ID code: '3ZD7' 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' --------------------------------------------------------------------------------- 4866 C1' G C 1 beta 4861 4867 4864 4889 C1' C C 2 beta 4884 4890 4887 4909 C1' G C 3 beta 4904 4910 4907 4932 C1' C C 4 beta 4927 4933 4930 4952 C1' G C 5 beta 4947 4953 4950 4975 C1' C C 6 beta 4970 4976 4973 4995 C1' G C 7 beta 4990 4996 4993 5018 C1' C C 8 beta 5013 5019 5016 5038 C1' G C 9 beta 5033 5039 5036 5061 C1' C C 10 beta 5056 5062 5059 5079 C1' G D 1 beta 5074 5080 5077 5102 C1' C D 2 beta 5097 5103 5100 5122 C1' G D 3 beta 5117 5123 5120 5145 C1' C D 4 beta 5140 5146 5143 5165 C1' G D 5 beta 5160 5166 5163 5188 C1' C D 6 beta 5183 5189 5186 5208 C1' G D 7 beta 5203 5209 5206 5231 C1' C D 8 beta 5226 5232 5229 5251 C1' G D 9 beta 5246 5252 5249 5274 C1' C D 10 beta 5269 5275 5272 5302 C1' ADP A1924 beta 5297 5303 5300 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4864 C2' G C 1 OK 4866 4862 4865 4887 C2' C C 2 OK 4889 4885 4888 4907 C2' G C 3 OK 4909 4905 4908 4930 C2' C C 4 OK 4932 4928 4931 4950 C2' G C 5 OK 4952 4948 4951 4973 C2' C C 6 OK 4975 4971 4974 4993 C2' G C 7 OK 4995 4991 4994 5016 C2' C C 8 OK 5018 5014 5017 5036 C2' G C 9 OK 5038 5034 5037 5059 C2' C C 10 OK 5061 5057 5060 5077 C2' G D 1 OK 5079 5075 5078 5100 C2' C D 2 OK 5102 5098 5101 5120 C2' G D 3 OK 5122 5118 5121 5143 C2' C D 4 OK 5145 5141 5144 5163 C2' G D 5 OK 5165 5161 5164 5186 C2' C D 6 OK 5188 5184 5187 5206 C2' G D 7 OK 5208 5204 5207 5229 C2' C D 8 OK 5231 5227 5230 5249 C2' G D 9 OK 5251 5247 5250 5272 C2' C D 10 OK 5274 5270 5273 5300 C2' ADP A1924 OK 5302 5298 5301 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4862 C3' G C 1 OK 4860 4863 4864 4885 C3' C C 2 OK 4883 4886 4887 4905 C3' G C 3 OK 4903 4906 4907 4928 C3' C C 4 OK 4926 4929 4930 4948 C3' G C 5 OK 4946 4949 4950 4971 C3' C C 6 OK 4969 4972 4973 4991 C3' G C 7 OK 4989 4992 4993 5014 C3' C C 8 OK 5012 5015 5016 5034 C3' G C 9 OK 5032 5035 5036 5057 C3' C C 10 OK 5055 5058 5059 5075 C3' G D 1 OK 5073 5076 5077 5098 C3' C D 2 OK 5096 5099 5100 5118 C3' G D 3 OK 5116 5119 5120 5141 C3' C D 4 OK 5139 5142 5143 5161 C3' G D 5 OK 5159 5162 5163 5184 C3' C D 6 OK 5182 5185 5186 5204 C3' G D 7 OK 5202 5205 5206 5227 C3' C D 8 OK 5225 5228 5229 5247 C3' G D 9 OK 5245 5248 5249 5270 C3' C D 10 OK 5268 5271 5272 5298 C3' ADP A1924 OK 5296 5299 5300 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4860 C4' G C 1 OK 4862 4859 4861 4883 C4' C C 2 OK 4885 4882 4884 4903 C4' G C 3 OK 4905 4902 4904 4926 C4' C C 4 OK 4928 4925 4927 4946 C4' G C 5 OK 4948 4945 4947 4969 C4' C C 6 OK 4971 4968 4970 4989 C4' G C 7 OK 4991 4988 4990 5012 C4' C C 8 OK 5014 5011 5013 5032 C4' G C 9 OK 5034 5031 5033 5055 C4' C C 10 OK 5057 5054 5056 5073 C4' G D 1 OK 5075 5072 5074 5096 C4' C D 2 OK 5098 5095 5097 5116 C4' G D 3 OK 5118 5115 5117 5139 C4' C D 4 OK 5141 5138 5140 5159 C4' G D 5 OK 5161 5158 5160 5182 C4' C D 6 OK 5184 5181 5183 5202 C4' G D 7 OK 5204 5201 5203 5225 C4' C D 8 OK 5227 5224 5226 5245 C4' G D 9 OK 5247 5244 5246 5268 C4' C D 10 OK 5270 5267 5269 5296 C4' ADP A1924 OK 5298 5295 5297 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4859 C5' G C 1 4858 4860 4882 C5' C C 2 4881 4883 4902 C5' G C 3 4901 4903 4925 C5' C C 4 4924 4926 4945 C5' G C 5 4944 4946 4968 C5' C C 6 4967 4969 4988 C5' G C 7 4987 4989 5011 C5' C C 8 5010 5012 5031 C5' G C 9 5030 5032 5054 C5' C C 10 5053 5055 5072 C5' G D 1 5071 5073 5095 C5' C D 2 5094 5096 5115 C5' G D 3 5114 5116 5138 C5' C D 4 5137 5139 5158 C5' G D 5 5157 5159 5181 C5' C D 6 5180 5182 5201 C5' G D 7 5200 5202 5224 C5' C D 8 5223 5225 5244 C5' G D 9 5243 5245 5267 C5' C D 10 5266 5268 5295 C5' ADP A1924 5294 5296 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4878 P C C 2 distorted distorted 4863 4879 4880 4881 4898 P G C 3 distorted distorted 4886 4899 4900 4901 4921 P C C 4 distorted distorted 4906 4922 4923 4924 4941 P G C 5 OK OK 4929 4942 4943 4944 4964 P C C 6 distorted distorted 4949 4965 4966 4967 4984 P G C 7 distorted distorted 4972 4985 4986 4987 5007 P C C 8 OK OK 4992 5008 5009 5010 5027 P G C 9 distorted distorted 5015 5028 5029 5030 5050 P C C 10 distorted distorted 5035 5051 5052 5053 5091 P C D 2 distorted distorted 5076 5092 5093 5094 5111 P G D 3 distorted distorted 5099 5112 5113 5114 5134 P C D 4 distorted distorted 5119 5135 5136 5137 5154 P G D 5 distorted distorted 5142 5155 5156 5157 5177 P C D 6 distorted distorted 5162 5178 5179 5180 5197 P G D 7 distorted distorted 5185 5198 5199 5200 5220 P C D 8 distorted distorted 5205 5221 5222 5223 5240 P G D 9 distorted distorted 5228 5241 5242 5243 5263 P C D 10 distorted distorted 5248 5264 5265 5266 ---------------------------------------------------------------------------------