0.029040 0.000000 0.000000 0.000000 0.023159 0.000000 0.000000 0.000000 0.013810 0.00000 0.00000 0.00000 van Aalten, D.M.F. Erlanson, D.A. Verdine, G.L. Joshua-Tor, L. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 16 90.00 90.00 90.00 34.435 43.180 72.412 Ca 2 40.078 CALCIUM ION non-polymer C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O7 P 347.221 y 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking C12 H18 N5 O7 P S 407.339 n N2-ETHANETHIOL-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE DNA linking H2 O 18.015 WATER non-polymer N 1 N CA N 2 N O N 3 N P N 4 N O N 5 N O N 6 N O N 7 N C N 8 R C N 9 N O N 10 S C N 11 N O N 12 N C N 13 R C Y 14 N N Y 15 N C Y 16 N N Y 17 N C Y 18 N C N 19 N N Y 20 N N Y 21 N C Y 22 N N Y 23 N C N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N O N 39 N P N 40 N O N 41 N O N 42 N O N 43 N C N 44 R C N 45 N O N 46 S C N 47 N O N 48 N C N 49 R C N 50 N N N 51 N C N 52 N O N 53 N N N 54 N C N 55 N N N 56 N C N 57 N C N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N O N 73 N P N 74 N O N 75 N O N 76 N O N 77 N C N 78 R C N 79 N O N 80 S C N 81 N O N 82 N C N 83 R C Y 84 N N Y 85 N C Y 86 N N Y 87 N C N 88 N C N 89 N O N 90 N N N 91 N C N 92 N N N 93 N N Y 94 N C N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N H N 108 N H N 109 N O N 110 N P N 111 N O N 112 N O N 113 N O N 114 N C N 115 R C N 116 N O N 117 S C N 118 N O N 119 N C N 120 R C N 121 N N N 122 N C N 123 N O N 124 N N N 125 N C N 126 N O N 127 N C N 128 N C N 129 N C N 130 N H N 131 N H N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N H N 145 N P N 146 N O N 147 N O N 148 N O N 149 N O N 150 N C N 151 R C N 152 N O N 153 S C N 154 N O N 155 N C N 156 R C Y 157 N N Y 158 N C Y 159 N N Y 160 N C N 161 N C N 162 N O N 163 N N N 164 N C N 165 N N N 166 N N Y 167 N C N 168 N C N 169 N C N 170 N S N 171 N H N 172 N H N 173 N H N 174 N H N 175 N H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 N H N 184 N H N 185 N H N 186 N H N 187 N H N 188 N H N 189 N O N 190 N H N 191 N H N 1 N sing N 2 N sing N 3 N doub N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing Y 24 N sing Y 25 N sing Y 26 N doub N 27 N sing Y 28 N sing Y 29 N sing Y 30 N doub N 31 N sing Y 32 N doub N 33 N sing N 34 N sing Y 35 N sing Y 36 N doub N 37 N sing Y 38 N sing N 39 N sing N 40 N sing N 41 N doub N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N doub N 65 N sing N 66 N doub N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N doub N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N doub N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing Y 97 N sing Y 98 N sing Y 99 N doub N 100 N sing Y 101 N sing N 102 N sing Y 103 N doub N 104 N doub N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N doub N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N doub N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N doub N 139 N sing N 140 N sing N 141 N sing N 142 N doub N 143 N sing N 144 N sing N 145 N doub N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N doub N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing Y 173 N sing Y 174 N sing Y 175 N doub N 176 N sing Y 177 N sing N 178 N sing Y 179 N doub N 180 N doub N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N doub N 186 N sing N 187 N sing N 188 N sing N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 96 11809 11814 10.1073/pnas.96.21.11809 10518532 A structural snapshot of base-pair opening in DNA. 1999 10.2210/pdb1cw9/pdb pdb_00001cw9 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 IMAGE PLATE 1998-03-02 MARRESEARCH SINGLE WAVELENGTH M x-ray 1 1.0800 1.0 X26C NSLS 1.0800 SYNCHROTRON NSLS BEAMLINE X26C 3106.110 5'-D(*CP*CP*AP*GP*(G47)P*CP*CP*TP*GP*G)-3' 4 syn polymer 40.078 CALCIUM ION 1 syn non-polymer 18.015 water 271 nat water no yes (DC)(DC)(DA)(DG)(G47)(DC)(DC)(DT)(DG)(DG) CCAGGCCTGG A,B,C,D polydeoxyribonucleotide n n n n n n n n n n 1 2.13 45. VAPOR DIFFUSION, HANGING DROP 7.0 MPD, CALCIUM CHLORIDE, SODIUM CHLORIDE, SPERMINE TETRACHLORIDE, SODIUM CACODYLATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K 277 CACL2 1 NACL 1 SPERMINE 1 SODIUM CACODYLATE 1 MPD 1 MPD 2 -2.554 1 19 A 1 B 10 1.920 A_DC1:DG10_B 1 -15.186 0.199 0.186 -0.138 1.111 1 19 A 2 B 9 -0.466 A_DC2:DG9_B 2 -8.912 0.262 0.025 -0.109 2.958 1 20 A 3 B 8 0.982 A_DA3:DT8_B 3 -5.269 0.027 0.329 -0.016 11.999 1 19 A 4 B 7 -1.080 A_DG4:DC7_B 4 -6.704 -0.085 0.331 -0.177 0.860 1 19 A 5 B 6 3.018 A_G475:DC6_B 5 -15.214 -0.452 0.294 -0.085 -2.401 1 19 A 6 B 5 1.213 A_DC6:G475_B 6 -8.750 0.343 0.273 -0.110 -12.779 1 19 A 7 B 4 -2.503 A_DC7:DG4_B 7 -8.194 0.143 0.468 -0.123 -1.558 1 20 A 8 B 3 -1.130 A_DT8:DA3_B 8 -6.799 -0.030 0.119 -0.089 -4.843 1 19 A 9 B 2 1.381 A_DG9:DC2_B 9 -15.199 -0.289 0.078 -0.119 1.602 1 19 A 10 B 1 1.486 A_DG10:DC1_B 10 -18.142 -0.137 0.174 -0.157 -7.445 1 19 C 1 D 10 0.520 C_DC1:DG10_D 11 -11.540 0.082 0.226 -0.137 2.444 1 19 C 2 D 9 -0.983 C_DC2:DG9_D 12 -8.081 0.200 -0.068 -0.159 4.393 1 20 C 3 D 8 -2.085 C_DA3:DT8_D 13 -8.323 0.124 0.167 -0.139 8.521 1 19 C 4 D 7 0.224 C_DG4:DC7_D 14 -11.911 -0.172 0.373 -0.175 4.770 1 19 C 5 D 6 0.582 C_G475:DC6_D 15 -7.001 -0.208 0.344 -0.126 6.150 C 6 D 5 56.064 C_DC6:G475_D 16 -32.191 1.676 0.533 2.570 -11.194 1 19 C 7 D 4 -0.632 C_DC7:DG4_D 17 -8.217 0.184 0.312 -0.096 -6.728 1 20 C 8 D 3 1.748 C_DT8:DA3_D 18 -10.293 -0.017 0.229 -0.159 -5.381 1 19 C 9 D 2 -0.620 C_DG9:DC2_D 19 -9.394 -0.285 0.075 -0.133 5.620 1 19 C 10 D 1 2.490 C_DG10:DC1_D 20 -12.557 -0.142 0.244 -0.070 3.562 41.012 A A 1 2 5.440 B B 10 9 3.394 3.786 0.208 2.233 AA_DC1DC2:DG9DG10_BB 1 7.548 -10.845 40.170 2.744 0.588 3.006 45.525 A A 2 3 -5.423 B B 9 8 3.264 -4.188 0.033 2.707 AA_DC2DA3:DT8DG9_BB 2 -3.229 4.181 45.233 3.852 -0.315 3.204 24.460 A A 3 4 12.537 B B 8 7 3.158 5.269 0.412 0.646 AA_DA3DG4:DC7DT8_BB 3 -0.985 2.344 23.874 -0.088 -1.274 3.571 41.186 A A 4 5 2.315 B B 7 6 3.563 1.628 -0.081 0.239 AA_DG4G475:DC6DC7_BB 4 -1.111 1.579 41.141 0.148 -0.016 3.417 35.708 A A 5 6 8.953 B B 6 5 3.468 5.469 -0.069 -0.067 AA_G475DC6:G475DC6_BB 5 0.920 -1.505 35.289 -0.946 0.254 3.502 45.481 A A 6 7 -4.845 B B 5 4 3.604 -3.742 -0.046 1.160 AA_DC6DC7:DG4G475_BB 6 -1.346 1.743 45.316 1.860 -0.070 3.084 24.638 A A 7 8 9.980 B B 4 3 3.079 4.229 -0.432 0.683 AA_DC7DT8:DA3DG4_BB 7 2.738 -6.461 24.125 0.367 1.811 2.938 50.513 A A 8 9 -7.242 B B 3 2 3.310 -6.166 -0.006 3.053 AA_DT8DG9:DC2DA3_BB 8 1.371 -1.610 50.142 3.997 0.100 3.245 34.635 A A 9 10 11.540 B B 2 1 3.210 6.814 0.686 0.983 AA_DG9DG10:DC1DC2_BB 9 -3.865 6.546 33.764 0.602 -1.747 3.032 30.008 C C 1 2 16.814 D D 10 9 3.079 8.552 -0.199 0.530 CC_DC1DC2:DG9DG10_DD 10 4.869 -9.573 28.383 -0.669 1.348 2.954 50.573 C C 2 3 -6.928 D D 9 8 3.264 -5.907 -0.051 2.665 CC_DC2DA3:DT8DG9_DD 11 -1.038 1.218 50.239 3.518 -0.010 3.216 27.765 C C 3 4 8.045 D D 8 7 3.199 3.846 0.095 0.436 CC_DA3DG4:DC7DT8_DD 12 -1.770 3.702 27.446 -0.004 -0.618 3.338 37.386 C C 4 5 5.412 D D 7 6 3.326 3.463 0.806 -0.108 CC_DG4G475:DC6DC7_DD 13 1.849 -2.890 37.187 -0.634 -1.009 3.883 40.233 C C 5 6 13.013 D D 6 5 3.392 8.821 2.625 0.516 CC_G475DC6:G475DC6_DD 14 8.442 -12.453 38.409 -0.391 -2.725 3.748 31.818 C C 6 7 19.239 D D 5 4 3.534 10.335 -2.796 0.214 CC_DC6DC7:DG4G475_DD 15 -4.189 7.799 29.847 -1.784 4.219 3.216 27.666 C C 7 8 10.972 D D 4 3 3.181 5.216 -0.394 0.518 CC_DC7DT8:DA3DG4_DD 16 0.426 -0.897 27.176 -0.164 0.925 2.876 50.260 C C 8 9 -7.530 D D 3 2 3.232 -6.380 -0.255 2.846 CC_DT8DG9:DC2DA3_DD 17 -1.349 1.592 49.862 3.780 0.209 3.060 31.051 C C 9 10 22.735 D D 2 1 3.102 11.812 0.556 0.878 CC_DG9DG10:DC1DC2_DD 18 -5.464 10.516 28.253 -0.604 -2.077 software chem_comp_atom chem_comp_bond database_2 pdbx_struct_conn_angle struct_conn struct_site pdbx_initial_refinement_model repository Initial release Version format compliance Version format compliance Structure summary Refinement description Data collection Database references Derived calculations Refinement description 1 0 1999-10-14 1 1 2008-04-27 1 2 2011-07-13 1 3 2017-02-01 1 4 2017-10-04 1 5 2024-02-07 1 6 2024-04-03 _software.classification _software.name _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.value _struct_conn.conn_type_id _struct_conn.id _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 1999-08-26 REL CA CALCIUM ION HOH water CROSSLINKED DNA WAS SYNTHESIZED BY THE CONVERTIBLE NUCLEOSIDE APPROACH sample 1BD1 BDJ017 PDB experimental model CA 1 2 CA CA 11 A HOH 2 3 HOH HOH 12 A HOH 303 3 HOH HOH 13 A HOH 305 3 HOH HOH 14 A HOH 308 3 HOH HOH 15 A HOH 313 3 HOH HOH 16 A HOH 318 3 HOH HOH 17 A HOH 324 3 HOH HOH 18 A HOH 327 3 HOH HOH 19 A HOH 329 3 HOH HOH 20 A HOH 334 3 HOH HOH 21 A HOH 336 3 HOH HOH 22 A HOH 339 3 HOH HOH 23 A HOH 342 3 HOH HOH 24 A HOH 346 3 HOH HOH 25 A HOH 349 3 HOH HOH 26 A HOH 351 3 HOH HOH 27 A HOH 352 3 HOH HOH 28 A HOH 354 3 HOH HOH 29 A HOH 355 3 HOH HOH 30 A HOH 357 3 HOH HOH 31 A HOH 358 3 HOH HOH 32 A HOH 381 3 HOH HOH 33 A HOH 384 3 HOH HOH 34 A HOH 385 3 HOH HOH 35 A HOH 389 3 HOH HOH 36 A HOH 410 3 HOH HOH 37 A HOH 418 3 HOH HOH 38 A HOH 420 3 HOH HOH 39 A HOH 422 3 HOH HOH 40 A HOH 426 3 HOH HOH 41 A HOH 427 3 HOH HOH 42 A HOH 431 3 HOH HOH 43 A HOH 433 3 HOH HOH 44 A HOH 438 3 HOH HOH 45 A HOH 439 3 HOH HOH 46 A HOH 457 3 HOH HOH 47 A HOH 461 3 HOH HOH 48 A HOH 463 3 HOH HOH 49 A HOH 464 3 HOH HOH 50 A HOH 465 3 HOH HOH 51 A HOH 468 3 HOH HOH 52 A HOH 470 3 HOH HOH 53 A HOH 476 3 HOH HOH 54 A HOH 481 3 HOH HOH 55 A HOH 496 3 HOH HOH 56 A HOH 502 3 HOH HOH 57 A HOH 514 3 HOH HOH 58 A HOH 516 3 HOH HOH 59 A HOH 519 3 HOH HOH 60 A HOH 528 3 HOH HOH 61 A HOH 543 3 HOH HOH 62 A HOH 544 3 HOH HOH 63 A HOH 548 3 HOH HOH 64 A HOH 552 3 HOH HOH 65 A HOH 556 3 HOH HOH 66 A HOH 567 3 HOH HOH 67 A HOH 574 3 HOH HOH 68 A HOH 581 3 HOH HOH 69 A HOH 583 3 HOH HOH 70 A HOH 584 3 HOH HOH 71 A HOH 590 3 HOH HOH 72 A HOH 595 3 HOH HOH 73 A HOH 600 3 HOH HOH 74 A HOH 606 3 HOH HOH 75 A HOH 608 3 HOH HOH 76 A HOH 615 3 HOH HOH 77 A HOH 617 3 HOH HOH 78 A HOH 621 3 HOH HOH 79 A HOH 623 3 HOH HOH 80 A HOH 639 3 HOH HOH 81 A HOH 641 3 HOH HOH 82 A HOH 644 3 HOH HOH 83 A HOH 654 3 HOH HOH 84 A HOH 659 3 HOH HOH 85 A HOH 660 3 HOH HOH 86 A HOH 690 3 HOH HOH 87 A HOH 696 3 HOH HOH 88 A HOH 304 3 HOH HOH 304 B HOH 306 3 HOH HOH 306 B HOH 316 3 HOH HOH 316 B HOH 326 3 HOH HOH 326 B HOH 328 3 HOH HOH 328 B HOH 331 3 HOH HOH 331 B HOH 333 3 HOH HOH 333 B HOH 338 3 HOH HOH 338 B HOH 345 3 HOH HOH 345 B HOH 347 3 HOH HOH 347 B HOH 348 3 HOH HOH 348 B HOH 353 3 HOH HOH 353 B HOH 356 3 HOH HOH 356 B HOH 359 3 HOH HOH 359 B HOH 363 3 HOH HOH 363 B HOH 366 3 HOH HOH 366 B HOH 367 3 HOH HOH 367 B HOH 369 3 HOH HOH 369 B HOH 380 3 HOH HOH 380 B HOH 382 3 HOH HOH 382 B HOH 386 3 HOH HOH 386 B HOH 392 3 HOH HOH 392 B HOH 393 3 HOH HOH 393 B HOH 395 3 HOH HOH 395 B HOH 397 3 HOH HOH 397 B HOH 419 3 HOH HOH 419 B HOH 421 3 HOH HOH 421 B HOH 424 3 HOH HOH 424 B HOH 428 3 HOH HOH 428 B HOH 434 3 HOH HOH 434 B HOH 449 3 HOH HOH 449 B HOH 450 3 HOH HOH 450 B HOH 452 3 HOH HOH 452 B HOH 458 3 HOH HOH 458 B HOH 467 3 HOH HOH 467 B HOH 474 3 HOH HOH 474 B HOH 475 3 HOH HOH 475 B HOH 492 3 HOH HOH 492 B HOH 493 3 HOH HOH 493 B HOH 501 3 HOH HOH 501 B HOH 507 3 HOH HOH 507 B HOH 509 3 HOH HOH 509 B HOH 510 3 HOH HOH 510 B HOH 513 3 HOH HOH 513 B HOH 523 3 HOH HOH 523 B HOH 530 3 HOH HOH 530 B HOH 533 3 HOH HOH 533 B HOH 537 3 HOH HOH 537 B HOH 541 3 HOH HOH 541 B HOH 545 3 HOH HOH 545 B HOH 572 3 HOH HOH 572 B HOH 573 3 HOH HOH 573 B HOH 587 3 HOH HOH 587 B HOH 588 3 HOH HOH 588 B HOH 593 3 HOH HOH 593 B HOH 596 3 HOH HOH 596 B HOH 599 3 HOH HOH 599 B HOH 603 3 HOH HOH 603 B HOH 609 3 HOH HOH 609 B HOH 631 3 HOH HOH 631 B HOH 636 3 HOH HOH 636 B HOH 637 3 HOH HOH 637 B HOH 638 3 HOH HOH 638 B HOH 649 3 HOH HOH 649 B HOH 651 3 HOH HOH 651 B HOH 669 3 HOH HOH 669 B HOH 698 3 HOH HOH 698 B HOH 706 3 HOH HOH 706 B HOH 4 3 HOH HOH 11 C HOH 302 3 HOH HOH 12 C HOH 309 3 HOH HOH 13 C HOH 310 3 HOH HOH 14 C HOH 311 3 HOH HOH 15 C HOH 312 3 HOH HOH 16 C HOH 315 3 HOH HOH 17 C HOH 319 3 HOH HOH 18 C HOH 320 3 HOH HOH 19 C HOH 322 3 HOH HOH 20 C HOH 323 3 HOH HOH 21 C HOH 325 3 HOH HOH 22 C HOH 330 3 HOH HOH 23 C HOH 332 3 HOH HOH 24 C HOH 350 3 HOH HOH 25 C HOH 360 3 HOH HOH 26 C HOH 362 3 HOH HOH 27 C HOH 364 3 HOH HOH 28 C HOH 368 3 HOH HOH 29 C HOH 378 3 HOH HOH 30 C HOH 390 3 HOH HOH 31 C HOH 411 3 HOH HOH 32 C HOH 412 3 HOH HOH 33 C HOH 413 3 HOH HOH 34 C HOH 425 3 HOH HOH 35 C HOH 429 3 HOH HOH 36 C HOH 430 3 HOH HOH 37 C HOH 432 3 HOH HOH 38 C HOH 436 3 HOH HOH 39 C HOH 440 3 HOH HOH 40 C HOH 447 3 HOH HOH 41 C HOH 453 3 HOH HOH 42 C HOH 456 3 HOH HOH 43 C HOH 460 3 HOH HOH 44 C HOH 466 3 HOH HOH 45 C HOH 480 3 HOH HOH 46 C HOH 485 3 HOH HOH 47 C HOH 497 3 HOH HOH 48 C HOH 518 3 HOH HOH 49 C HOH 521 3 HOH HOH 50 C HOH 522 3 HOH HOH 51 C HOH 538 3 HOH HOH 52 C HOH 542 3 HOH HOH 53 C HOH 546 3 HOH HOH 54 C HOH 549 3 HOH HOH 55 C HOH 557 3 HOH HOH 56 C HOH 558 3 HOH HOH 57 C HOH 563 3 HOH HOH 58 C HOH 569 3 HOH HOH 59 C HOH 580 3 HOH HOH 60 C HOH 586 3 HOH HOH 61 C HOH 591 3 HOH HOH 62 C HOH 592 3 HOH HOH 63 C HOH 594 3 HOH HOH 64 C HOH 601 3 HOH HOH 65 C HOH 612 3 HOH HOH 66 C HOH 624 3 HOH HOH 67 C HOH 625 3 HOH HOH 68 C HOH 640 3 HOH HOH 69 C HOH 653 3 HOH HOH 70 C HOH 656 3 HOH HOH 71 C HOH 3 3 HOH HOH 11 D HOH 314 3 HOH HOH 12 D HOH 321 3 HOH HOH 13 D HOH 335 3 HOH HOH 14 D HOH 337 3 HOH HOH 15 D HOH 361 3 HOH HOH 16 D HOH 371 3 HOH HOH 17 D HOH 372 3 HOH HOH 18 D HOH 373 3 HOH HOH 19 D HOH 374 3 HOH HOH 20 D HOH 375 3 HOH HOH 21 D HOH 376 3 HOH HOH 22 D HOH 377 3 HOH HOH 23 D HOH 383 3 HOH HOH 24 D HOH 391 3 HOH HOH 25 D HOH 394 3 HOH HOH 26 D HOH 398 3 HOH HOH 27 D HOH 401 3 HOH HOH 28 D HOH 402 3 HOH HOH 29 D HOH 403 3 HOH HOH 30 D HOH 406 3 HOH HOH 31 D HOH 407 3 HOH HOH 32 D HOH 408 3 HOH HOH 33 D HOH 414 3 HOH HOH 34 D HOH 415 3 HOH HOH 35 D HOH 416 3 HOH HOH 36 D HOH 423 3 HOH HOH 37 D HOH 435 3 HOH HOH 38 D HOH 437 3 HOH HOH 39 D HOH 441 3 HOH HOH 40 D HOH 443 3 HOH HOH 41 D HOH 444 3 HOH HOH 42 D HOH 448 3 HOH HOH 43 D HOH 451 3 HOH HOH 44 D HOH 462 3 HOH HOH 45 D HOH 469 3 HOH HOH 46 D HOH 477 3 HOH HOH 47 D HOH 478 3 HOH HOH 48 D HOH 479 3 HOH HOH 49 D HOH 487 3 HOH HOH 50 D HOH 504 3 HOH HOH 51 D HOH 508 3 HOH HOH 52 D HOH 520 3 HOH HOH 53 D HOH 525 3 HOH HOH 54 D HOH 531 3 HOH HOH 55 D HOH 535 3 HOH HOH 56 D HOH 547 3 HOH HOH 57 D HOH 553 3 HOH HOH 58 D HOH 555 3 HOH HOH 59 D HOH 565 3 HOH HOH 60 D HOH 571 3 HOH HOH 61 D HOH 576 3 HOH HOH 62 D HOH 585 3 HOH HOH 63 D HOH 597 3 HOH HOH 64 D HOH 602 3 HOH HOH 65 D HOH 604 3 HOH HOH 66 D HOH 619 3 HOH HOH 67 D HOH 630 3 HOH HOH 68 D HOH 643 3 HOH HOH 69 D HOH 652 3 HOH HOH 70 D HOH 661 3 HOH HOH 71 D HOH 667 3 HOH HOH 72 D HOH 668 3 HOH HOH 73 D HOH 678 3 HOH HOH 74 D HOH 685 3 HOH HOH 75 D C 1 n 1 DC 1 A C 2 n 2 DC 2 A A 3 n 3 DA 3 A G 4 n 4 DG 4 A +G 5 n 5 G47 5 A C 6 n 6 DC 6 A C 7 n 7 DC 7 A T 8 n 8 DT 8 A G 9 n 9 DG 9 A G 10 n 10 DG 10 A C 1 n 1 DC 1 B C 2 n 2 DC 2 B A 3 n 3 DA 3 B G 4 n 4 DG 4 B +G 5 n 5 G47 5 B C 6 n 6 DC 6 B C 7 n 7 DC 7 B T 8 n 8 DT 8 B G 9 n 9 DG 9 B G 10 n 10 DG 10 B C 1 n 1 DC 1 C C 2 n 2 DC 2 C A 3 n 3 DA 3 C G 4 n 4 DG 4 C +G 5 n 5 G47 5 C C 6 n 6 DC 6 C C 7 n 7 DC 7 C T 8 n 8 DT 8 C G 9 n 9 DG 9 C G 10 n 10 DG 10 C C 1 n 1 DC 1 D C 2 n 2 DC 2 D A 3 n 3 DA 3 D G 4 n 4 DG 4 D +G 5 n 5 G47 5 D C 6 n 6 DC 6 D C 7 n 7 DC 7 D T 8 n 8 DT 8 D G 9 n 9 DG 9 D G 10 n 10 DG 10 D author_defined_assembly 2 dimeric author_defined_assembly 2 dimeric A G47 5 A O6 G47 5 1_555 A CA 11 E CA CA 1_555 A HOH 16 F O HOH 1_555 78.1 A G47 5 A O6 G47 5 1_555 A CA 11 E CA CA 1_555 A HOH 21 F O HOH 1_555 122.2 A HOH 16 F O HOH 1_555 A CA 11 E CA CA 1_555 A HOH 21 F O HOH 1_555 80.8 A G47 5 A O6 G47 5 1_555 A CA 11 E CA CA 1_555 A HOH 26 F O HOH 1_555 73.4 A HOH 16 F O HOH 1_555 A CA 11 E CA CA 1_555 A HOH 26 F O HOH 1_555 95.0 A HOH 21 F O HOH 1_555 A CA 11 E CA CA 1_555 A HOH 26 F O HOH 1_555 161.9 A G47 5 A O6 G47 5 1_555 A CA 11 E CA CA 1_555 A HOH 30 F O HOH 1_555 142.8 A HOH 16 F O HOH 1_555 A CA 11 E CA CA 1_555 A HOH 30 F O HOH 1_555 78.3 A HOH 21 F O HOH 1_555 A CA 11 E CA CA 1_555 A HOH 30 F O HOH 1_555 81.3 A HOH 26 F O HOH 1_555 A CA 11 E CA CA 1_555 A HOH 30 F O HOH 1_555 80.6 A G47 5 A O6 G47 5 1_555 A CA 11 E CA CA 1_555 B G47 5 B O6 G47 5 1_555 72.1 A HOH 16 F O HOH 1_555 A CA 11 E CA CA 1_555 B G47 5 B O6 G47 5 1_555 123.2 A HOH 21 F O HOH 1_555 A CA 11 E CA CA 1_555 B G47 5 B O6 G47 5 1_555 76.3 A HOH 26 F O HOH 1_555 A CA 11 E CA CA 1_555 B G47 5 B O6 G47 5 1_555 119.9 A HOH 30 F O HOH 1_555 A CA 11 E CA CA 1_555 B G47 5 B O6 G47 5 1_555 145.0 A G47 5 A O6 G47 5 1_555 A CA 11 E CA CA 1_555 B HOH 359 G O HOH 1_555 119.2 A HOH 16 F O HOH 1_555 A CA 11 E CA CA 1_555 B HOH 359 G O HOH 1_555 157.1 A HOH 21 F O HOH 1_555 A CA 11 E CA CA 1_555 B HOH 359 G O HOH 1_555 99.7 A HOH 26 F O HOH 1_555 A CA 11 E CA CA 1_555 B HOH 359 G O HOH 1_555 77.5 A HOH 30 F O HOH 1_555 A CA 11 E CA CA 1_555 B HOH 359 G O HOH 1_555 79.2 B G47 5 B O6 G47 5 1_555 A CA 11 E CA CA 1_555 B HOH 359 G O HOH 1_555 78.5 A G47 5 A G47 5 DG B G47 5 B G47 5 DG C G47 5 C G47 5 DG D G47 5 D G47 5 DG 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 1 A DC 2 0.068 SIDE CHAIN 1 A DA 3 0.056 SIDE CHAIN 1 A DC 7 0.073 SIDE CHAIN 1 A DG 9 0.095 SIDE CHAIN 1 B DA 3 0.052 SIDE CHAIN 1 B DC 6 0.059 SIDE CHAIN 1 B DC 7 0.088 SIDE CHAIN 1 C DA 3 0.069 SIDE CHAIN 1 C DC 7 0.101 SIDE CHAIN 1 C DG 9 0.062 SIDE CHAIN 1 A B O5' OP1 DC DC 1 6 2.18 1_555 4_456 DNA-RNA_REP.PARAM DNA-RNA.TOP 18.3 3.895 0.000 0.000 -2.358 0.000 -1.537 MAXIMUM LIKELIHOOD. 0.232 0.203 0.2031 0.2031 1.55 13.0 782 15525 15525 5 95.7 RANDOM 1 RESTRAINED CNS THROUGHOUT 0.0 0.0 MOLECULAR REPLACEMENT BDJ017 CNS NUCLEIC ACID PARAMETERS USING SOFT VAN DER WAALS PARAMETERS (PARKINSON ET AL., ACTA D, 52, 57-64 (1996)). FLAT - CNS CALCULATED MASK 1.55 13.0 271 1092 1 820 0 0.009 1.53 3.938 4.824 2.875 3.828 1.61 5 98.0 14.7 1.55 13.0 1CW9 62990 62990 0.0 0.0 0.078 1 9.0 4.0 95.5 0.32 1.55 1.61 3.0 1 4.0 98.0 phasing AMoRE refinement CNS data collection MAR345 data scaling SCALEPACK DNA DECAMER WITH AN ENGINEERED CROSSLINK IN THE MINOR GROOVE 1 N N 1 N N 1 N N 1 N N 2 N N 3 N N 3 N N 3 N N 3 N N covale 1.598 both A DG 4 A O3' DG 4 1_555 A G47 5 A P G47 5 1_555 covale 1.600 one A G47 5 A O3' G47 5 1_555 A DC 6 A P DC 6 1_555 covale 2.091 none A G47 5 A SG G47 5 1_555 B G47 5 B SG G47 5 1_555 covale 1.608 both B DG 4 B O3' DG 4 1_555 B G47 5 B P G47 5 1_555 covale 1.605 one B G47 5 B O3' G47 5 1_555 B DC 6 B P DC 6 1_555 covale 1.601 both C DG 4 C O3' DG 4 1_555 C G47 5 C P G47 5 1_555 covale 1.600 one C G47 5 C O3' G47 5 1_555 C DC 6 C P DC 6 1_555 covale 2.145 none C G47 5 C SG G47 5 1_555 D G47 5 D SG G47 5 1_555 covale 1.610 both D DG 4 D O3' DG 4 1_555 D G47 5 D P G47 5 1_555 covale 1.592 one D G47 5 D O3' G47 5 1_555 D DC 6 D P DC 6 1_555 metalc 2.513 A G47 5 A O6 G47 5 1_555 A CA 11 E CA CA 1_555 metalc 2.442 A CA 11 E CA CA 1_555 A HOH 16 F O HOH 1_555 metalc 2.319 A CA 11 E CA CA 1_555 A HOH 21 F O HOH 1_555 metalc 2.365 A CA 11 E CA CA 1_555 A HOH 26 F O HOH 1_555 metalc 2.492 A CA 11 E CA CA 1_555 A HOH 30 F O HOH 1_555 metalc 2.542 A CA 11 E CA CA 1_555 B G47 5 B O6 G47 5 1_555 metalc 2.413 A CA 11 E CA CA 1_555 B HOH 359 G O HOH 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 10 B N1 DG 10 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 10 B O6 DG 10 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 10 B N2 DG 10 1_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 B DG 9 B N1 DG 9 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 B DG 9 B O6 DG 9 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 B DG 9 B N2 DG 9 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 B DT 8 B N3 DT 8 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 B DT 8 B O4 DT 8 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B DC 7 B N3 DC 7 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 7 B O2 DC 7 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B DC 7 B N4 DC 7 1_555 hydrog WATSON-CRICK A G47 5 A N1 G47 5 1_555 B DC 6 B N3 DC 6 1_555 hydrog WATSON-CRICK A G47 5 A N2 G47 5 1_555 B DC 6 B O2 DC 6 1_555 hydrog WATSON-CRICK A G47 5 A O6 G47 5 1_555 B DC 6 B N4 DC 6 1_555 hydrog WATSON-CRICK A DC 6 A N3 DC 6 1_555 B G47 5 B N1 G47 5 1_555 hydrog WATSON-CRICK A DC 6 A N4 DC 6 1_555 B G47 5 B O6 G47 5 1_555 hydrog WATSON-CRICK A DC 6 A O2 DC 6 1_555 B G47 5 B N2 G47 5 1_555 hydrog WATSON-CRICK A DC 7 A N3 DC 7 1_555 B DG 4 B N1 DG 4 1_555 hydrog WATSON-CRICK A DC 7 A N4 DC 7 1_555 B DG 4 B O6 DG 4 1_555 hydrog WATSON-CRICK A DC 7 A O2 DC 7 1_555 B DG 4 B N2 DG 4 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 B DA 3 B N1 DA 3 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 B DA 3 B N6 DA 3 1_555 hydrog WATSON-CRICK A DG 9 A N1 DG 9 1_555 B DC 2 B N3 DC 2 1_555 hydrog WATSON-CRICK A DG 9 A N2 DG 9 1_555 B DC 2 B O2 DC 2 1_555 hydrog WATSON-CRICK A DG 9 A O6 DG 9 1_555 B DC 2 B N4 DC 2 1_555 hydrog WATSON-CRICK A DG 10 A N1 DG 10 1_555 B DC 1 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 10 A N2 DG 10 1_555 B DC 1 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 10 A O6 DG 10 1_555 B DC 1 B N4 DC 1 1_555 hydrog WATSON-CRICK C DC 1 C N3 DC 1 1_555 D DG 10 D N1 DG 10 1_555 hydrog WATSON-CRICK C DC 1 C N4 DC 1 1_555 D DG 10 D O6 DG 10 1_555 hydrog WATSON-CRICK C DC 1 C O2 DC 1 1_555 D DG 10 D N2 DG 10 1_555 hydrog WATSON-CRICK C DC 2 C N3 DC 2 1_555 D DG 9 D N1 DG 9 1_555 hydrog WATSON-CRICK C DC 2 C N4 DC 2 1_555 D DG 9 D O6 DG 9 1_555 hydrog WATSON-CRICK C DC 2 C O2 DC 2 1_555 D DG 9 D N2 DG 9 1_555 hydrog WATSON-CRICK C DA 3 C N1 DA 3 1_555 D DT 8 D N3 DT 8 1_555 hydrog WATSON-CRICK C DA 3 C N6 DA 3 1_555 D DT 8 D O4 DT 8 1_555 hydrog WATSON-CRICK C DG 4 C N1 DG 4 1_555 D DC 7 D N3 DC 7 1_555 hydrog WATSON-CRICK C DG 4 C N2 DG 4 1_555 D DC 7 D O2 DC 7 1_555 hydrog WATSON-CRICK C DG 4 C O6 DG 4 1_555 D DC 7 D N4 DC 7 1_555 hydrog WATSON-CRICK C G47 5 C N1 G47 5 1_555 D DC 6 D N3 DC 6 1_555 hydrog WATSON-CRICK C G47 5 C N2 G47 5 1_555 D DC 6 D O2 DC 6 1_555 hydrog WATSON-CRICK C G47 5 C O6 G47 5 1_555 D DC 6 D N4 DC 6 1_555 hydrog DC-G47 PAIR C DC 6 C O2 DC 6 1_555 D G47 5 D N2 G47 5 1_555 hydrog WATSON-CRICK C DC 7 C N3 DC 7 1_555 D DG 4 D N1 DG 4 1_555 hydrog WATSON-CRICK C DC 7 C N4 DC 7 1_555 D DG 4 D O6 DG 4 1_555 hydrog WATSON-CRICK C DC 7 C O2 DC 7 1_555 D DG 4 D N2 DG 4 1_555 hydrog WATSON-CRICK C DT 8 C N3 DT 8 1_555 D DA 3 D N1 DA 3 1_555 hydrog WATSON-CRICK C DT 8 C O4 DT 8 1_555 D DA 3 D N6 DA 3 1_555 hydrog WATSON-CRICK C DG 9 C N1 DG 9 1_555 D DC 2 D N3 DC 2 1_555 hydrog WATSON-CRICK C DG 9 C N2 DG 9 1_555 D DC 2 D O2 DC 2 1_555 hydrog WATSON-CRICK C DG 9 C O6 DG 9 1_555 D DC 2 D N4 DC 2 1_555 hydrog WATSON-CRICK C DG 10 C N1 DG 10 1_555 D DC 1 D N3 DC 1 1_555 hydrog WATSON-CRICK C DG 10 C N2 DG 10 1_555 D DC 1 D O2 DC 1 1_555 hydrog WATSON-CRICK C DG 10 C O6 DG 10 1_555 D DC 1 D N4 DC 1 1_555 DNA CROSSLINKED DOUBLE-HELICAL DNA, BASE-PAIR OPENING, PARTIAL BASE FLIPPING., DNA 1CW9 PDB 1 1CW9 1 10 1CW9 1 10 1CW9 A 1 1 10 1 10 1CW9 1 10 1CW9 B 1 1 10 1 10 1CW9 1 10 1CW9 C 1 1 10 1 10 1CW9 1 10 1CW9 D 1 1 10 BINDING SITE FOR RESIDUE CA A 11 A CA 11 Software 7 A G47 5 A G47 5 7 1_555 A HOH 16 F HOH 7 1_555 A HOH 21 F HOH 7 1_555 A HOH 26 F HOH 7 1_555 A HOH 30 F HOH 7 1_555 B G47 5 B G47 5 7 1_555 B HOH 359 G HOH 7 1_555 19 orthorhombic P 21 21 21