25 45 P G T 4 distorted distorted 30 46 47 48 70 P C P 1 distorted distorted 71 72 73 90 P C P 2 distorted distorted 78 91 92 93 ---------------------------------------------------------------------------------