ID code: '2XFM' 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' --------------------------------------------------------------------------------- 1970 C1' A B 1 alpha beta 1965 1987 1971 1968 2004 C1' C B 2 alpha beta 1999 2019 2005 2002 2035 C1' C B 3 alpha beta 2030 2050 2036 2033 2066 C1' G B 4 alpha beta 2061 2084 2067 2064 2100 C1' A B 5 alpha beta 2095 2117 2101 2098 2133 C1' C B 6 alpha beta 2128 2148 2134 2131 2164 C1' U B 7 alpha beta 2159 2179 2165 2162 2191 C1' OMU B 8 alpha beta 2198 2207 2183 2192 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1968 C2' A B 1 OK OK 1970 1966 1985 1969 2002 C2' C B 2 OK OK 2004 2000 2017 2003 2033 C2' C B 3 OK OK 2035 2031 2048 2034 2064 C2' G B 4 OK OK 2066 2062 2082 2065 2098 C2' A B 5 OK OK 2100 2096 2115 2099 2131 C2' C B 6 OK OK 2133 2129 2146 2132 2162 C2' U B 7 OK OK 2164 2160 2177 2163 2192 C2' OMU B 8 OK OK 2191 2195 2208 2193 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1966 C3' A B 1 OK OK 1964 1984 1967 1968 2000 C3' C B 2 OK OK 1998 2016 2001 2002 2031 C3' C B 3 OK OK 2029 2047 2032 2033 2062 C3' G B 4 OK OK 2060 2081 2063 2064 2096 C3' A B 5 OK OK 2094 2114 2097 2098 2129 C3' C B 6 OK OK 2127 2145 2130 2131 2160 C3' U B 7 OK OK 2158 2176 2161 2162 2195 C3' OMU B 8 OK OK 2196 2212 2197 2192 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1964 C4' A B 1 OK OK 1966 1983 1963 1965 1998 C4' C B 2 OK OK 2000 2015 1997 1999 2029 C4' C B 3 OK OK 2031 2046 2028 2030 2060 C4' G B 4 OK OK 2062 2080 2059 2061 2094 C4' A B 5 OK OK 2096 2113 2093 2095 2127 C4' C B 6 OK OK 2129 2144 2126 2128 2158 C4' U B 7 OK OK 2160 2175 2157 2159 2196 C4' OMU B 8 OK OK 2195 2213 2199 2198 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1963 C5' A B 1 distorted distorted 1962 1981 1982 1964 1997 C5' C B 2 OK OK 1996 2013 2014 1998 2028 C5' C B 3 OK OK 2027 2044 2045 2029 2059 C5' G B 4 OK OK 2058 2078 2079 2060 2093 C5' A B 5 OK OK 2092 2111 2112 2094 2126 C5' C B 6 distorted distorted 2125 2142 2143 2127 2157 C5' U B 7 distorted distorted 2156 2173 2174 2158 2199 C5' OMU B 8 OK OK 2200 2215 2216 2196 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1993 P C B 2 OK OK 1967 1994 1995 1996 2024 P C B 3 OK OK 2001 2025 2026 2027 2055 P G B 4 distorted distorted 2032 2056 2057 2058 2089 P A B 5 distorted distorted 2063 2090 2091 2092 2122 P C B 6 distorted distorted 2097 2123 2124 2125 2153 P U B 7 distorted distorted 2130 2154 2155 2156 2201 P OMU B 8 distorted distorted 2161 2202 2203 2200 ---------------------------------------------------------------------------------