ID code: '2QCH' 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' --------------------------------------------------------------------------------- 3989 C1' 5IU A 1 beta 4014 4001 4010 4009 C1' UMP A 2 beta 4014 4001 4010 4031 C1' 5IU B 3 beta 4056 4043 4052 4051 C1' UMP B 4 beta 4056 4043 4052 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 3990 C2' 5IU A 1 4009 4011 4010 C2' UMP A 2 4009 4011 4032 C2' 5IU B 3 4051 4053 4052 C2' UMP B 4 4051 4053 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3991 C3' 5IU A 1 OK 4012 4013 4010 4011 C3' UMP A 2 OK 4012 4013 4010 4033 C3' 5IU B 3 OK 4054 4055 4052 4053 C3' UMP B 4 OK 4054 4055 4052 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3992 C4' 5IU A 1 OK 4011 4015 4014 4012 C4' UMP A 2 OK 4011 4015 4014 4034 C4' 5IU B 3 OK 4053 4057 4056 4054 C4' UMP B 4 OK 4053 4057 4056 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 3995 C5' 5IU A 1 4016 4012 4015 C5' UMP A 2 4016 4012 4037 C5' 5IU B 3 4058 4054 4057 C5' UMP B 4 4058 4054 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3997 P 5IU A 1 OK OK 4018 4019 4016 4017 P UMP A 2 OK OK 4018 4019 4016 4039 P 5IU B 3 OK OK 4060 4061 4058 4059 P UMP B 4 OK OK 4060 4061 4058 ---------------------------------------------------------------------------------