ID code: '2ADB' 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' --------------------------------------------------------------------------------- 1982 C1' C B 299 alpha beta 1977 1997 1983 1980 2014 C1' U B 300 alpha beta 2009 2029 2015 2012 2044 C1' C B 301 alpha beta 2039 2059 2045 2042 2075 C1' U B 302 alpha beta 2070 2090 2076 2073 2105 C1' C B 303 alpha beta 2100 2120 2106 2103 2136 C1' U B 304 alpha beta 2131 2152 2137 2134 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1980 C2' C B 299 OK OK 1982 1978 1995 1981 2012 C2' U B 300 OK OK 2014 2010 2027 2013 2042 C2' C B 301 OK OK 2044 2040 2057 2043 2073 C2' U B 302 OK OK 2075 2071 2088 2074 2103 C2' C B 303 OK OK 2105 2101 2118 2104 2134 C2' U B 304 OK OK 2136 2132 2150 2135 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1978 C3' C B 299 OK OK 1976 1994 1979 1980 2010 C3' U B 300 OK OK 2008 2026 2011 2012 2040 C3' C B 301 OK OK 2038 2056 2041 2042 2071 C3' U B 302 OK OK 2069 2087 2072 2073 2101 C3' C B 303 OK OK 2099 2117 2102 2103 2132 C3' U B 304 OK OK 2130 2148 2133 2134 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1976 C4' C B 299 OK OK 1978 1993 1975 1977 2008 C4' U B 300 OK OK 2010 2025 2007 2009 2038 C4' C B 301 OK OK 2040 2055 2037 2039 2069 C4' U B 302 OK OK 2071 2086 2068 2070 2099 C4' C B 303 OK OK 2101 2116 2098 2100 2130 C4' U B 304 OK OK 2132 2147 2129 2131 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1975 C5' C B 299 OK OK 1974 1991 1992 1976 2007 C5' U B 300 OK OK 2006 2023 2024 2008 2037 C5' C B 301 OK OK 2036 2053 2054 2038 2068 C5' U B 302 OK OK 2067 2084 2085 2069 2098 C5' C B 303 OK OK 2097 2114 2115 2099 2129 C5' U B 304 OK OK 2128 2145 2146 2130 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2003 P U B 300 distorted distorted 1979 2004 2005 2006 2033 P C B 301 distorted distorted 2011 2034 2035 2036 2064 P U B 302 distorted distorted 2041 2065 2066 2067 2094 P C B 303 distorted distorted 2072 2095 2096 2097 2125 P U B 304 distorted distorted 2102 2126 2127 2128 ---------------------------------------------------------------------------------