ID code: '3L26' 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' --------------------------------------------------------------------------------- 1948 C1' C C 1 beta 1943 1949 1946 1968 C1' G C 2 beta 1963 1969 1966 1991 C1' C C 3 beta 1986 1992 1989 2011 C1' A C 4 beta 2006 2012 2009 2033 C1' U C 5 beta 2028 2034 2031 2053 C1' G C 6 beta 2048 2054 2051 2076 C1' C C 7 beta 2071 2077 2074 2096 C1' G C 8 beta 2091 2097 2094 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1946 C2' C C 1 OK 1948 1944 1947 1966 C2' G C 2 OK 1968 1964 1967 1989 C2' C C 3 OK 1991 1987 1990 2009 C2' A C 4 OK 2011 2007 2010 2031 C2' U C 5 OK 2033 2029 2032 2051 C2' G C 6 OK 2053 2049 2052 2074 C2' C C 7 OK 2076 2072 2075 2094 C2' G C 8 OK 2096 2092 2095 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1944 C3' C C 1 OK 1942 1945 1946 1964 C3' G C 2 OK 1962 1965 1966 1987 C3' C C 3 OK 1985 1988 1989 2007 C3' A C 4 OK 2005 2008 2009 2029 C3' U C 5 OK 2027 2030 2031 2049 C3' G C 6 OK 2047 2050 2051 2072 C3' C C 7 OK 2070 2073 2074 2092 C3' G C 8 OK 2090 2093 2094 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1942 C4' C C 1 OK 1944 1941 1943 1962 C4' G C 2 OK 1964 1961 1963 1985 C4' C C 3 OK 1987 1984 1986 2005 C4' A C 4 OK 2007 2004 2006 2027 C4' U C 5 OK 2029 2026 2028 2047 C4' G C 6 OK 2049 2046 2048 2070 C4' C C 7 OK 2072 2069 2071 2090 C4' G C 8 OK 2092 2089 2091 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1941 C5' C C 1 1940 1942 1961 C5' G C 2 1960 1962 1984 C5' C C 3 1983 1985 2004 C5' A C 4 2003 2005 2026 C5' U C 5 2025 2027 2046 C5' G C 6 2045 2047 2069 C5' C C 7 2068 2070 2089 C5' G C 8 2088 2090 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1957 P G C 2 distorted distorted 1945 1958 1959 1960 1980 P C C 3 distorted distorted 1965 1981 1982 1983 2000 P A C 4 distorted distorted 1988 2001 2002 2003 2022 P U C 5 distorted distorted 2008 2023 2024 2025 2042 P G C 6 distorted distorted 2030 2043 2044 2045 2065 P C C 7 distorted distorted 2050 2066 2067 2068 2085 P G C 8 distorted distorted 2073 2086 2087 2088 ---------------------------------------------------------------------------------