ID code: '1ZC5' 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' G A 1 alpha beta 7 30 13 10 46 C1' G A 2 alpha beta 41 64 47 44 80 C1' C A 3 alpha beta 75 95 81 78 111 C1' G A 4 alpha beta 106 129 112 109 145 C1' A A 5 alpha beta 140 162 146 143 178 C1' U A 6 alpha beta 173 193 179 176 208 C1' C A 7 alpha beta 203 223 209 206 239 C1' U A 8 alpha beta 234 254 240 237 269 C1' G A 9 alpha beta 264 287 270 267 303 C1' G A 10 alpha beta 298 321 304 301 337 C1' C A 11 alpha beta 332 352 338 335 368 C1' C A 12 alpha beta 363 383 369 366 399 C1' U A 13 alpha beta 394 414 400 397 429 C1' U A 14 alpha beta 424 444 430 427 459 C1' C A 15 alpha beta 454 474 460 457 490 C1' C A 16 alpha beta 485 505 491 488 521 C1' U A 17 alpha beta 516 536 522 519 551 C1' A A 18 alpha beta 546 568 552 549 584 C1' C A 19 alpha beta 579 599 585 582 615 C1' A A 20 alpha beta 610 632 616 613 648 C1' A A 21 alpha beta 643 665 649 646 681 C1' G A 22 alpha beta 676 699 682 679 715 C1' G A 23 alpha beta 710 733 716 713 749 C1' G A 24 alpha beta 744 767 750 747 783 C1' A A 25 alpha beta 778 800 784 781 816 C1' A A 26 alpha beta 811 833 817 814 849 C1' G A 27 alpha beta 844 867 850 847 883 C1' G A 28 alpha beta 878 901 884 881 917 C1' C A 29 alpha beta 912 932 918 915 948 C1' C A 30 alpha beta 943 963 949 946 979 C1' A A 31 alpha beta 974 996 980 977 1012 C1' G A 32 alpha beta 1007 1030 1013 1010 1046 C1' G A 33 alpha beta 1041 1064 1047 1044 1080 C1' G A 34 alpha beta 1075 1098 1081 1078 1114 C1' A A 35 alpha beta 1109 1131 1115 1112 1147 C1' A A 36 alpha beta 1142 1164 1148 1145 1180 C1' U A 37 alpha beta 1175 1195 1181 1178 1210 C1' U A 38 alpha beta 1205 1225 1211 1208 1240 C1' G A 39 alpha beta 1235 1258 1241 1238 1274 C1' C A 40 alpha beta 1269 1289 1275 1272 1305 C1' C A 41 alpha beta 1300 1320 1306 1303 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 1 OK OK 12 8 28 11 44 C2' G A 2 OK OK 46 42 62 45 78 C2' C A 3 OK OK 80 76 93 79 109 C2' G A 4 OK OK 111 107 127 110 143 C2' A A 5 OK OK 145 141 160 144 176 C2' U A 6 OK OK 178 174 191 177 206 C2' C A 7 OK OK 208 204 221 207 237 C2' U A 8 OK OK 239 235 252 238 267 C2' G A 9 OK OK 269 265 285 268 301 C2' G A 10 OK OK 303 299 319 302 335 C2' C A 11 OK OK 337 333 350 336 366 C2' C A 12 OK OK 368 364 381 367 397 C2' U A 13 OK OK 399 395 412 398 427 C2' U A 14 OK OK 429 425 442 428 457 C2' C A 15 OK OK 459 455 472 458 488 C2' C A 16 OK OK 490 486 503 489 519 C2' U A 17 OK OK 521 517 534 520 549 C2' A A 18 OK OK 551 547 566 550 582 C2' C A 19 OK OK 584 580 597 583 613 C2' A A 20 OK OK 615 611 630 614 646 C2' A A 21 OK OK 648 644 663 647 679 C2' G A 22 OK OK 681 677 697 680 713 C2' G A 23 OK OK 715 711 731 714 747 C2' G A 24 OK OK 749 745 765 748 781 C2' A A 25 OK OK 783 779 798 782 814 C2' A A 26 OK OK 816 812 831 815 847 C2' G A 27 OK OK 849 845 865 848 881 C2' G A 28 OK OK 883 879 899 882 915 C2' C A 29 OK OK 917 913 930 916 946 C2' C A 30 OK OK 948 944 961 947 977 C2' A A 31 OK OK 979 975 994 978 1010 C2' G A 32 OK OK 1012 1008 1028 1011 1044 C2' G A 33 OK OK 1046 1042 1062 1045 1078 C2' G A 34 OK OK 1080 1076 1096 1079 1112 C2' A A 35 OK OK 1114 1110 1129 1113 1145 C2' A A 36 OK OK 1147 1143 1162 1146 1178 C2' U A 37 OK OK 1180 1176 1193 1179 1208 C2' U A 38 OK OK 1210 1206 1223 1209 1238 C2' G A 39 OK OK 1240 1236 1256 1239 1272 C2' C A 40 OK OK 1274 1270 1287 1273 1303 C2' C A 41 OK OK 1305 1301 1318 1304 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 1 OK OK 6 27 9 10 42 C3' G A 2 OK OK 40 61 43 44 76 C3' C A 3 OK OK 74 92 77 78 107 C3' G A 4 OK OK 105 126 108 109 141 C3' A A 5 OK OK 139 159 142 143 174 C3' U A 6 OK OK 172 190 175 176 204 C3' C A 7 OK OK 202 220 205 206 235 C3' U A 8 OK OK 233 251 236 237 265 C3' G A 9 OK OK 263 284 266 267 299 C3' G A 10 OK OK 297 318 300 301 333 C3' C A 11 OK OK 331 349 334 335 364 C3' C A 12 OK OK 362 380 365 366 395 C3' U A 13 OK OK 393 411 396 397 425 C3' U A 14 OK OK 423 441 426 427 455 C3' C A 15 OK OK 453 471 456 457 486 C3' C A 16 OK OK 484 502 487 488 517 C3' U A 17 OK OK 515 533 518 519 547 C3' A A 18 OK OK 545 565 548 549 580 C3' C A 19 OK OK 578 596 581 582 611 C3' A A 20 OK OK 609 629 612 613 644 C3' A A 21 OK OK 642 662 645 646 677 C3' G A 22 OK OK 675 696 678 679 711 C3' G A 23 OK OK 709 730 712 713 745 C3' G A 24 OK OK 743 764 746 747 779 C3' A A 25 OK OK 777 797 780 781 812 C3' A A 26 OK OK 810 830 813 814 845 C3' G A 27 OK OK 843 864 846 847 879 C3' G A 28 OK OK 877 898 880 881 913 C3' C A 29 OK OK 911 929 914 915 944 C3' C A 30 OK OK 942 960 945 946 975 C3' A A 31 OK OK 973 993 976 977 1008 C3' G A 32 OK OK 1006 1027 1009 1010 1042 C3' G A 33 OK OK 1040 1061 1043 1044 1076 C3' G A 34 OK OK 1074 1095 1077 1078 1110 C3' A A 35 OK OK 1108 1128 1111 1112 1143 C3' A A 36 OK OK 1141 1161 1144 1145 1176 C3' U A 37 OK OK 1174 1192 1177 1178 1206 C3' U A 38 OK OK 1204 1222 1207 1208 1236 C3' G A 39 OK OK 1234 1255 1237 1238 1270 C3' C A 40 OK OK 1268 1286 1271 1272 1301 C3' C A 41 OK OK 1299 1317 1302 1303 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 1 OK OK 8 26 5 7 40 C4' G A 2 OK OK 42 60 39 41 74 C4' C A 3 OK OK 76 91 73 75 105 C4' G A 4 OK OK 107 125 104 106 139 C4' A A 5 OK OK 141 158 138 140 172 C4' U A 6 OK OK 174 189 171 173 202 C4' C A 7 OK OK 204 219 201 203 233 C4' U A 8 OK OK 235 250 232 234 263 C4' G A 9 OK OK 265 283 262 264 297 C4' G A 10 OK OK 299 317 296 298 331 C4' C A 11 OK OK 333 348 330 332 362 C4' C A 12 OK OK 364 379 361 363 393 C4' U A 13 OK OK 395 410 392 394 423 C4' U A 14 OK OK 425 440 422 424 453 C4' C A 15 OK OK 455 470 452 454 484 C4' C A 16 OK OK 486 501 483 485 515 C4' U A 17 OK OK 517 532 514 516 545 C4' A A 18 OK OK 547 564 544 546 578 C4' C A 19 OK OK 580 595 577 579 609 C4' A A 20 OK OK 611 628 608 610 642 C4' A A 21 OK OK 644 661 641 643 675 C4' G A 22 OK OK 677 695 674 676 709 C4' G A 23 OK OK 711 729 708 710 743 C4' G A 24 OK OK 745 763 742 744 777 C4' A A 25 OK OK 779 796 776 778 810 C4' A A 26 OK OK 812 829 809 811 843 C4' G A 27 OK OK 845 863 842 844 877 C4' G A 28 OK OK 879 897 876 878 911 C4' C A 29 OK OK 913 928 910 912 942 C4' C A 30 OK OK 944 959 941 943 973 C4' A A 31 OK OK 975 992 972 974 1006 C4' G A 32 OK OK 1008 1026 1005 1007 1040 C4' G A 33 OK OK 1042 1060 1039 1041 1074 C4' G A 34 OK OK 1076 1094 1073 1075 1108 C4' A A 35 OK OK 1110 1127 1107 1109 1141 C4' A A 36 OK OK 1143 1160 1140 1142 1174 C4' U A 37 OK OK 1176 1191 1173 1175 1204 C4' U A 38 OK OK 1206 1221 1203 1205 1234 C4' G A 39 OK OK 1236 1254 1233 1235 1268 C4' C A 40 OK OK 1270 1285 1267 1269 1299 C4' C A 41 OK OK 1301 1316 1298 1300 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 1 OK OK 4 24 25 6 39 C5' G A 2 OK OK 38 58 59 40 73 C5' C A 3 OK OK 72 89 90 74 104 C5' G A 4 OK OK 103 123 124 105 138 C5' A A 5 OK OK 137 156 157 139 171 C5' U A 6 OK OK 170 187 188 172 201 C5' C A 7 OK OK 200 217 218 202 232 C5' U A 8 OK OK 231 248 249 233 262 C5' G A 9 OK OK 261 281 282 263 296 C5' G A 10 OK OK 295 315 316 297 330 C5' C A 11 OK OK 329 346 347 331 361 C5' C A 12 OK OK 360 377 378 362 392 C5' U A 13 OK OK 391 408 409 393 422 C5' U A 14 OK OK 421 438 439 423 452 C5' C A 15 OK OK 451 468 469 453 483 C5' C A 16 OK OK 482 499 500 484 514 C5' U A 17 OK OK 513 530 531 515 544 C5' A A 18 OK OK 543 562 563 545 577 C5' C A 19 OK OK 576 593 594 578 608 C5' A A 20 OK OK 607 626 627 609 641 C5' A A 21 OK OK 640 659 660 642 674 C5' G A 22 OK OK 673 693 694 675 708 C5' G A 23 OK OK 707 727 728 709 742 C5' G A 24 OK OK 741 761 762 743 776 C5' A A 25 OK OK 775 794 795 777 809 C5' A A 26 OK OK 808 827 828 810 842 C5' G A 27 OK OK 841 861 862 843 876 C5' G A 28 OK OK 875 895 896 877 910 C5' C A 29 OK OK 909 926 927 911 941 C5' C A 30 OK OK 940 957 958 942 972 C5' A A 31 OK OK 971 990 991 973 1005 C5' G A 32 OK OK 1004 1024 1025 1006 1039 C5' G A 33 OK OK 1038 1058 1059 1040 1073 C5' G A 34 OK OK 1072 1092 1093 1074 1107 C5' A A 35 OK OK 1106 1125 1126 1108 1140 C5' A A 36 OK OK 1139 1158 1159 1141 1173 C5' U A 37 OK OK 1172 1189 1190 1174 1203 C5' U A 38 OK OK 1202 1219 1220 1204 1233 C5' G A 39 OK OK 1232 1252 1253 1234 1267 C5' C A 40 OK OK 1266 1283 1284 1268 1298 C5' C A 41 OK OK 1297 1314 1315 1299 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 1 OK OK 2 3 4 35 P G A 2 distorted distorted 9 36 37 38 69 P C A 3 distorted distorted 43 70 71 72 100 P G A 4 distorted distorted 77 101 102 103 134 P A A 5 distorted distorted 108 135 136 137 167 P U A 6 distorted distorted 142 168 169 170 197 P C A 7 distorted distorted 175 198 199 200 228 P U A 8 distorted distorted 205 229 230 231 258 P G A 9 distorted distorted 236 259 260 261 292 P G A 10 distorted distorted 266 293 294 295 326 P C A 11 distorted distorted 300 327 328 329 357 P C A 12 distorted distorted 334 358 359 360 388 P U A 13 distorted distorted 365 389 390 391 418 P U A 14 distorted distorted 396 419 420 421 448 P C A 15 distorted distorted 426 449 450 451 479 P C A 16 distorted distorted 456 480 481 482 510 P U A 17 distorted distorted 487 511 512 513 540 P A A 18 distorted distorted 518 541 542 543 573 P C A 19 distorted distorted 548 574 575 576 604 P A A 20 distorted distorted 581 605 606 607 637 P A A 21 distorted distorted 612 638 639 640 670 P G A 22 distorted distorted 645 671 672 673 704 P G A 23 distorted distorted 678 705 706 707 738 P G A 24 distorted distorted 712 739 740 741 772 P A A 25 distorted distorted 746 773 774 775 805 P A A 26 distorted distorted 780 806 807 808 838 P G A 27 distorted distorted 813 839 840 841 872 P G A 28 distorted distorted 846 873 874 875 906 P C A 29 distorted distorted 880 907 908 909 937 P C A 30 distorted distorted 914 938 939 940 968 P A A 31 distorted distorted 945 969 970 971 1001 P G A 32 distorted distorted 976 1002 1003 1004 1035 P G A 33 distorted distorted 1009 1036 1037 1038 1069 P G A 34 distorted distorted 1043 1070 1071 1072 1103 P A A 35 distorted distorted 1077 1104 1105 1106 1136 P A A 36 distorted distorted 1111 1137 1138 1139 1169 P U A 37 distorted distorted 1144 1170 1171 1172 1199 P U A 38 distorted distorted 1177 1200 1201 1202 1229 P G A 39 distorted distorted 1207 1230 1231 1232 1263 P C A 40 distorted distorted 1237 1264 1265 1266 1294 P C A 41 distorted distorted 1271 1295 1296 1297 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