ID code: '4LJ0' 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' --------------------------------------------------------------------------------- 1994 C1' A C 1 alpha beta 1989 2011 1995 1992 2028 C1' A C 2 alpha beta 2023 2045 2029 2026 2061 C1' A C 3 alpha beta 2056 2078 2062 2059 2094 C1' A C 4 alpha beta 2089 2111 2095 2092 2128 C1' A D 1 alpha beta 2123 2145 2129 2126 2161 C1' A D 2 alpha beta 2156 2178 2162 2159 2194 C1' A D 3 alpha beta 2189 2211 2195 2192 2227 C1' A D 4 alpha beta 2222 2244 2228 2225 2261 C1' A E 1 alpha beta 2256 2278 2262 2259 2294 C1' A E 2 alpha beta 2289 2311 2295 2292 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1992 C2' A C 1 OK OK 1994 1990 2009 1993 2026 C2' A C 2 OK OK 2028 2024 2043 2027 2059 C2' A C 3 OK OK 2061 2057 2076 2060 2092 C2' A C 4 OK OK 2094 2090 2109 2093 2126 C2' A D 1 OK OK 2128 2124 2143 2127 2159 C2' A D 2 OK OK 2161 2157 2176 2160 2192 C2' A D 3 OK OK 2194 2190 2209 2193 2225 C2' A D 4 OK OK 2227 2223 2242 2226 2259 C2' A E 1 OK OK 2261 2257 2276 2260 2292 C2' A E 2 OK OK 2294 2290 2309 2293 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1990 C3' A C 1 OK OK 1988 2008 1991 1992 2024 C3' A C 2 OK OK 2022 2042 2025 2026 2057 C3' A C 3 OK OK 2055 2075 2058 2059 2090 C3' A C 4 OK OK 2088 2108 2091 2092 2124 C3' A D 1 OK OK 2122 2142 2125 2126 2157 C3' A D 2 OK OK 2155 2175 2158 2159 2190 C3' A D 3 OK OK 2188 2208 2191 2192 2223 C3' A D 4 OK OK 2221 2241 2224 2225 2257 C3' A E 1 OK OK 2255 2275 2258 2259 2290 C3' A E 2 OK OK 2288 2308 2291 2292 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1988 C4' A C 1 OK OK 1990 2007 1987 1989 2022 C4' A C 2 OK OK 2024 2041 2021 2023 2055 C4' A C 3 OK OK 2057 2074 2054 2056 2088 C4' A C 4 OK OK 2090 2107 2087 2089 2122 C4' A D 1 OK OK 2124 2141 2121 2123 2155 C4' A D 2 OK OK 2157 2174 2154 2156 2188 C4' A D 3 OK OK 2190 2207 2187 2189 2221 C4' A D 4 OK OK 2223 2240 2220 2222 2255 C4' A E 1 OK OK 2257 2274 2254 2256 2288 C4' A E 2 OK OK 2290 2307 2287 2289 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1987 C5' A C 1 OK OK 1986 2005 2006 1988 2021 C5' A C 2 OK OK 2020 2039 2040 2022 2054 C5' A C 3 OK OK 2053 2072 2073 2055 2087 C5' A C 4 OK OK 2086 2105 2106 2088 2121 C5' A D 1 OK OK 2120 2139 2140 2122 2154 C5' A D 2 OK OK 2153 2172 2173 2155 2187 C5' A D 3 OK OK 2186 2205 2206 2188 2220 C5' A D 4 OK OK 2219 2238 2239 2221 2254 C5' A E 1 OK OK 2253 2272 2273 2255 2287 C5' A E 2 OK OK 2286 2305 2306 2288 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2017 P A C 2 distorted distorted 1991 2018 2019 2020 2050 P A C 3 distorted distorted 2025 2051 2052 2053 2083 P A C 4 distorted distorted 2058 2084 2085 2086 2117 P A D 1 distorted distorted 2118 2119 2120 2150 P A D 2 distorted distorted 2125 2151 2152 2153 2183 P A D 3 distorted distorted 2158 2184 2185 2186 2216 P A D 4 distorted distorted 2191 2217 2218 2219 2250 P A E 1 distorted distorted 2251 2252 2253 2283 P A E 2 distorted distorted 2258 2284 2285 2286 ---------------------------------------------------------------------------------