ID code: '4AY2' 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' --------------------------------------------------------------------------------- 5029 C1' GTP C 1 beta 5024 5030 5027 5052 C1' G C 2 beta 5047 5053 5050 5075 C1' C C 3 beta 5070 5076 5073 5095 C1' G C 4 beta 5090 5096 5093 5118 C1' C C 5 beta 5113 5119 5116 5138 C1' G C 6 beta 5133 5139 5136 5161 C1' G C 7 beta 5156 5162 5159 5184 C1' C C 8 beta 5179 5185 5182 5204 C1' U C 9 beta 5199 5205 5202 5224 C1' U C 10 beta 5219 5225 5222 5244 C1' C C 11 beta 5239 5245 5242 5264 C1' G C 12 beta 5259 5265 5262 5287 C1' G C 13 beta 5282 5288 5285 5310 C1' C C 14 beta 5305 5311 5308 5330 C1' C C 15 beta 5325 5331 5328 5350 C1' G C 16 beta 5345 5351 5348 5373 C1' C C 17 beta 5368 5374 5371 5393 C1' G C 18 beta 5388 5394 5391 5416 C1' C C 19 beta 5411 5417 5414 5436 C1' C C 20 beta 5431 5437 5434 5462 C1' ADP A1924 beta 5463 5464 5460 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5027 C2' GTP C 1 OK 5029 5025 5028 5050 C2' G C 2 OK 5052 5048 5051 5073 C2' C C 3 OK 5075 5071 5074 5093 C2' G C 4 OK 5095 5091 5094 5116 C2' C C 5 OK 5118 5114 5117 5136 C2' G C 6 OK 5138 5134 5137 5159 C2' G C 7 OK 5161 5157 5160 5182 C2' C C 8 OK 5184 5180 5183 5202 C2' U C 9 OK 5204 5200 5203 5222 C2' U C 10 OK 5224 5220 5223 5242 C2' C C 11 OK 5244 5240 5243 5262 C2' G C 12 OK 5264 5260 5263 5285 C2' G C 13 OK 5287 5283 5286 5308 C2' C C 14 OK 5310 5306 5309 5328 C2' C C 15 OK 5330 5326 5329 5348 C2' G C 16 OK 5350 5346 5349 5371 C2' C C 17 OK 5373 5369 5372 5391 C2' G C 18 OK 5393 5389 5392 5414 C2' C C 19 OK 5416 5412 5415 5434 C2' C C 20 OK 5436 5432 5435 5460 C2' ADP A1924 OK 5462 5458 5461 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5025 C3' GTP C 1 OK 5023 5026 5027 5048 C3' G C 2 OK 5046 5049 5050 5071 C3' C C 3 OK 5069 5072 5073 5091 C3' G C 4 OK 5089 5092 5093 5114 C3' C C 5 OK 5112 5115 5116 5134 C3' G C 6 OK 5132 5135 5136 5157 C3' G C 7 OK 5155 5158 5159 5180 C3' C C 8 OK 5178 5181 5182 5200 C3' U C 9 OK 5198 5201 5202 5220 C3' U C 10 OK 5218 5221 5222 5240 C3' C C 11 OK 5238 5241 5242 5260 C3' G C 12 OK 5258 5261 5262 5283 C3' G C 13 OK 5281 5284 5285 5306 C3' C C 14 OK 5304 5307 5308 5326 C3' C C 15 OK 5324 5327 5328 5346 C3' G C 16 OK 5344 5347 5348 5369 C3' C C 17 OK 5367 5370 5371 5389 C3' G C 18 OK 5387 5390 5391 5412 C3' C C 19 OK 5410 5413 5414 5432 C3' C C 20 OK 5430 5433 5434 5458 C3' ADP A1924 OK 5457 5459 5460 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5023 C4' GTP C 1 OK 5025 5022 5024 5046 C4' G C 2 OK 5048 5045 5047 5069 C4' C C 3 OK 5071 5068 5070 5089 C4' G C 4 OK 5091 5088 5090 5112 C4' C C 5 OK 5114 5111 5113 5132 C4' G C 6 OK 5134 5131 5133 5155 C4' G C 7 OK 5157 5154 5156 5178 C4' C C 8 OK 5180 5177 5179 5198 C4' U C 9 OK 5200 5197 5199 5218 C4' U C 10 OK 5220 5217 5219 5238 C4' C C 11 OK 5240 5237 5239 5258 C4' G C 12 OK 5260 5257 5259 5281 C4' G C 13 OK 5283 5280 5282 5304 C4' C C 14 OK 5306 5303 5305 5324 C4' C C 15 OK 5326 5323 5325 5344 C4' G C 16 OK 5346 5343 5345 5367 C4' C C 17 OK 5369 5366 5368 5387 C4' G C 18 OK 5389 5386 5388 5410 C4' C C 19 OK 5412 5409 5411 5430 C4' C C 20 OK 5432 5429 5431 5457 C4' ADP A1924 OK 5458 5456 5463 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5022 C5' GTP C 1 5021 5023 5045 C5' G C 2 5044 5046 5068 C5' C C 3 5067 5069 5088 C5' G C 4 5087 5089 5111 C5' C C 5 5110 5112 5131 C5' G C 6 5130 5132 5154 C5' G C 7 5153 5155 5177 C5' C C 8 5176 5178 5197 C5' U C 9 5196 5198 5217 C5' U C 10 5216 5218 5237 C5' C C 11 5236 5238 5257 C5' G C 12 5256 5258 5280 C5' G C 13 5279 5281 5303 C5' C C 14 5302 5304 5323 C5' C C 15 5322 5324 5343 C5' G C 16 5342 5344 5366 C5' C C 17 5365 5367 5386 C5' G C 18 5385 5387 5409 C5' C C 19 5408 5410 5429 C5' C C 20 5428 5430 5456 C5' ADP A1924 5455 5457 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5041 P G C 2 distorted distorted 5026 5042 5043 5044 5064 P C C 3 distorted distorted 5049 5065 5066 5067 5084 P G C 4 distorted distorted 5072 5085 5086 5087 5107 P C C 5 distorted distorted 5092 5108 5109 5110 5127 P G C 6 distorted distorted 5115 5128 5129 5130 5150 P G C 7 distorted distorted 5135 5151 5152 5153 5173 P C C 8 distorted distorted 5158 5174 5175 5176 5193 P U C 9 distorted distorted 5181 5194 5195 5196 5213 P U C 10 distorted distorted 5201 5214 5215 5216 5233 P C C 11 distorted distorted 5221 5234 5235 5236 5253 P G C 12 distorted distorted 5241 5254 5255 5256 5276 P G C 13 distorted distorted 5261 5277 5278 5279 5299 P C C 14 distorted distorted 5284 5300 5301 5302 5319 P C C 15 distorted distorted 5307 5320 5321 5322 5339 P G C 16 distorted distorted 5327 5340 5341 5342 5362 P C C 17 distorted distorted 5347 5363 5364 5365 5382 P G C 18 distorted distorted 5370 5383 5384 5385 5405 P C C 19 distorted distorted 5390 5406 5407 5408 5425 P C C 20 distorted distorted 5413 5426 5427 5428 ---------------------------------------------------------------------------------