ID code: '2NRE' 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' --------------------------------------------------------------------------------- 12 C1' A F 5 beta 7 13 10 34 C1' G F 6 beta 29 35 32 57 C1' G F 7 beta 52 58 55 80 C1' U F 8 beta 75 81 78 100 C1' G F 9 beta 95 101 98 123 C1' G F 10 beta 118 124 121 146 C1' U F 11 beta 141 147 144 166 C1' G F 12 beta 161 167 164 189 C1' G F 13 beta 184 190 187 212 C1' A F 14 beta 207 213 210 234 C1' A F 15 beta 229 235 232 256 C1' U F 16 beta 251 257 254 276 C1' U F 17 beta 271 277 274 296 C1' G F 18 beta 291 297 294 319 C1' G F 19 beta 314 320 317 342 C1' U F 20 beta 337 343 340 362 C1' A F 20 beta 357 363 360 384 C1' G F 21 beta 379 385 382 407 C1' A F 22 beta 402 408 405 429 C1' C F 23 beta 424 430 427 449 C1' A F 24 beta 444 450 447 471 C1' C F 25 beta 466 472 469 491 C1' G F 26 beta 486 492 489 514 C1' C F 27 beta 509 515 512 534 C1' U F 28 beta 529 535 532 554 C1' A F 29 beta 549 555 552 576 C1' C F 30 beta 571 577 574 596 C1' C F 31 beta 591 597 594 616 C1' G F 39 beta 611 617 614 639 C1' G F 40 beta 634 640 637 662 C1' U F 41 beta 657 663 660 682 C1' A F 42 beta 677 683 680 704 C1' G F 43 beta 699 705 702 727 C1' U F 44 beta 722 728 725 747 C1' U F 48 beta 742 748 745 767 C1' A F 49 beta 762 768 765 789 C1' C F 50 beta 784 790 787 809 C1' G F 51 beta 804 810 807 832 C1' G F 52 beta 827 833 830 855 C1' G F 53 beta 850 856 853 878 C1' U F 54 beta 873 879 876 898 C1' U F 55 beta 893 899 896 918 C1' C F 56 beta 913 919 916 938 C1' A F 57 beta 933 939 936 960 C1' A F 58 beta 955 961 958 982 C1' G F 59 beta 977 983 980 1005 C1' U F 60 beta 1000 1006 1003 1025 C1' C F 61 beta 1020 1026 1023 1045 C1' C F 62 beta 1040 1046 1043 1065 C1' C F 63 beta 1060 1066 1063 1085 C1' G F 64 beta 1080 1086 1083 1108 C1' U F 65 beta 1103 1109 1106 1128 C1' C F 66 beta 1123 1129 1126 1148 C1' C F 67 beta 1143 1149 1146 1168 C1' U F 68 beta 1163 1169 1166 1188 C1' C F 69 beta 1183 1189 1186 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' A F 5 OK 12 8 11 32 C2' G F 6 OK 34 30 33 55 C2' G F 7 OK 57 53 56 78 C2' U F 8 OK 80 76 79 98 C2' G F 9 OK 100 96 99 121 C2' G F 10 OK 123 119 122 144 C2' U F 11 OK 146 142 145 164 C2' G F 12 OK 166 162 165 187 C2' G F 13 OK 189 185 188 210 C2' A F 14 OK 212 208 211 232 C2' A F 15 OK 234 230 233 254 C2' U F 16 OK 256 252 255 274 C2' U F 17 OK 276 272 275 294 C2' G F 18 OK 296 292 295 317 C2' G F 19 OK 319 315 318 340 C2' U F 20 OK 342 338 341 360 C2' A F 20 OK 362 358 361 382 C2' G F 21 OK 384 380 383 405 C2' A F 22 OK 407 403 406 427 C2' C F 23 OK 429 425 428 447 C2' A F 24 OK 449 445 448 469 C2' C F 25 OK 471 467 470 489 C2' G F 26 OK 491 487 490 512 C2' C F 27 OK 514 510 513 532 C2' U F 28 OK 534 530 533 552 C2' A F 29 OK 554 550 553 574 C2' C F 30 OK 576 572 575 594 C2' C F 31 OK 596 592 595 614 C2' G F 39 OK 616 612 615 637 C2' G F 40 OK 639 635 638 660 C2' U F 41 OK 662 658 661 680 C2' A F 42 OK 682 678 681 702 C2' G F 43 OK 704 700 703 725 C2' U F 44 OK 727 723 726 745 C2' U F 48 OK 747 743 746 765 C2' A F 49 OK 767 763 766 787 C2' C F 50 OK 789 785 788 807 C2' G F 51 OK 809 805 808 830 C2' G F 52 OK 832 828 831 853 C2' G F 53 OK 855 851 854 876 C2' U F 54 OK 878 874 877 896 C2' U F 55 OK 898 894 897 916 C2' C F 56 OK 918 914 917 936 C2' A F 57 OK 938 934 937 958 C2' A F 58 OK 960 956 959 980 C2' G F 59 OK 982 978 981 1003 C2' U F 60 OK 1005 1001 1004 1023 C2' C F 61 OK 1025 1021 1024 1043 C2' C F 62 OK 1045 1041 1044 1063 C2' C F 63 OK 1065 1061 1064 1083 C2' G F 64 OK 1085 1081 1084 1106 C2' U F 65 OK 1108 1104 1107 1126 C2' C F 66 OK 1128 1124 1127 1146 C2' C F 67 OK 1148 1144 1147 1166 C2' U F 68 OK 1168 1164 1167 1186 C2' C F 69 OK 1188 1184 1187 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' A F 5 OK 6 9 10 30 C3' G F 6 OK 28 31 32 53 C3' G F 7 OK 51 54 55 76 C3' U F 8 OK 74 77 78 96 C3' G F 9 OK 94 97 98 119 C3' G F 10 OK 117 120 121 142 C3' U F 11 OK 140 143 144 162 C3' G F 12 OK 160 163 164 185 C3' G F 13 OK 183 186 187 208 C3' A F 14 OK 206 209 210 230 C3' A F 15 OK 228 231 232 252 C3' U F 16 OK 250 253 254 272 C3' U F 17 OK 270 273 274 292 C3' G F 18 OK 290 293 294 315 C3' G F 19 OK 313 316 317 338 C3' U F 20 OK 336 339 340 358 C3' A F 20 OK 356 359 360 380 C3' G F 21 OK 378 381 382 403 C3' A F 22 OK 401 404 405 425 C3' C F 23 OK 423 426 427 445 C3' A F 24 OK 443 446 447 467 C3' C F 25 OK 465 468 469 487 C3' G F 26 OK 485 488 489 510 C3' C F 27 OK 508 511 512 530 C3' U F 28 OK 528 531 532 550 C3' A F 29 OK 548 551 552 572 C3' C F 30 OK 570 573 574 592 C3' C F 31 OK 590 593 594 612 C3' G F 39 OK 610 613 614 635 C3' G F 40 OK 633 636 637 658 C3' U F 41 OK 656 659 660 678 C3' A F 42 OK 676 679 680 700 C3' G F 43 OK 698 701 702 723 C3' U F 44 OK 721 724 725 743 C3' U F 48 OK 741 744 745 763 C3' A F 49 OK 761 764 765 785 C3' C F 50 OK 783 786 787 805 C3' G F 51 OK 803 806 807 828 C3' G F 52 OK 826 829 830 851 C3' G F 53 OK 849 852 853 874 C3' U F 54 OK 872 875 876 894 C3' U F 55 OK 892 895 896 914 C3' C F 56 OK 912 915 916 934 C3' A F 57 OK 932 935 936 956 C3' A F 58 OK 954 957 958 978 C3' G F 59 OK 976 979 980 1001 C3' U F 60 OK 999 1002 1003 1021 C3' C F 61 OK 1019 1022 1023 1041 C3' C F 62 OK 1039 1042 1043 1061 C3' C F 63 OK 1059 1062 1063 1081 C3' G F 64 OK 1079 1082 1083 1104 C3' U F 65 OK 1102 1105 1106 1124 C3' C F 66 OK 1122 1125 1126 1144 C3' C F 67 OK 1142 1145 1146 1164 C3' U F 68 OK 1162 1165 1166 1184 C3' C F 69 OK 1182 1185 1186 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' A F 5 OK 8 5 7 28 C4' G F 6 OK 30 27 29 51 C4' G F 7 OK 53 50 52 74 C4' U F 8 OK 76 73 75 94 C4' G F 9 OK 96 93 95 117 C4' G F 10 OK 119 116 118 140 C4' U F 11 OK 142 139 141 160 C4' G F 12 OK 162 159 161 183 C4' G F 13 OK 185 182 184 206 C4' A F 14 OK 208 205 207 228 C4' A F 15 OK 230 227 229 250 C4' U F 16 OK 252 249 251 270 C4' U F 17 OK 272 269 271 290 C4' G F 18 OK 292 289 291 313 C4' G F 19 OK 315 312 314 336 C4' U F 20 OK 338 335 337 356 C4' A F 20 OK 358 355 357 378 C4' G F 21 OK 380 377 379 401 C4' A F 22 OK 403 400 402 423 C4' C F 23 OK 425 422 424 443 C4' A F 24 OK 445 442 444 465 C4' C F 25 OK 467 464 466 485 C4' G F 26 OK 487 484 486 508 C4' C F 27 OK 510 507 509 528 C4' U F 28 OK 530 527 529 548 C4' A F 29 OK 550 547 549 570 C4' C F 30 OK 572 569 571 590 C4' C F 31 OK 592 589 591 610 C4' G F 39 OK 612 609 611 633 C4' G F 40 OK 635 632 634 656 C4' U F 41 OK 658 655 657 676 C4' A F 42 OK 678 675 677 698 C4' G F 43 OK 700 697 699 721 C4' U F 44 OK 723 720 722 741 C4' U F 48 OK 743 740 742 761 C4' A F 49 OK 763 760 762 783 C4' C F 50 OK 785 782 784 803 C4' G F 51 OK 805 802 804 826 C4' G F 52 OK 828 825 827 849 C4' G F 53 OK 851 848 850 872 C4' U F 54 OK 874 871 873 892 C4' U F 55 OK 894 891 893 912 C4' C F 56 OK 914 911 913 932 C4' A F 57 OK 934 931 933 954 C4' A F 58 OK 956 953 955 976 C4' G F 59 OK 978 975 977 999 C4' U F 60 OK 1001 998 1000 1019 C4' C F 61 OK 1021 1018 1020 1039 C4' C F 62 OK 1041 1038 1040 1059 C4' C F 63 OK 1061 1058 1060 1079 C4' G F 64 OK 1081 1078 1080 1102 C4' U F 65 OK 1104 1101 1103 1122 C4' C F 66 OK 1124 1121 1123 1142 C4' C F 67 OK 1144 1141 1143 1162 C4' U F 68 OK 1164 1161 1163 1182 C4' C F 69 OK 1184 1181 1183 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' A F 5 4 6 27 C5' G F 6 26 28 50 C5' G F 7 49 51 73 C5' U F 8 72 74 93 C5' G F 9 92 94 116 C5' G F 10 115 117 139 C5' U F 11 138 140 159 C5' G F 12 158 160 182 C5' G F 13 181 183 205 C5' A F 14 204 206 227 C5' A F 15 226 228 249 C5' U F 16 248 250 269 C5' U F 17 268 270 289 C5' G F 18 288 290 312 C5' G F 19 311 313 335 C5' U F 20 334 336 355 C5' A F 20 354 356 377 C5' G F 21 376 378 400 C5' A F 22 399 401 422 C5' C F 23 421 423 442 C5' A F 24 441 443 464 C5' C F 25 463 465 484 C5' G F 26 483 485 507 C5' C F 27 506 508 527 C5' U F 28 526 528 547 C5' A F 29 546 548 569 C5' C F 30 568 570 589 C5' C F 31 588 590 609 C5' G F 39 608 610 632 C5' G F 40 631 633 655 C5' U F 41 654 656 675 C5' A F 42 674 676 697 C5' G F 43 696 698 720 C5' U F 44 719 721 740 C5' U F 48 739 741 760 C5' A F 49 759 761 782 C5' C F 50 781 783 802 C5' G F 51 801 803 825 C5' G F 52 824 826 848 C5' G F 53 847 849 871 C5' U F 54 870 872 891 C5' U F 55 890 892 911 C5' C F 56 910 912 931 C5' A F 57 930 932 953 C5' A F 58 952 954 975 C5' G F 59 974 976 998 C5' U F 60 997 999 1018 C5' C F 61 1017 1019 1038 C5' C F 62 1037 1039 1058 C5' C F 63 1057 1059 1078 C5' G F 64 1077 1079 1101 C5' U F 65 1100 1102 1121 C5' C F 66 1120 1122 1141 C5' C F 67 1140 1142 1161 C5' U F 68 1160 1162 1181 C5' C F 69 1180 1182 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A F 5 OK OK 2 3 4 23 P G F 6 distorted distorted 9 24 25 26 46 P G F 7 distorted distorted 31 47 48 49 69 P U F 8 distorted distorted 54 70 71 72 89 P G F 9 distorted distorted 77 90 91 92 112 P G F 10 distorted distorted 97 113 114 115 135 P U F 11 distorted distorted 120 136 137 138 155 P G F 12 distorted distorted 143 156 157 158 178 P G F 13 distorted distorted 163 179 180 181 201 P A F 14 distorted distorted 186 202 203 204 223 P A F 15 distorted distorted 209 224 225 226 245 P U F 16 distorted distorted 231 246 247 248 265 P U F 17 distorted distorted 253 266 267 268 285 P G F 18 distorted distorted 273 286 287 288 308 P G F 19 distorted distorted 293 309 310 311 331 P U F 20 distorted distorted 316 332 333 334 351 P A F 20 distorted distorted 339 352 353 354 373 P G F 21 distorted distorted 359 374 375 376 396 P A F 22 distorted distorted 381 397 398 399 418 P C F 23 distorted distorted 404 419 420 421 438 P A F 24 distorted distorted 426 439 440 441 460 P C F 25 distorted distorted 446 461 462 463 480 P G F 26 distorted distorted 468 481 482 483 503 P C F 27 distorted distorted 488 504 505 506 523 P U F 28 distorted distorted 511 524 525 526 543 P A F 29 distorted distorted 531 544 545 546 565 P C F 30 distorted distorted 551 566 567 568 585 P C F 31 distorted distorted 573 586 587 588 605 P G F 39 distorted distorted 606 607 608 628 P G F 40 distorted distorted 613 629 630 631 651 P U F 41 distorted distorted 636 652 653 654 671 P A F 42 distorted distorted 659 672 673 674 693 P G F 43 distorted distorted 679 694 695 696 716 P U F 44 distorted distorted 701 717 718 719 736 P U F 48 distorted distorted 737 738 739 756 P A F 49 distorted distorted 744 757 758 759 778 P C F 50 distorted distorted 764 779 780 781 798 P G F 51 distorted distorted 786 799 800 801 821 P G F 52 distorted distorted 806 822 823 824 844 P G F 53 distorted distorted 829 845 846 847 867 P U F 54 distorted distorted 852 868 869 870 887 P U F 55 distorted distorted 875 888 889 890 907 P C F 56 distorted distorted 895 908 909 910 927 P A F 57 distorted distorted 915 928 929 930 949 P A F 58 distorted distorted 935 950 951 952 971 P G F 59 distorted distorted 957 972 973 974 994 P U F 60 distorted distorted 979 995 996 997 1014 P C F 61 distorted distorted 1002 1015 1016 1017 1034 P C F 62 distorted distorted 1022 1035 1036 1037 1054 P C F 63 distorted distorted 1042 1055 1056 1057 1074 P G F 64 distorted distorted 1062 1075 1076 1077 1097 P U F 65 distorted distorted 1082 1098 1099 1100 1117 P C F 66 distorted distorted 1105 1118 1119 1120 1137 P C F 67 distorted distorted 1125 1138 1139 1140 1157 P U F 68 distorted distorted 1145 1158 1159 1160 1177 P C F 69 distorted distorted 1165 1178 1179 1180 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