ID code: '2YKG' 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' --------------------------------------------------------------------------------- 5004 C1' G C 1 beta 4999 5005 5002 5027 C1' C C 2 beta 5022 5028 5025 5047 C1' G C 3 beta 5042 5048 5045 5070 C1' C C 4 beta 5065 5071 5068 5090 C1' G C 5 beta 5085 5091 5088 5113 C1' C C 6 beta 5108 5114 5111 5133 C1' G C 7 beta 5128 5134 5131 5156 C1' C C 8 beta 5151 5157 5154 5176 C1' G C 9 beta 5171 5177 5174 5199 C1' C C 10 beta 5194 5200 5197 5217 C1' G D 1 beta 5212 5218 5215 5240 C1' C D 2 beta 5235 5241 5238 5260 C1' G D 3 beta 5255 5261 5258 5283 C1' C D 4 beta 5278 5284 5281 5303 C1' G D 5 beta 5298 5304 5301 5326 C1' C D 6 beta 5321 5327 5324 5346 C1' G D 7 beta 5341 5347 5344 5369 C1' C D 8 beta 5364 5370 5367 5389 C1' G D 9 beta 5384 5390 5387 5412 C1' C D 10 beta 5407 5413 5410 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5002 C2' G C 1 OK 5004 5000 5003 5025 C2' C C 2 OK 5027 5023 5026 5045 C2' G C 3 OK 5047 5043 5046 5068 C2' C C 4 OK 5070 5066 5069 5088 C2' G C 5 OK 5090 5086 5089 5111 C2' C C 6 OK 5113 5109 5112 5131 C2' G C 7 OK 5133 5129 5132 5154 C2' C C 8 OK 5156 5152 5155 5174 C2' G C 9 OK 5176 5172 5175 5197 C2' C C 10 OK 5199 5195 5198 5215 C2' G D 1 OK 5217 5213 5216 5238 C2' C D 2 OK 5240 5236 5239 5258 C2' G D 3 OK 5260 5256 5259 5281 C2' C D 4 OK 5283 5279 5282 5301 C2' G D 5 OK 5303 5299 5302 5324 C2' C D 6 OK 5326 5322 5325 5344 C2' G D 7 OK 5346 5342 5345 5367 C2' C D 8 OK 5369 5365 5368 5387 C2' G D 9 OK 5389 5385 5388 5410 C2' C D 10 OK 5412 5408 5411 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5000 C3' G C 1 OK 4998 5001 5002 5023 C3' C C 2 OK 5021 5024 5025 5043 C3' G C 3 OK 5041 5044 5045 5066 C3' C C 4 OK 5064 5067 5068 5086 C3' G C 5 OK 5084 5087 5088 5109 C3' C C 6 OK 5107 5110 5111 5129 C3' G C 7 OK 5127 5130 5131 5152 C3' C C 8 OK 5150 5153 5154 5172 C3' G C 9 OK 5170 5173 5174 5195 C3' C C 10 OK 5193 5196 5197 5213 C3' G D 1 OK 5211 5214 5215 5236 C3' C D 2 OK 5234 5237 5238 5256 C3' G D 3 OK 5254 5257 5258 5279 C3' C D 4 OK 5277 5280 5281 5299 C3' G D 5 OK 5297 5300 5301 5322 C3' C D 6 OK 5320 5323 5324 5342 C3' G D 7 OK 5340 5343 5344 5365 C3' C D 8 OK 5363 5366 5367 5385 C3' G D 9 OK 5383 5386 5387 5408 C3' C D 10 OK 5406 5409 5410 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4998 C4' G C 1 OK 5000 4997 4999 5021 C4' C C 2 OK 5023 5020 5022 5041 C4' G C 3 OK 5043 5040 5042 5064 C4' C C 4 OK 5066 5063 5065 5084 C4' G C 5 OK 5086 5083 5085 5107 C4' C C 6 OK 5109 5106 5108 5127 C4' G C 7 OK 5129 5126 5128 5150 C4' C C 8 OK 5152 5149 5151 5170 C4' G C 9 OK 5172 5169 5171 5193 C4' C C 10 OK 5195 5192 5194 5211 C4' G D 1 OK 5213 5210 5212 5234 C4' C D 2 OK 5236 5233 5235 5254 C4' G D 3 OK 5256 5253 5255 5277 C4' C D 4 OK 5279 5276 5278 5297 C4' G D 5 OK 5299 5296 5298 5320 C4' C D 6 OK 5322 5319 5321 5340 C4' G D 7 OK 5342 5339 5341 5363 C4' C D 8 OK 5365 5362 5364 5383 C4' G D 9 OK 5385 5382 5384 5406 C4' C D 10 OK 5408 5405 5407 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4997 C5' G C 1 4996 4998 5020 C5' C C 2 5019 5021 5040 C5' G C 3 5039 5041 5063 C5' C C 4 5062 5064 5083 C5' G C 5 5082 5084 5106 C5' C C 6 5105 5107 5126 C5' G C 7 5125 5127 5149 C5' C C 8 5148 5150 5169 C5' G C 9 5168 5170 5192 C5' C C 10 5191 5193 5210 C5' G D 1 5209 5211 5233 C5' C D 2 5232 5234 5253 C5' G D 3 5252 5254 5276 C5' C D 4 5275 5277 5296 C5' G D 5 5295 5297 5319 C5' C D 6 5318 5320 5339 C5' G D 7 5338 5340 5362 C5' C D 8 5361 5363 5382 C5' G D 9 5381 5383 5405 C5' C D 10 5404 5406 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5016 P C C 2 distorted distorted 5001 5017 5018 5019 5036 P G C 3 distorted distorted 5024 5037 5038 5039 5059 P C C 4 distorted distorted 5044 5060 5061 5062 5079 P G C 5 distorted distorted 5067 5080 5081 5082 5102 P C C 6 distorted distorted 5087 5103 5104 5105 5122 P G C 7 distorted distorted 5110 5123 5124 5125 5145 P C C 8 distorted distorted 5130 5146 5147 5148 5165 P G C 9 distorted distorted 5153 5166 5167 5168 5188 P C C 10 distorted distorted 5173 5189 5190 5191 5229 P C D 2 distorted distorted 5214 5230 5231 5232 5249 P G D 3 distorted distorted 5237 5250 5251 5252 5272 P C D 4 distorted distorted 5257 5273 5274 5275 5292 P G D 5 distorted distorted 5280 5293 5294 5295 5315 P C D 6 distorted distorted 5300 5316 5317 5318 5335 P G D 7 distorted distorted 5323 5336 5337 5338 5358 P C D 8 distorted distorted 5343 5359 5360 5361 5378 P G D 9 distorted distorted 5366 5379 5380 5381 5401 P C D 10 distorted distorted 5386 5402 5403 5404 ---------------------------------------------------------------------------------