ID code: '3SYZ' 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' --------------------------------------------------------------------------------- 8720 C1' DG B 101 beta 8716 8721 8719 8742 C1' DA B 102 beta 8738 8743 8741 8763 C1' DC B 103 beta 8759 8764 8762 8782 C1' DC B 104 beta 8778 8783 8781 8801 C1' DA B 105 beta 8797 8802 8800 8822 C1' DC B 106 beta 8818 8823 8821 8841 C1' DG B 107 beta 8837 8842 8840 8863 C1' DG B 108 beta 8859 8864 8862 8885 C1' DC B 109 beta 8881 8886 8884 8904 C1' DG B 110 beta 8900 8905 8903 8926 C1' DC B 111 beta 8922 8927 8925 8943 C1' DOC B 112 alpha beta 8947 8957 8935 8944 8973 C1' DA C 201 beta 8969 8974 8972 8994 C1' DA C 202 beta 8990 8995 8993 9015 C1' DA C 203 beta 9011 9016 9014 9033 C1' BMN C 204 9044 9034 9059 C1' DG C 205 beta 9055 9060 9058 9081 C1' DG C 206 beta 9077 9082 9080 9103 C1' DC C 207 beta 9099 9104 9102 9122 C1' DG C 208 beta 9118 9123 9121 9144 C1' DC C 209 beta 9140 9145 9143 9163 C1' DC C 210 beta 9159 9164 9162 9182 C1' DG C 211 beta 9178 9183 9181 9204 C1' DT C 212 beta 9200 9205 9203 9224 C1' DG C 213 beta 9220 9225 9223 9246 C1' DG C 214 beta 9242 9247 9245 9268 C1' DT C 215 beta 9264 9269 9267 9288 C1' DC C 216 beta 9284 9289 9287 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 8719 C2' DG B 101 8720 8717 8741 C2' DA B 102 8742 8739 8762 C2' DC B 103 8763 8760 8781 C2' DC B 104 8782 8779 8800 C2' DA B 105 8801 8798 8821 C2' DC B 106 8822 8819 8840 C2' DG B 107 8841 8838 8862 C2' DG B 108 8863 8860 8884 C2' DC B 109 8885 8882 8903 C2' DG B 110 8904 8901 8925 C2' DC B 111 8926 8923 8944 C2' DOC B 112 OK OK 8943 8945 8958 8959 8972 C2' DA C 201 8973 8970 8993 C2' DA C 202 8994 8991 9014 C2' DA C 203 9015 9012 9034 C2' BMN C 204 9033 9040 9058 C2' DG C 205 9059 9056 9080 C2' DG C 206 9081 9078 9102 C2' DC C 207 9103 9100 9121 C2' DG C 208 9122 9119 9143 C2' DC C 209 9144 9141 9162 C2' DC C 210 9163 9160 9181 C2' DG C 211 9182 9179 9203 C2' DT C 212 9204 9201 9223 C2' DG C 213 9224 9221 9245 C2' DG C 214 9246 9243 9267 C2' DT C 215 9268 9265 9287 C2' DC C 216 9288 9285 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8717 C3' DG B 101 OK 8715 8718 8719 8739 C3' DA B 102 OK 8737 8740 8741 8760 C3' DC B 103 OK 8758 8761 8762 8779 C3' DC B 104 OK 8777 8780 8781 8798 C3' DA B 105 OK 8796 8799 8800 8819 C3' DC B 106 OK 8817 8820 8821 8838 C3' DG B 107 OK 8836 8839 8840 8860 C3' DG B 108 OK 8858 8861 8862 8882 C3' DC B 109 OK 8880 8883 8884 8901 C3' DG B 110 OK 8899 8902 8903 8923 C3' DC B 111 OK 8921 8924 8925 8945 C3' DOC B 112 8946 8944 8970 C3' DA C 201 OK 8968 8971 8972 8991 C3' DA C 202 OK 8989 8992 8993 9012 C3' DA C 203 OK 9010 9013 9014 9040 C3' BMN C 204 OK 9043 9036 9034 9056 C3' DG C 205 OK 9054 9057 9058 9078 C3' DG C 206 OK 9076 9079 9080 9100 C3' DC C 207 OK 9098 9101 9102 9119 C3' DG C 208 OK 9117 9120 9121 9141 C3' DC C 209 OK 9139 9142 9143 9160 C3' DC C 210 OK 9158 9161 9162 9179 C3' DG C 211 OK 9177 9180 9181 9201 C3' DT C 212 OK 9199 9202 9203 9221 C3' DG C 213 OK 9219 9222 9223 9243 C3' DG C 214 OK 9241 9244 9245 9265 C3' DT C 215 OK 9263 9266 9267 9285 C3' DC C 216 OK 9283 9286 9287 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 8715 C4' DG B 101 OK 8717 8714 8716 8737 C4' DA B 102 OK 8739 8736 8738 8758 C4' DC B 103 OK 8760 8757 8759 8777 C4' DC B 104 OK 8779 8776 8778 8796 C4' DA B 105 OK 8798 8795 8797 8817 C4' DC B 106 OK 8819 8816 8818 8836 C4' DG B 107 OK 8838 8835 8837 8858 C4' DG B 108 OK 8860 8857 8859 8880 C4' DC B 109 OK 8882 8879 8881 8899 C4' DG B 110 OK 8901 8898 8900 8921 C4' DC B 111 OK 8923 8920 8922 8946 C4' DOC B 112 OK OK 8945 8962 8948 8947 8968 C4' DA C 201 OK 8970 8967 8969 8989 C4' DA C 202 OK 8991 8988 8990 9010 C4' DA C 203 OK 9012 9009 9011 9043 C4' BMN C 204 OK 9040 9045 9044 9054 C4' DG C 205 OK 9056 9053 9055 9076 C4' DG C 206 OK 9078 9075 9077 9098 C4' DC C 207 OK 9100 9097 9099 9117 C4' DG C 208 OK 9119 9116 9118 9139 C4' DC C 209 OK 9141 9138 9140 9158 C4' DC C 210 OK 9160 9157 9159 9177 C4' DG C 211 OK 9179 9176 9178 9199 C4' DT C 212 OK 9201 9198 9200 9219 C4' DG C 213 OK 9221 9218 9220 9241 C4' DG C 214 OK 9243 9240 9242 9263 C4' DT C 215 OK 9265 9262 9264 9283 C4' DC C 216 OK 9285 9282 9284 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 8714 C5' DG B 101 8713 8715 8736 C5' DA B 102 8735 8737 8757 C5' DC B 103 8756 8758 8776 C5' DC B 104 8775 8777 8795 C5' DA B 105 8794 8796 8816 C5' DC B 106 8815 8817 8835 C5' DG B 107 8834 8836 8857 C5' DG B 108 8856 8858 8879 C5' DC B 109 8878 8880 8898 C5' DG B 110 8897 8899 8920 C5' DC B 111 8919 8921 8948 C5' DOC B 112 distorted distorted 8949 8963 8964 8946 8967 C5' DA C 201 8966 8968 8988 C5' DA C 202 8987 8989 9009 C5' DA C 203 9008 9010 9045 C5' BMN C 204 9046 9043 9053 C5' DG C 205 9052 9054 9075 C5' DG C 206 9074 9076 9097 C5' DC C 207 9096 9098 9116 C5' DG C 208 9115 9117 9138 C5' DC C 209 9137 9139 9157 C5' DC C 210 9156 9158 9176 C5' DG C 211 9175 9177 9198 C5' DT C 212 9197 9199 9218 C5' DG C 213 9217 9219 9240 C5' DG C 214 9239 9241 9262 C5' DT C 215 9261 9263 9282 C5' DC C 216 9281 9283 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 8732 P DA B 102 distorted distorted 8718 8733 8734 8735 8753 P DC B 103 distorted distorted 8740 8754 8755 8756 8772 P DC B 104 distorted distorted 8761 8773 8774 8775 8791 P DA B 105 distorted distorted 8780 8792 8793 8794 8812 P DC B 106 distorted distorted 8799 8813 8814 8815 8831 P DG B 107 distorted distorted 8820 8832 8833 8834 8853 P DG B 108 distorted distorted 8839 8854 8855 8856 8875 P DC B 109 distorted distorted 8861 8876 8877 8878 8894 P DG B 110 distorted distorted 8883 8895 8896 8897 8916 P DC B 111 distorted distorted 8902 8917 8918 8919 8950 P DOC B 112 OK OK 8924 8951 8952 8949 8984 P DA C 202 distorted distorted 8971 8985 8986 8987 9005 P DA C 203 distorted distorted 8992 9006 9007 9008 9027 P BMN C 204 OK OK 9013 9047 9048 9046 9049 P DG C 205 distorted distorted 9036 9050 9051 9052 9071 P DG C 206 distorted distorted 9057 9072 9073 9074 9093 P DC C 207 distorted distorted 9079 9094 9095 9096 9112 P DG C 208 distorted distorted 9101 9113 9114 9115 9134 P DC C 209 distorted distorted 9120 9135 9136 9137 9153 P DC C 210 distorted distorted 9142 9154 9155 9156 9172 P DG C 211 distorted distorted 9161 9173 9174 9175 9194 P DT C 212 distorted distorted 9180 9195 9196 9197 9214 P DG C 213 distorted distorted 9202 9215 9216 9217 9236 P DG C 214 distorted distorted 9222 9237 9238 9239 9258 P DT C 215 distorted distorted 9244 9259 9260 9261 9278 P DC C 216 distorted distorted 9266 9279 9280 9281 ---------------------------------------------------------------------------------