ID code: '3MJ0' 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' --------------------------------------------------------------------------------- 961 C1' C B 1 beta 956 962 959 981 C1' G B 2 beta 976 982 979 1004 C1' U B 3 beta 999 1005 1002 1024 C1' U B 4 beta 1019 1025 1022 1044 C1' A B 5 beta 1039 1045 1042 1066 C1' C B 6 beta 1061 1067 1064 1086 C1' G B 7 beta 1081 1087 1084 1109 C1' C B 8 beta 1104 1110 1107 1126 C1' OMU B 9 beta 1133 1118 1127 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 959 C2' C B 1 OK 961 957 960 979 C2' G B 2 OK 981 977 980 1002 C2' U B 3 OK 1004 1000 1003 1022 C2' U B 4 OK 1024 1020 1023 1042 C2' A B 5 OK 1044 1040 1043 1064 C2' C B 6 OK 1066 1062 1065 1084 C2' G B 7 OK 1086 1082 1085 1107 C2' C B 8 OK 1109 1105 1108 1127 C2' OMU B 9 OK 1126 1130 1128 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 957 C3' C B 1 OK 955 958 959 977 C3' G B 2 OK 975 978 979 1000 C3' U B 3 OK 998 1001 1002 1020 C3' U B 4 OK 1018 1021 1022 1040 C3' A B 5 OK 1038 1041 1042 1062 C3' C B 6 OK 1060 1063 1064 1082 C3' G B 7 OK 1080 1083 1084 1105 C3' C B 8 OK 1103 1106 1107 1130 C3' OMU B 9 OK 1131 1132 1127 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 955 C4' C B 1 OK 957 954 956 975 C4' G B 2 OK 977 974 976 998 C4' U B 3 OK 1000 997 999 1018 C4' U B 4 OK 1020 1017 1019 1038 C4' A B 5 OK 1040 1037 1039 1060 C4' C B 6 OK 1062 1059 1061 1080 C4' G B 7 OK 1082 1079 1081 1103 C4' C B 8 OK 1105 1102 1104 1131 C4' OMU B 9 OK 1130 1134 1133 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 954 C5' C B 1 953 955 974 C5' G B 2 973 975 997 C5' U B 3 996 998 1017 C5' U B 4 1016 1018 1037 C5' A B 5 1036 1038 1059 C5' C B 6 1058 1060 1079 C5' G B 7 1078 1080 1102 C5' C B 8 1101 1103 1134 C5' OMU B 9 1135 1131 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 970 P G B 2 distorted distorted 958 971 972 973 993 P U B 3 distorted distorted 978 994 995 996 1013 P U B 4 distorted distorted 1001 1014 1015 1016 1033 P A B 5 distorted distorted 1021 1034 1035 1036 1055 P C B 6 distorted distorted 1041 1056 1057 1058 1075 P G B 7 distorted distorted 1063 1076 1077 1078 1098 P C B 8 distorted distorted 1083 1099 1100 1101 1136 P OMU B 9 distorted distorted 1106 1137 1138 1135 ---------------------------------------------------------------------------------