ID code: '3ZD6' 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' --------------------------------------------------------------------------------- 4956 C1' G C 1 beta 4951 4957 4954 4979 C1' C C 2 beta 4974 4980 4977 4999 C1' G C 3 beta 4994 5000 4997 5022 C1' C C 4 beta 5017 5023 5020 5042 C1' G C 5 beta 5037 5043 5040 5065 C1' C C 6 beta 5060 5066 5063 5085 C1' G C 7 beta 5080 5086 5083 5108 C1' C C 8 beta 5103 5109 5106 5128 C1' G C 9 beta 5123 5129 5126 5151 C1' C C 10 beta 5146 5152 5149 5169 C1' G D 1 beta 5164 5170 5167 5192 C1' C D 2 beta 5187 5193 5190 5212 C1' G D 3 beta 5207 5213 5210 5235 C1' C D 4 beta 5230 5236 5233 5255 C1' G D 5 beta 5250 5256 5253 5278 C1' C D 6 beta 5273 5279 5276 5298 C1' G D 7 beta 5293 5299 5296 5321 C1' C D 8 beta 5316 5322 5319 5341 C1' G D 9 beta 5336 5342 5339 5364 C1' C D 10 beta 5359 5365 5362 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4954 C2' G C 1 OK 4956 4952 4955 4977 C2' C C 2 OK 4979 4975 4978 4997 C2' G C 3 OK 4999 4995 4998 5020 C2' C C 4 OK 5022 5018 5021 5040 C2' G C 5 OK 5042 5038 5041 5063 C2' C C 6 OK 5065 5061 5064 5083 C2' G C 7 OK 5085 5081 5084 5106 C2' C C 8 OK 5108 5104 5107 5126 C2' G C 9 OK 5128 5124 5127 5149 C2' C C 10 OK 5151 5147 5150 5167 C2' G D 1 OK 5169 5165 5168 5190 C2' C D 2 OK 5192 5188 5191 5210 C2' G D 3 OK 5212 5208 5211 5233 C2' C D 4 OK 5235 5231 5234 5253 C2' G D 5 OK 5255 5251 5254 5276 C2' C D 6 OK 5278 5274 5277 5296 C2' G D 7 OK 5298 5294 5297 5319 C2' C D 8 OK 5321 5317 5320 5339 C2' G D 9 OK 5341 5337 5340 5362 C2' C D 10 OK 5364 5360 5363 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4952 C3' G C 1 OK 4950 4953 4954 4975 C3' C C 2 OK 4973 4976 4977 4995 C3' G C 3 OK 4993 4996 4997 5018 C3' C C 4 OK 5016 5019 5020 5038 C3' G C 5 OK 5036 5039 5040 5061 C3' C C 6 OK 5059 5062 5063 5081 C3' G C 7 OK 5079 5082 5083 5104 C3' C C 8 OK 5102 5105 5106 5124 C3' G C 9 OK 5122 5125 5126 5147 C3' C C 10 OK 5145 5148 5149 5165 C3' G D 1 OK 5163 5166 5167 5188 C3' C D 2 OK 5186 5189 5190 5208 C3' G D 3 OK 5206 5209 5210 5231 C3' C D 4 OK 5229 5232 5233 5251 C3' G D 5 OK 5249 5252 5253 5274 C3' C D 6 OK 5272 5275 5276 5294 C3' G D 7 OK 5292 5295 5296 5317 C3' C D 8 OK 5315 5318 5319 5337 C3' G D 9 OK 5335 5338 5339 5360 C3' C D 10 OK 5358 5361 5362 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4950 C4' G C 1 OK 4952 4949 4951 4973 C4' C C 2 OK 4975 4972 4974 4993 C4' G C 3 OK 4995 4992 4994 5016 C4' C C 4 OK 5018 5015 5017 5036 C4' G C 5 OK 5038 5035 5037 5059 C4' C C 6 OK 5061 5058 5060 5079 C4' G C 7 OK 5081 5078 5080 5102 C4' C C 8 OK 5104 5101 5103 5122 C4' G C 9 OK 5124 5121 5123 5145 C4' C C 10 OK 5147 5144 5146 5163 C4' G D 1 OK 5165 5162 5164 5186 C4' C D 2 OK 5188 5185 5187 5206 C4' G D 3 OK 5208 5205 5207 5229 C4' C D 4 OK 5231 5228 5230 5249 C4' G D 5 OK 5251 5248 5250 5272 C4' C D 6 OK 5274 5271 5273 5292 C4' G D 7 OK 5294 5291 5293 5315 C4' C D 8 OK 5317 5314 5316 5335 C4' G D 9 OK 5337 5334 5336 5358 C4' C D 10 OK 5360 5357 5359 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4949 C5' G C 1 4948 4950 4972 C5' C C 2 4971 4973 4992 C5' G C 3 4991 4993 5015 C5' C C 4 5014 5016 5035 C5' G C 5 5034 5036 5058 C5' C C 6 5057 5059 5078 C5' G C 7 5077 5079 5101 C5' C C 8 5100 5102 5121 C5' G C 9 5120 5122 5144 C5' C C 10 5143 5145 5162 C5' G D 1 5161 5163 5185 C5' C D 2 5184 5186 5205 C5' G D 3 5204 5206 5228 C5' C D 4 5227 5229 5248 C5' G D 5 5247 5249 5271 C5' C D 6 5270 5272 5291 C5' G D 7 5290 5292 5314 C5' C D 8 5313 5315 5334 C5' G D 9 5333 5335 5357 C5' C D 10 5356 5358 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4968 P C C 2 distorted distorted 4953 4969 4970 4971 4988 P G C 3 distorted distorted 4976 4989 4990 4991 5011 P C C 4 distorted distorted 4996 5012 5013 5014 5031 P G C 5 OK OK 5019 5032 5033 5034 5054 P C C 6 distorted distorted 5039 5055 5056 5057 5074 P G C 7 distorted distorted 5062 5075 5076 5077 5097 P C C 8 OK OK 5082 5098 5099 5100 5117 P G C 9 distorted distorted 5105 5118 5119 5120 5140 P C C 10 distorted distorted 5125 5141 5142 5143 5181 P C D 2 distorted distorted 5166 5182 5183 5184 5201 P G D 3 distorted distorted 5189 5202 5203 5204 5224 P C D 4 distorted distorted 5209 5225 5226 5227 5244 P G D 5 distorted distorted 5232 5245 5246 5247 5267 P C D 6 distorted distorted 5252 5268 5269 5270 5287 P G D 7 distorted distorted 5275 5288 5289 5290 5310 P C D 8 distorted distorted 5295 5311 5312 5313 5330 P G D 9 distorted distorted 5318 5331 5332 5333 5353 P C D 10 distorted distorted 5338 5354 5355 5356 ---------------------------------------------------------------------------------