ID code: '5NKL' 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' --------------------------------------------------------------------------------- 8703 C1' DG B 101 alpha beta 8699 8721 8704 8702 8737 C1' DA B 102 alpha beta 8733 8754 8738 8736 8769 C1' DC B 103 alpha beta 8765 8784 8770 8768 8799 C1' DC B 104 alpha beta 8795 8814 8800 8798 8829 C1' DA B 105 alpha beta 8825 8846 8830 8828 8861 C1' DC B 106 alpha beta 8857 8876 8862 8860 8891 C1' DG B 107 alpha beta 8887 8909 8892 8890 8924 C1' DG B 108 alpha beta 8920 8942 8925 8923 8957 C1' DC B 109 alpha beta 8953 8972 8958 8956 8987 C1' DG B 110 alpha beta 8983 9005 8988 8986 9020 C1' DC B 111 alpha beta 9016 9035 9021 9019 9048 C1' DOC B 112 alpha beta 9052 9062 9040 9049 9078 C1' DA C 201 alpha beta 9074 9095 9079 9077 9111 C1' DA C 202 alpha beta 9107 9128 9112 9110 9143 C1' DA C 203 alpha beta 9139 9160 9144 9142 9165 C1' 91N C 204 9184 9170 9213 C1' DG C 205 alpha beta 9209 9231 9214 9212 9246 C1' DG C 206 alpha beta 9242 9264 9247 9245 9279 C1' DC C 207 alpha beta 9275 9294 9280 9278 9309 C1' DG C 208 alpha beta 9305 9327 9310 9308 9342 C1' DC C 209 alpha beta 9338 9357 9343 9341 9372 C1' DC C 210 alpha beta 9368 9387 9373 9371 9402 C1' DG C 211 alpha beta 9398 9420 9403 9401 9435 C1' DT C 212 alpha beta 9431 9451 9436 9434 9467 C1' DG C 213 alpha beta 9463 9485 9468 9466 9500 C1' DG C 214 alpha beta 9496 9518 9501 9499 9533 C1' DT C 215 alpha beta 9529 9549 9534 9532 9565 C1' DC C 216 alpha beta 9561 9581 9566 9564 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 8702 C2' DG B 101 OK OK 8703 8700 8719 8720 8736 C2' DA B 102 OK OK 8737 8734 8752 8753 8768 C2' DC B 103 OK OK 8769 8766 8782 8783 8798 C2' DC B 104 OK OK 8799 8796 8812 8813 8828 C2' DA B 105 OK OK 8829 8826 8844 8845 8860 C2' DC B 106 OK OK 8861 8858 8874 8875 8890 C2' DG B 107 OK OK 8891 8888 8907 8908 8923 C2' DG B 108 OK OK 8924 8921 8940 8941 8956 C2' DC B 109 OK OK 8957 8954 8970 8971 8986 C2' DG B 110 OK OK 8987 8984 9003 9004 9019 C2' DC B 111 OK OK 9020 9017 9033 9034 9049 C2' DOC B 112 OK OK 9048 9050 9063 9064 9077 C2' DA C 201 OK OK 9078 9075 9093 9094 9110 C2' DA C 202 OK OK 9111 9108 9126 9127 9142 C2' DA C 203 OK OK 9143 9140 9158 9159 9170 C2' 91N C 204 9165 9171 9212 C2' DG C 205 OK OK 9213 9210 9229 9230 9245 C2' DG C 206 OK OK 9246 9243 9262 9263 9278 C2' DC C 207 OK OK 9279 9276 9292 9293 9308 C2' DG C 208 OK OK 9309 9306 9325 9326 9341 C2' DC C 209 OK OK 9342 9339 9355 9356 9371 C2' DC C 210 OK OK 9372 9369 9385 9386 9401 C2' DG C 211 OK OK 9402 9399 9418 9419 9434 C2' DT C 212 OK OK 9435 9432 9449 9450 9466 C2' DG C 213 OK OK 9467 9464 9483 9484 9499 C2' DG C 214 OK OK 9500 9497 9516 9517 9532 C2' DT C 215 OK OK 9533 9530 9547 9548 9564 C2' DC C 216 OK OK 9565 9562 9579 9580 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8700 C3' DG B 101 OK OK 8698 8718 8701 8702 8734 C3' DA B 102 OK OK 8732 8751 8735 8736 8766 C3' DC B 103 OK OK 8764 8781 8767 8768 8796 C3' DC B 104 OK OK 8794 8811 8797 8798 8826 C3' DA B 105 OK OK 8824 8843 8827 8828 8858 C3' DC B 106 OK OK 8856 8873 8859 8860 8888 C3' DG B 107 OK OK 8886 8906 8889 8890 8921 C3' DG B 108 OK OK 8919 8939 8922 8923 8954 C3' DC B 109 OK OK 8952 8969 8955 8956 8984 C3' DG B 110 OK OK 8982 9002 8985 8986 9017 C3' DC B 111 OK OK 9015 9032 9018 9019 9050 C3' DOC B 112 9051 9049 9075 C3' DA C 201 OK OK 9073 9092 9076 9077 9108 C3' DA C 202 OK OK 9106 9125 9109 9110 9140 C3' DA C 203 OK OK 9138 9157 9141 9142 9171 C3' 91N C 204 OK 9173 9183 9170 9210 C3' DG C 205 OK OK 9208 9228 9211 9212 9243 C3' DG C 206 OK OK 9241 9261 9244 9245 9276 C3' DC C 207 OK OK 9274 9291 9277 9278 9306 C3' DG C 208 OK OK 9304 9324 9307 9308 9339 C3' DC C 209 OK OK 9337 9354 9340 9341 9369 C3' DC C 210 OK OK 9367 9384 9370 9371 9399 C3' DG C 211 OK OK 9397 9417 9400 9401 9432 C3' DT C 212 OK OK 9430 9448 9433 9434 9464 C3' DG C 213 OK OK 9462 9482 9465 9466 9497 C3' DG C 214 OK OK 9495 9515 9498 9499 9530 C3' DT C 215 OK OK 9528 9546 9531 9532 9562 C3' DC C 216 OK OK 9560 9577 9563 9564 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 8698 C4' DG B 101 OK OK 8700 8717 8697 8699 8732 C4' DA B 102 OK OK 8734 8750 8731 8733 8764 C4' DC B 103 OK OK 8766 8780 8763 8765 8794 C4' DC B 104 OK OK 8796 8810 8793 8795 8824 C4' DA B 105 OK OK 8826 8842 8823 8825 8856 C4' DC B 106 OK OK 8858 8872 8855 8857 8886 C4' DG B 107 OK OK 8888 8905 8885 8887 8919 C4' DG B 108 OK OK 8921 8938 8918 8920 8952 C4' DC B 109 OK OK 8954 8968 8951 8953 8982 C4' DG B 110 OK OK 8984 9001 8981 8983 9015 C4' DC B 111 OK OK 9017 9031 9014 9016 9051 C4' DOC B 112 OK OK 9050 9067 9053 9052 9073 C4' DA C 201 OK OK 9075 9091 9072 9074 9106 C4' DA C 202 OK OK 9108 9124 9105 9107 9138 C4' DA C 203 OK OK 9140 9156 9137 9139 9173 C4' 91N C 204 OK 9171 9175 9184 9208 C4' DG C 205 OK OK 9210 9227 9207 9209 9241 C4' DG C 206 OK OK 9243 9260 9240 9242 9274 C4' DC C 207 OK OK 9276 9290 9273 9275 9304 C4' DG C 208 OK OK 9306 9323 9303 9305 9337 C4' DC C 209 OK OK 9339 9353 9336 9338 9367 C4' DC C 210 OK OK 9369 9383 9366 9368 9397 C4' DG C 211 OK OK 9399 9416 9396 9398 9430 C4' DT C 212 OK OK 9432 9447 9429 9431 9462 C4' DG C 213 OK OK 9464 9481 9461 9463 9495 C4' DG C 214 OK OK 9497 9514 9494 9496 9528 C4' DT C 215 OK OK 9530 9545 9527 9529 9560 C4' DC C 216 OK OK 9562 9576 9559 9561 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 8697 C5' DG B 101 OK OK 8696 8715 8716 8698 8731 C5' DA B 102 OK OK 8730 8748 8749 8732 8763 C5' DC B 103 OK OK 8762 8778 8779 8764 8793 C5' DC B 104 OK OK 8792 8808 8809 8794 8823 C5' DA B 105 OK OK 8822 8840 8841 8824 8855 C5' DC B 106 OK OK 8854 8870 8871 8856 8885 C5' DG B 107 OK OK 8884 8903 8904 8886 8918 C5' DG B 108 OK OK 8917 8936 8937 8919 8951 C5' DC B 109 OK OK 8950 8966 8967 8952 8981 C5' DG B 110 OK OK 8980 8999 9000 8982 9014 C5' DC B 111 OK OK 9013 9029 9030 9015 9053 C5' DOC B 112 distorted distorted 9054 9068 9069 9051 9072 C5' DA C 201 OK OK 9071 9089 9090 9073 9105 C5' DA C 202 OK OK 9104 9122 9123 9106 9137 C5' DA C 203 OK OK 9136 9154 9155 9138 9175 C5' 91N C 204 9185 9173 9207 C5' DG C 205 OK OK 9206 9225 9226 9208 9240 C5' DG C 206 OK OK 9239 9258 9259 9241 9273 C5' DC C 207 OK OK 9272 9288 9289 9274 9303 C5' DG C 208 OK OK 9302 9321 9322 9304 9336 C5' DC C 209 OK OK 9335 9351 9352 9337 9366 C5' DC C 210 OK OK 9365 9381 9382 9367 9396 C5' DG C 211 OK OK 9395 9414 9415 9397 9429 C5' DT C 212 OK OK 9428 9445 9446 9430 9461 C5' DG C 213 OK OK 9460 9479 9480 9462 9494 C5' DG C 214 OK OK 9493 9512 9513 9495 9527 C5' DT C 215 OK OK 9526 9543 9544 9528 9559 C5' DC C 216 OK OK 9558 9574 9575 9560 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 8727 P DA B 102 distorted distorted 8701 8728 8729 8730 8759 P DC B 103 distorted distorted 8735 8760 8761 8762 8789 P DC B 104 distorted distorted 8767 8790 8791 8792 8819 P DA B 105 distorted distorted 8797 8820 8821