ID code: '3I62' 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' --------------------------------------------------------------------------------- 4015 C1' U B 1 beta 4010 4016 4013 4035 C1' U B 2 beta 4030 4036 4033 4048 C1' U B 3 beta 4043 4049 4046 4068 C1' U B 4 beta 4063 4069 4066 4088 C1' U B 5 beta 4083 4089 4086 4108 C1' U B 6 beta 4103 4109 4106 4128 C1' U B 7 beta 4123 4129 4126 4148 C1' U B 8 beta 4143 4149 4146 4168 C1' U B 9 beta 4163 4169 4166 4188 C1' U B 10 beta 4183 4189 4186 4214 C1' ADP A1000 beta 4209 4215 4212 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4013 C2' U B 1 OK 4015 4011 4014 4033 C2' U B 2 OK 4035 4031 4034 4046 C2' U B 3 OK 4048 4044 4047 4066 C2' U B 4 OK 4068 4064 4067 4086 C2' U B 5 OK 4088 4084 4087 4106 C2' U B 6 OK 4108 4104 4107 4126 C2' U B 7 OK 4128 4124 4127 4146 C2' U B 8 OK 4148 4144 4147 4166 C2' U B 9 OK 4168 4164 4167 4186 C2' U B 10 OK 4188 4184 4187 4212 C2' ADP A1000 OK 4214 4210 4213 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4011 C3' U B 1 OK 4009 4012 4013 4031 C3' U B 2 OK 4029 4032 4033 4044 C3' U B 3 OK 4042 4045 4046 4064 C3' U B 4 OK 4062 4065 4066 4084 C3' U B 5 OK 4082 4085 4086 4104 C3' U B 6 OK 4102 4105 4106 4124 C3' U B 7 OK 4122 4125 4126 4144 C3' U B 8 OK 4142 4145 4146 4164 C3' U B 9 OK 4162 4165 4166 4184 C3' U B 10 OK 4182 4185 4186 4210 C3' ADP A1000 OK 4208 4211 4212 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4009 C4' U B 1 OK 4011 4008 4010 4029 C4' U B 2 OK 4031 4028 4030 4042 C4' U B 3 OK 4044 4041 4043 4062 C4' U B 4 OK 4064 4061 4063 4082 C4' U B 5 OK 4084 4081 4083 4102 C4' U B 6 OK 4104 4101 4103 4122 C4' U B 7 OK 4124 4121 4123 4142 C4' U B 8 OK 4144 4141 4143 4162 C4' U B 9 OK 4164 4161 4163 4182 C4' U B 10 OK 4184 4181 4183 4208 C4' ADP A1000 OK 4210 4207 4209 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4008 C5' U B 1 4007 4009 4028 C5' U B 2 4027 4029 4041 C5' U B 3 4040 4042 4061 C5' U B 4 4060 4062 4081 C5' U B 5 4080 4082 4101 C5' U B 6 4100 4102 4121 C5' U B 7 4120 4122 4141 C5' U B 8 4140 4142 4161 C5' U B 9 4160 4162 4181 C5' U B 10 4180 4182 4207 C5' ADP A1000 4206 4208 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4024 P U B 2 distorted distorted 4012 4025 4026 4027 4037 P U B 3 distorted distorted 4032 4038 4039 4040 4057 P U B 4 distorted distorted 4045 4058 4059 4060 4077 P U B 5 distorted distorted 4065 4078 4079 4080 4097 P U B 6 distorted distorted 4085 4098 4099 4100 4117 P U B 7 distorted distorted 4105 4118 4119 4120 4137 P U B 8 distorted distorted 4125 4138 4139 4140 4157 P U B 9 distorted distorted 4145 4158 4159 4160 4177 P U B 10 distorted distorted 4165 4178 4179 4180 ---------------------------------------------------------------------------------