ID code: '1DNK' 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' --------------------------------------------------------------------------------- 1991 C1' G B 301 beta 1987 1992 1990 2013 C1' G B 302 beta 2009 2014 2012 2035 C1' T B 303 beta 2031 2036 2034 2055 C1' A B 304 beta 2051 2056 2054 2076 C1' T B 305 beta 2072 2077 2075 2096 C1' A B 306 beta 2092 2097 2095 2117 C1' C B 307 beta 2113 2118 2116 2156 C1' G C 310 beta 2152 2157 2155 2178 C1' T C 311 beta 2174 2179 2177 2198 C1' A C 312 beta 2194 2199 2197 2219 C1' T C 313 beta 2215 2220 2218 2239 C1' A C 314 beta 2235 2240 2238 2260 C1' C C 315 beta 2256 2261 2259 2279 C1' C C 316 beta 2275 2280 2278 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1990 C2' G B 301 1991 1988 2012 C2' G B 302 2013 2010 2034 C2' T B 303 2035 2032 2054 C2' A B 304 2055 2052 2075 C2' T B 305 2076 2073 2095 C2' A B 306 2096 2093 2116 C2' C B 307 2117 2114 2155 C2' G C 310 2156 2153 2177 C2' T C 311 2178 2175 2197 C2' A C 312 2198 2195 2218 C2' T C 313 2219 2216 2238 C2' A C 314 2239 2236 2259 C2' C C 315 2260 2257 2278 C2' C C 316 2279 2276 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1988 C3' G B 301 OK 1986 1989 1990 2010 C3' G B 302 OK 2008 2011 2012 2032 C3' T B 303 OK 2030 2033 2034 2052 C3' A B 304 OK 2050 2053 2054 2073 C3' T B 305 OK 2071 2074 2075 2093 C3' A B 306 OK 2091 2094 2095 2114 C3' C B 307 OK 2112 2115 2116 2153 C3' G C 310 OK 2151 2154 2155 2175 C3' T C 311 OK 2173 2176 2177 2195 C3' A C 312 OK 2193 2196 2197 2216 C3' T C 313 OK 2214 2217 2218 2236 C3' A C 314 OK 2234 2237 2238 2257 C3' C C 315 OK 2255 2258 2259 2276 C3' C C 316 OK 2274 2277 2278 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1986 C4' G B 301 OK 1988 1985 1987 2008 C4' G B 302 OK 2010 2007 2009 2030 C4' T B 303 OK 2032 2029 2031 2050 C4' A B 304 OK 2052 2049 2051 2071 C4' T B 305 OK 2073 2070 2072 2091 C4' A B 306 OK 2093 2090 2092 2112 C4' C B 307 OK 2114 2111 2113 2151 C4' G C 310 OK 2153 2150 2152 2173 C4' T C 311 OK 2175 2172 2174 2193 C4' A C 312 OK 2195 2192 2194 2214 C4' T C 313 OK 2216 2213 2215 2234 C4' A C 314 OK 2236 2233 2235 2255 C4' C C 315 OK 2257 2254 2256 2274 C4' C C 316 OK 2276 2273 2275 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1985 C5' G B 301 1984 1986 2007 C5' G B 302 2006 2008 2029 C5' T B 303 2028 2030 2049 C5' A B 304 2048 2050 2070 C5' T B 305 2069 2071 2090 C5' A B 306 2089 2091 2111 C5' C B 307 2110 2112 2150 C5' G C 310 2149 2151 2172 C5' T C 311 2171 2173 2192 C5' A C 312 2191 2193 2213 C5' T C 313 2212 2214 2233 C5' A C 314 2232 2234 2254 C5' C C 315 2253 2255 2273 C5' C C 316 2272 2274 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2003 P G B 302 distorted distorted 1989 2004 2005 2006 2025 P T B 303 distorted distorted 2011 2026 2027 2028 2045 P A B 304 distorted distorted 2033 2046 2047 2048 2066 P T B 305 distorted distorted 2053 2067 2068 2069 2086 P A B 306 distorted distorted 2074 2087 2088 2089 2107 P C B 307 OK OK 2094 2108 2109 2110 2168 P T C 311 distorted distorted 2154 2169 2170 2171 2188 P A C 312 distorted distorted 2176 2189 2190 2191 2209 P T C 313 distorted distorted 2196 2210 2211 2212 2229 P A C 314 distorted distorted 2217 2230 2231 2232 2250 P C C 315 distorted distorted 2237 2251 2252 2253 2269 P C C 316 distorted distorted 2258 2270 2271 2272 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