ID code: '3RR7' 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' --------------------------------------------------------------------------------- 4092 C1' DG B 101 beta 4088 4093 4091 4114 C1' DA B 102 beta 4110 4115 4113 4135 C1' DC B 103 beta 4131 4136 4134 4154 C1' DC B 104 beta 4150 4155 4153 4173 C1' DA B 105 beta 4169 4174 4172 4194 C1' DC B 106 beta 4190 4195 4193 4213 C1' DG B 107 beta 4209 4214 4212 4235 C1' DG B 108 beta 4231 4236 4234 4257 C1' DC B 109 beta 4253 4258 4256 4276 C1' DG B 110 beta 4272 4277 4275 4298 C1' DC B 111 beta 4294 4299 4297 4315 C1' DOC B 112 beta 4319 4307 4316 4336 C1' DA C 202 beta 4332 4337 4335 4357 C1' DA C 203 beta 4353 4358 4356 4376 C1' 3DR C 204 4375 4372 4389 C1' DG C 205 beta 4385 4390 4388 4411 C1' DG C 206 beta 4407 4412 4410 4433 C1' DC C 207 beta 4429 4434 4432 4452 C1' DG C 208 beta 4448 4453 4451 4474 C1' DC C 209 beta 4470 4475 4473 4493 C1' DC C 210 beta 4489 4494 4492 4512 C1' DG C 211 beta 4508 4513 4511 4534 C1' DT C 212 beta 4530 4535 4533 4554 C1' DG C 213 beta 4550 4555 4553 4576 C1' DG C 214 beta 4572 4577 4575 4598 C1' DT C 215 beta 4594 4599 4597 4618 C1' DC C 216 beta 4614 4619 4617 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4091 C2' DG B 101 4092 4089 4113 C2' DA B 102 4114 4111 4134 C2' DC B 103 4135 4132 4153 C2' DC B 104 4154 4151 4172 C2' DA B 105 4173 4170 4193 C2' DC B 106 4194 4191 4212 C2' DG B 107 4213 4210 4234 C2' DG B 108 4235 4232 4256 C2' DC B 109 4257 4254 4275 C2' DG B 110 4276 4273 4297 C2' DC B 111 4298 4295 4316 C2' DOC B 112 4315 4317 4335 C2' DA C 202 4336 4333 4356 C2' DA C 203 4357 4354 4372 C2' 3DR C 204 4376 4377 4388 C2' DG C 205 4389 4386 4410 C2' DG C 206 4411 4408 4432 C2' DC C 207 4433 4430 4451 C2' DG C 208 4452 4449 4473 C2' DC C 209 4474 4471 4492 C2' DC C 210 4493 4490 4511 C2' DG C 211 4512 4509 4533 C2' DT C 212 4534 4531 4553 C2' DG C 213 4554 4551 4575 C2' DG C 214 4576 4573 4597 C2' DT C 215 4598 4595 4617 C2' DC C 216 4618 4615 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4089 C3' DG B 101 OK 4087 4090 4091 4111 C3' DA B 102 OK 4109 4112 4113 4132 C3' DC B 103 OK 4130 4133 4134 4151 C3' DC B 104 OK 4149 4152 4153 4170 C3' DA B 105 OK 4168 4171 4172 4191 C3' DC B 106 OK 4189 4192 4193 4210 C3' DG B 107 OK 4208 4211 4212 4232 C3' DG B 108 OK 4230 4233 4234 4254 C3' DC B 109 OK 4252 4255 4256 4273 C3' DG B 110 OK 4271 4274 4275 4295 C3' DC B 111 OK 4293 4296 4297 4317 C3' DOC B 112 4318 4316 4333 C3' DA C 202 OK 4331 4334 4335 4354 C3' DA C 203 OK 4352 4355 4356 4377 C3' 3DR C 204 OK 4374 4378 4372 4386 C3' DG C 205 OK 4384 4387 4388 4408 C3' DG C 206 OK 4406 4409 4410 4430 C3' DC C 207 OK 4428 4431 4432 4449 C3' DG C 208 OK 4447 4450 4451 4471 C3' DC C 209 OK 4469 4472 4473 4490 C3' DC C 210 OK 4488 4491 4492 4509 C3' DG C 211 OK 4507 4510 4511 4531 C3' DT C 212 OK 4529 4532 4533 4551 C3' DG C 213 OK 4549 4552 4553 4573 C3' DG C 214 OK 4571 4574 4575 4595 C3' DT C 215 OK 4593 4596 4597 4615 C3' DC C 216 OK 4613 4616 4617 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4087 C4' DG B 101 OK 4089 4086 4088 4109 C4' DA B 102 OK 4111 4108 4110 4130 C4' DC B 103 OK 4132 4129 4131 4149 C4' DC B 104 OK 4151 4148 4150 4168 C4' DA B 105 OK 4170 4167 4169 4189 C4' DC B 106 OK 4191 4188 4190 4208 C4' DG B 107 OK 4210 4207 4209 4230 C4' DG B 108 OK 4232 4229 4231 4252 C4' DC B 109 OK 4254 4251 4253 4271 C4' DG B 110 OK 4273 4270 4272 4293 C4' DC B 111 OK 4295 4292 4294 4318 C4' DOC B 112 OK 4317 4320 4319 4331 C4' DA C 202 OK 4333 4330 4332 4352 C4' DA C 203 OK 4354 4351 4353 4374 C4' 3DR C 204 OK 4377 4373 4375 4384 C4' DG C 205 OK 4386 4383 4385 4406 C4' DG C 206 OK 4408 4405 4407 4428 C4' DC C 207 OK 4430 4427 4429 4447 C4' DG C 208 OK 4449 4446 4448 4469 C4' DC C 209 OK 4471 4468 4470 4488 C4' DC C 210 OK 4490 4487 4489 4507 C4' DG C 211 OK 4509 4506 4508 4529 C4' DT C 212 OK 4531 4528 4530 4549 C4' DG C 213 OK 4551 4548 4550 4571 C4' DG C 214 OK 4573 4570 4572 4593 C4' DT C 215 OK 4595 4592 4594 4613 C4' DC C 216 OK 4615 4612 4614 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4086 C5' DG B 101 4085 4087 4108 C5' DA B 102 4107 4109 4129 C5' DC B 103 4128 4130 4148 C5' DC B 104 4147 4149 4167 C5' DA B 105 4166 4168 4188 C5' DC B 106 4187 4189 4207 C5' DG B 107 4206 4208 4229 C5' DG B 108 4228 4230 4251 C5' DC B 109 4250 4252 4270 C5' DG B 110 4269 4271 4292 C5' DC B 111 4291 4293 4320 C5' DOC B 112 4321 4318 4330 C5' DA C 202 4329 4331 4351 C5' DA C 203 4350 4352 4373 C5' 3DR C 204 4368 4374 4383 C5' DG C 205 4382 4384 4405 C5' DG C 206 4404 4406 4427 C5' DC C 207 4426 4428 4446 C5' DG C 208 4445 4447 4468 C5' DC C 209 4467 4469 4487 C5' DC C 210 4486 4488 4506 C5' DG C 211 4505 4507 4528 C5' DT C 212 4527 4529 4548 C5' DG C 213 4547 4549 4570 C5' DG C 214 4569 4571 4592 C5' DT C 215 4591 4593 4612 C5' DC C 216 4611 4613 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4104 P DA B 102 distorted distorted 4090 4105 4106 4107 4125 P DC B 103 distorted distorted 4112 4126 4127 4128 4144 P DC B 104 distorted distorted 4133 4145 4146 4147 4163 P DA B 105 distorted distorted 4152 4164 4165 4166 4184 P DC B 106 distorted distorted 4171 4185 4186 4187 4203 P DG B 107 distorted distorted 4192 4204 4205 4206 4225 P DG B 108 distorted distorted 4211 4226 4227 4228 4247 P DC B 109 distorted distorted 4233 4248 4249 4250 4266 P DG B 110 distorted distorted 4255 4267 4268 4269 4288 P DC B 111 distorted distorted 4274 4289 4290 4291 4322 P DOC B 112 distorted distorted 4296 4323 4324 4321 4326 P DA C 202 OK OK 4327 4328 4329 4347 P DA C 203 distorted distorted 4334 4348 4349 4350 4369 P 3DR C 204 distorted distorted 4355 4370 4371 4368 4379 P DG C 205 distorted distorted 4378 4380 4381 4382 4401 P DG C 206 distorted distorted 4387 4402 4403 4404 4423 P DC C 207 distorted distorted 4409 4424 4425 4426 4442 P DG C 208 distorted distorted 4431 4443 4444 4445 4464 P DC C 209 distorted distorted 4450 4465 4466 4467 4483 P DC C 210 distorted distorted 4472 4484 4485 4486 4502 P DG C 211 distorted distorted 4491 4503 4504 4505 4524 P DT C 212 distorted distorted 4510 4525 4526 4527 4544 P DG C 213 distorted distorted 4532 4545 4546 4547 4566 P DG C 214 distorted distorted 4552 4567 4568 4569 4588 P DT C 215 distorted distorted 4574 4589 4590 4591 4608 P DC C 216 distorted distorted 4596 4609 4610 4611 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