ID code: '3ZD5' 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' --------------------------------------------------------------------------------- 17 C1' GDP A 1 beta 12 18 15 40 C1' G A 2 beta 35 41 38 63 C1' A A 3 beta 58 64 61 85 C1' U A 4 beta 80 86 83 105 C1' G A 5 beta 100 106 103 128 C1' U A 6 beta 123 129 126 148 C1' A A 7 beta 143 149 146 170 C1' C A 8 beta 165 171 168 190 C1' U A 9 beta 185 191 188 210 C1' A A 10 beta 205 211 208 232 C1' C A 11 beta 227 233 230 252 C1' C A 12 beta 247 253 250 272 C1' A A 13 beta 267 273 270 294 C1' G A 14 beta 289 295 292 317 C1' C A 15 beta 312 318 315 337 C1' U A 16 beta 332 338 335 357 C1' G A 17 beta 352 358 355 380 C1' A A 18 beta 375 381 378 402 C1' U A 19 beta 397 403 400 422 C1' G A 20 beta 417 423 420 445 C1' A A 21 beta 440 446 443 467 C1' G A 22 beta 462 468 465 490 C1' U A 23 beta 485 491 488 510 C1' C A 24 beta 505 511 508 530 C1' C A 25 beta 525 531 528 550 C1' C A 26 beta 545 551 548 570 C1' A A 27 beta 565 571 568 592 C1' A A 28 beta 587 593 590 614 C1' A A 29 beta 609 615 612 636 C1' U A 30 beta 631 637 634 656 C1' A A 31 beta 651 657 654 678 C1' G A 32 beta 673 679 676 701 C1' G A 33 beta 696 702 699 724 C1' A A 34 beta 719 725 722 746 C1' C A 35 beta 741 747 744 766 C1' G A 36 beta 761 767 764 789 C1' A A 37 beta 784 790 787 811 C1' A A 38 beta 806 812 809 833 C1' A A 39 beta 828 834 831 855 C1' C A 40 beta 850 856 853 875 C1' G A 41 beta 870 876 873 898 C1' C A 42 beta 893 899 896 918 C1' C A 43 beta 913 919 916 936 C1' G B 1 beta 931 937 934 959 C1' G B 2 beta 954 960 957 982 C1' C B 3 beta 977 983 980 1002 C1' G B 4 beta 997 1003 1000 1025 C1' U B 5 beta 1020 1026 1023 1042 C1' OMC B 6 beta 1048 1034 1043 1066 C1' C B 7 beta 1061 1067 1064 1086 C1' U B 8 beta 1081 1087 1084 1106 C1' G B 9 beta 1101 1107 1104 1129 C1' G B 10 beta 1124 1130 1127 1152 C1' 5BU B 11 beta 1147 1153 1150 1173 C1' A B 12 beta 1168 1174 1171 1195 C1' U B 13 beta 1190 1196 1193 1215 C1' C B 14 beta 1210 1216 1213 1235 C1' C B 15 beta 1230 1236 1233 1255 C1' A B 16 beta 1250 1256 1253 1277 C1' A B 17 beta 1272 1278 1275 1299 C1' 5BU B 18 beta 1294 1300 1297 1320 C1' C B 19 beta 1315 1321 1318 1339 C1' DC B 20 beta 1335 1340 1338 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 15 C2' GDP A 1 OK 17 13 16 38 C2' G A 2 OK 40 36 39 61 C2' A A 3 OK 63 59 62 83 C2' U A 4 OK 85 81 84 103 C2' G A 5 OK 105 101 104 126 C2' U A 6 OK 128 124 127 146 C2' A A 7 OK 148 144 147 168 C2' C A 8 OK 170 166 169 188 C2' U A 9 OK 190 186 189 208 C2' A A 10 OK 210 206 209 230 C2' C A 11 OK 232 228 231 250 C2' C A 12 OK 252 248 251 270 C2' A A 13 OK 272 268 271 292 C2' G A 14 OK 294 290 293 315 C2' C A 15 OK 317 313 316 335 C2' U A 16 OK 337 333 336 355 C2' G A 17 OK 357 353 356 378 C2' A A 18 OK 380 376 379 400 C2' U A 19 OK 402 398 401 420 C2' G A 20 OK 422 418 421 443 C2' A A 21 OK 445 441 444 465 C2' G A 22 OK 467 463 466 488 C2' U A 23 OK 490 486 489 508 C2' C A 24 OK 510 506 509 528 C2' C A 25 OK 530 526 529 548 C2' C A 26 OK 550 546 549 568 C2' A A 27 OK 570 566 569 590 C2' A A 28 OK 592 588 591 612 C2' A A 29 OK 614 610 613 634 C2' U A 30 OK 636 632 635 654 C2' A A 31 OK 656 652 655 676 C2' G A 32 OK 678 674 677 699 C2' G A 33 OK 701 697 700 722 C2' A A 34 OK 724 720 723 744 C2' C A 35 OK 746 742 745 764 C2' G A 36 OK 766 762 765 787 C2' A A 37 OK 789 785 788 809 C2' A A 38 OK 811 807 810 831 C2' A A 39 OK 833 829 832 853 C2' C A 40 OK 855 851 854 873 C2' G A 41 OK 875 871 874 896 C2' C A 42 OK 898 894 897 916 C2' C A 43 OK 918 914 917 934 C2' G B 1 OK 936 932 935 957 C2' G B 2 OK 959 955 958 980 C2' C B 3 OK 982 978 981 1000 C2' G B 4 OK 1002 998 1001 1023 C2' U B 5 OK 1025 1021 1024 1043 C2' OMC B 6 OK 1042 1046 1044 1064 C2' C B 7 OK 1066 1062 1065 1084 C2' U B 8 OK 1086 1082 1085 1104 C2' G B 9 OK 1106 1102 1105 1127 C2' G B 10 OK 1129 1125 1128 1150 C2' 5BU B 11 OK 1152 1148 1151 1171 C2' A B 12 OK 1173 1169 1172 1193 C2' U B 13 OK 1195 1191 1194 1213 C2' C B 14 OK 1215 1211 1214 1233 C2' C B 15 OK 1235 1231 1234 1253 C2' A B 16 OK 1255 1251 1254 1275 C2' A B 17 OK 1277 1273 1276 1297 C2' 5BU B 18 OK 1299 1295 1298 1318 C2' C B 19 OK 1320 1316 1319 1338 C2' DC B 20 1339 1336 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 13 C3' GDP A 1 OK 11 14 15 36 C3' G A 2 OK 34 37 38 59 C3' A A 3 OK 57 60 61 81 C3' U A 4 OK 79 82 83 101 C3' G A 5 OK 99 102 103 124 C3' U A 6 OK 122 125 126 144 C3' A A 7 OK 142 145 146 166 C3' C A 8 OK 164 167 168 186 C3' U A 9 OK 184 187 188 206 C3' A A 10 OK 204 207 208 228 C3' C A 11 OK 226 229 230 248 C3' C A 12 OK 246 249 250 268 C3' A A 13 OK 266 269 270 290 C3' G A 14 OK 288 291 292 313 C3' C A 15 OK 311 314 315 333 C3' U A 16 OK 331 334 335 353 C3' G A 17 OK 351 354 355 376 C3' A A 18 OK 374 377 378 398 C3' U A 19 OK 396 399 400 418 C3' G A 20 OK 416 419 420 441 C3' A A 21 OK 439 442 443 463 C3' G A 22 OK 461 464 465 486 C3' U A 23 OK 484 487 488 506 C3' C A 24 OK 504 507 508 526 C3' C A 25 OK 524 527 528 546 C3' C A 26 OK 544 547 548 566 C3' A A 27 OK 564 567 568 588 C3' A A 28 OK 586 589 590 610 C3' A A 29 OK 608 611 612 632 C3' U A 30 OK 630 633 634 652 C3' A A 31 OK 650 653 654 674 C3' G A 32 OK 672 675 676 697 C3' G A 33 OK 695 698 699 720 C3' A A 34 OK 718 721 722 742 C3' C A 35 OK 740 743 744 762 C3' G A 36 OK 760 763 764 785 C3' A A 37 OK 783 786 787 807 C3' A A 38 OK 805 808 809 829 C3' A A 39 OK 827 830 831 851 C3' C A 40 OK 849 852 853 871 C3' G A 41 OK 869 872 873 894 C3' C A 42 OK 892 895 896 914 C3' C A 43 OK 912 915 916 932 C3' G B 1 OK 930 933 934 955 C3' G B 2 OK 953 956 957 978 C3' C B 3 OK 976 979 980 998 C3' G B 4 OK 996 999 1000 1021 C3' U B 5 OK 1019 1022 1023 1046 C3' OMC B 6 OK 1047 1049 1043 1062 C3' C B 7 OK 1060 1063 1064 1082 C3' U B 8 OK 1080 1083 1084 1102 C3' G B 9 OK 1100 1103 1104 1125 C3' G B 10 OK 1123 1126 1127 1148 C3' 5BU B 11 OK 1146 1149 1150 1169 C3' A B 12 OK 1167 1170 1171 1191 C3' U B 13 OK 1189 1192 1193 1211 C3' C B 14 OK 1209 1212 1213 1231 C3' C B 15 OK 1229 1232 1233 1251 C3' A B 16 OK 1249 1252 1253 1273 C3' A B 17 OK 1271 1274 1275 1295 C3' 5BU B 18 OK 1293 1296 1297 1316 C3' C B 19 OK 1314 1317 1318 1336 C3' DC B 20 OK 1334 1337 1338 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 11 C4' GDP A 1 OK 13 10 12 34 C4' G A 2 OK 36 33 35 57 C4' A A 3 OK 59 56 58 79 C4' U A 4 OK 81 78 80 99 C4' G A 5 OK 101 98 100 122 C4' U A 6 OK 124 121 123 142 C4' A A 7 OK 144 141 143 164 C4' C A 8 OK 166 163 165 184 C4' U A 9 OK 186 183 185 204 C4' A A 10 OK 206 203 205 226 C4' C A 11 OK 228 225 227 246 C4' C A 12 OK 248 245 247 266 C4' A A 13 OK 268 265 267 288 C4' G A 14 OK 290 287 289 311 C4' C A 15 OK 313 310 312 331 C4' U A 16 OK 333 330 332 351 C4' G A 17 OK 353 350 352 374 C4' A A 18 OK 376 373 375 396 C4' U A 19 OK 398 395 397 416 C4' G A 20 OK 418 415 417 439 C4' A A 21 OK 441 438 440 461 C4' G A 22 OK 463 460 462 484 C4' U A 23 OK 486 483 485 504 C4' C A 24 OK 506 503 505 524 C4' C A 25 OK 526 523 525 544 C4' C A 26 OK 546 543 545 564 C4' A A 27 OK 566 563 565 586 C4' A A 28 OK 588 585 587 608 C4' A A 29 OK 610 607 609 630 C4' U A 30 OK 632 629 631 650 C4' A A 31 OK 652 649 651 672 C4' G A 32 OK 674 671 673 695 C4' G A 33 OK 697 694 696 718 C4' A A 34 OK 720 717 719 740 C4' C A 35 OK 742 739 741 760 C4' G A 36 OK 762 759 761 783 C4' A A 37 OK 785 782 784 805 C4' A A 38 OK 807 804 806 827 C4' A A 39 OK 829 826 828 849 C4' C A 40 OK 851 848 850 869 C4' G A 41 OK 871 868 870 892 C4' C A 42 OK 894 891 893 912 C4' C A 43 OK 914 911 913 930 C4' G B 1 OK 932 929 931 953 C4' G B 2 OK 955 952 954 976 C4' C B 3 OK 978 975 977 996 C4' G B 4 OK 998 995 997 1019 C4' U B 5 OK 1021 1018 1020 1047 C4' OMC B 6 OK 1046 1050 1048 1060 C4' C B 7 OK 1062 1059 1061 1080 C4' U B 8 OK 1082 1079 1081 1100 C4' G B 9 OK 1102 1099 1101 1123 C4' G B 10 OK 1125 1122 1124 1146 C4' 5BU B 11 OK 1148 1145 1147 1167 C4' A B 12 OK 1169 1166 1168 1189 C4' U B 13 OK 1191 1188 1190 1209 C4' C B 14 OK 1211 1208 1210 1229 C4' C B 15 OK 1231 1228 1230 1249 C4' A B 16 OK 1251 1248 1250 1271 C4' A B 17 OK 1273 1270 1272 1293 C4' 5BU B 18 OK 1295 1292 1294 1314 C4' C B 19 OK 1316 1313 1315 1334 C4' DC B 20 OK 1336 1333 1335 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 10 C5' GDP A 1 9 11 33 C5' G A 2 32 34 56 C5' A A 3 55 57 78 C5' U A 4 77 79 98 C5' G A 5 97 99 121 C5' U A 6 120 122 141 C5' A A 7 140 142 163 C5' C A 8 162 164 183 C5' U A 9 182 184 203 C5' A A 10 202 204 225 C5' C A 11 224 226 245 C5' C A 12 244 246 265 C5' A A 13 264 266 287 C5' G A 14 286 288 310 C5' C A 15 309 311 330 C5' U A 16 329 331 350 C5' G A 17 349 351 373 C5' A A 18 372 374 395 C5' U A 19 394 396 415 C5' G A 20 414 416 438 C5' A A 21 437 439 460 C5' G A 22 459 461 483 C5' U A 23 482 484 503 C5' C A 24 502 504 523 C5' C A 25 522 524 543 C5' C A 26 542 544 563 C5' A A 27 562 564 585 C5' A A 28 584 586 607 C5' A A 29 606 608 629 C5' U A 30 628 630 649 C5' A A 31 648 650 671 C5' G A 32 670 672 694 C5' G A 33 693 695 717 C5' A A 34 716 718 739 C5' C A 35 738 740 759 C5' G A 36 758 760 782 C5' A A 37 781 783 804 C5' A A 38 803 805 826 C5' A A 39 825 827 848 C5' C A 40 847 849 868 C5' G A 41 867 869 891 C5' C A 42 890 892 911 C5' C A 43 910 912 929 C5' G B 1 928 930 952 C5' G B 2 951 953 975 C5' C B 3 974 976 995 C5' G B 4 994 996 1018 C5' U B 5 1017 1019 1050 C5' OMC B 6 1051 1047 1059 C5' C B 7 1058 1060 1079 C5' U B 8 1078 1080 1099 C5' G B 9 1098 1100 1122 C5' G B 10 1121 1123 1145 C5' 5BU B 11 1144 1146 1166 C5' A B 12 1165 1167 1188 C5' U B 13 1187 1189 1208 C5' C B 14 1207 1209 1228 C5' C B 15 1227 1229 1248 C5' A B 16 1247 1249 1270 C5' A B 17 1269 1271 1292 C5' 5BU B 18 1291 1293 1313 C5' C B 19 1312 1314 1333 C5' DC B 20 1332 1334 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 29 P G A 2 distorted distorted 14 30 31 32 52 P A A 3 distorted distorted 37 53 54 55 74 P U A 4 distorted distorted 60 75 76 77 94 P G A 5 distorted distorted 82 95 96 97 117 P U A 6 distorted distorted 102 118 119 120 137 P A A 7 distorted distorted 125 138 139 140 159 P C A 8 distorted distorted 145 160 161 162 179 P U A 9 distorted distorted 167 180 181 182 199 P A A 10 distorted distorted 187 200 201 202 221 P C A 11 distorted distorted 207 222 223 224 241 P C A 12 distorted distorted 229 242 243 244 261 P A A 13 distorted distorted 249 262 263 264 283 P G A 14 distorted distorted 269 284 285 286 306 P C A 15 distorted distorted 291 307 308 309 326 P U A 16 distorted distorted 314 327 328 329 346 P G A 17 distorted distorted 334 347 348 349 369 P A A 18 distorted distorted 354 370 371 372 391 P U A 19 distorted distorted 377 392 393 394 411 P G A 20 distorted distorted 399 412 413 414 434 P A A 21 distorted distorted 419 435 436 437 456 P G A 22 distorted distorted 442 457 458 459 479 P U A 23 distorted distorted 464 480 481 482 499 P C A 24 distorted distorted 487 500 501 502 519 P C A 25 distorted distorted 507 520 521 522 539 P C A 26 distorted distorted 527 540 541 542 559 P A A 27 distorted distorted 547 560 561 562 581 P A A 28 distorted distorted 567 582 583 584 603 P A A 29 distorted distorted 589 604 605 606 625 P U A 30 distorted distorted 611 626 627 628 645 P A A 31 distorted distorted 633 646 647 648 667 P G A 32 distorted distorted 653 668 669 670 690 P G A 33 distorted distorted 675 691 692 693 713 P A A 34 distorted distorted 698 714 715 716 735 P C A 35 distorted distorted 721 736 737 738 755 P G A 36 distorted distorted 743 756 757 758 778 P A A 37 distorted distorted 763 779 780 781 800 P A A 38 distorted distorted 786 801 802 803 822 P A A 39 distorted distorted 808 823 824 825 844 P C A 40 distorted distorted 830 845 846 847 864 P G A 41 distorted distorted 852 865 866 867 887 P C A 42 distorted distorted 872 888 889 890 907 P C A 43 distorted distorted 895 908 909 910 948 P G B 2 distorted distorted 933 949 950 951 971 P C B 3 distorted distorted 956 972 973 974 991 P G B 4 distorted distorted 979 992 993 994 1014 P U B 5 distorted distorted 999 1015 1016 1017 1052 P OMC B 6 distorted distorted 1022 1053 1054 1051 1055 P C B 7 distorted distorted 1049 1056 1057 1058 1075 P U B 8 distorted distorted 1063 1076 1077 1078 1095 P G B 9 distorted distorted 1083 1096 1097 1098 1118 P G B 10 distorted distorted 1103 1119 1120 1121 1141 P 5BU B 11 distorted distorted 1126 1142 1143 1144 1162 P A B 12 distorted distorted 1149 1163 1164 1165 1184 P U B 13 distorted distorted 1170 1185 1186 1187 1204 P C B 14 distorted distorted 1192 1205 1206 1207 1224 P C B 15 distorted distorted 1212 1225 1226 1227 1244 P A B 16 distorted distorted 1232 1245 1246 1247 1266 P A B 17 distorted distorted 1252 1267 1268 1269 1288 P 5BU B 18 distorted distorted 1274 1289 1290 1291 1309 P C B 19 distorted distorted 1296 1310 1311 1312 1329 P DC B 20 distorted distorted 1317 1330 1331 1332 ---------------------------------------------------------------------------------