0.013986 0.000000 0.000000 0.000000 0.013986 0.000000 0.000000 0.000000 0.016770 0.00000 0.00000 0.00000 Vargason, J.M. Eichman, B.F. Ho, P.S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 40 90.00 90.00 90.00 71.500 71.500 59.630 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 H2 O 18.015 WATER non-polymer C10 H26 N4 202.340 SPERMINE non-polymer N 1 N O N 2 N P N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 S C N 10 N O N 11 N C N 12 R C N 13 N N N 14 N C N 15 N O N 16 N N N 17 N C N 18 N N N 19 N C N 20 N C N 21 N H N 22 N H N 23 N H 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 O N 36 N P N 37 N O N 38 N O N 39 N O N 40 N C N 41 R C N 42 N O N 43 S C N 44 N O N 45 N C N 46 R C Y 47 N N Y 48 N C Y 49 N N Y 50 N C N 51 N C N 52 N O N 53 N N N 54 N C N 55 N N N 56 N N Y 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 H N 74 N H N 75 N N N 76 N C N 77 N C N 78 N C N 79 N N N 80 N C N 81 N C N 82 N C N 83 N C N 84 N N N 85 N C N 86 N C N 87 N C N 88 N N N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N H 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 H N 110 N H N 111 N H N 112 N H N 113 N H N 114 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 N 24 N sing N 25 N sing N 26 N doub N 27 N sing N 28 N doub N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N doub N 39 N sing N 40 N sing N 41 N sing 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 Y 59 N sing Y 60 N sing Y 61 N doub N 62 N sing Y 63 N sing N 64 N sing Y 65 N doub 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 sing 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 N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing US Nat.Struct.Biol. NSBIEW 2024 1072-8368 7 758 761 10.1038/78985 10966645 The extended and eccentric E-DNA structure induced by cytosine methylation or bromination. 2000 10.2210/pdb1f6c/pdb pdb_00001f6c 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 298 1 IMAGE PLATE 1998-10-30 RIGAKU RAXIS IV SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU RU300 1810.205 DNA (5'-D(*GP*GP*CP*GP*CP*C)-3') 5 syn polymer 202.340 SPERMINE 2 syn non-polymer 18.015 water 16 nat water no no (DG)(DG)(DC)(DG)(DC)(DC) GGCGCC A,B,C,D,E polydeoxyribonucleotide n n n n n n 1 4.00 69.23 VAPOR DIFFUSION, SITTING DROP 6.0 MGCL2, SPERMINE, SODIUM CACODYLATE, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K 298 SODIUM CACODYLATE 1 SPERMINE 1 MGCL2 1 MGCL2 2 1.543 1 19 B 7 C 18 -1.820 B_DG7:DC18_C 1 -4.144 0.076 0.163 -0.138 -0.211 1 19 B 8 C 17 -1.725 B_DG8:DC17_C 2 -4.869 0.582 0.108 -0.186 1.601 1 19 B 9 C 16 4.576 B_DC9:DG16_C 3 -5.984 0.457 0.093 -0.447 -2.533 1 19 B 10 C 15 3.918 B_DG10:DC15_C 4 -11.745 0.461 -0.342 -0.514 -4.650 1 19 B 11 C 14 -4.387 B_DC11:DG14_C 5 -4.573 -0.299 0.186 -0.534 -1.597 1 19 B 12 C 13 0.300 B_DC12:DG13_C 6 2.752 -0.232 0.176 -0.332 1.794 1 19 E 25 D 24 -0.573 E_DG25:DC24_D 7 -5.826 -0.962 0.255 -0.640 5.111 1 19 E 26 D 23 -2.208 E_DG26:DC23_D 8 2.409 -0.614 0.247 -0.183 2.526 1 19 E 27 D 22 -6.676 E_DC27:DG22_D 9 -8.369 0.290 0.085 -0.209 -5.506 1 19 E 28 D 21 -6.549 E_DG28:DC21_D 10 -4.485 1.026 0.103 -0.420 1.558 1 19 E 29 D 20 1.474 E_DC29:DG20_D 11 -2.965 0.819 0.232 -0.673 -6.280 1 19 E 30 D 19 4.322 E_DC30:DG19_D 12 -3.817 0.747 0.335 -0.590 1.108 1 19 A 1 A 6 -3.407 A_DG1:DC6_A 13 5.423 -0.423 -0.156 -0.470 -9.666 1 19 A 2 A 5 -1.629 A_DG2:DC5_A 14 -7.442 0.175 -0.291 -0.418 0.180 1 19 A 3 A 4 2.339 A_DC3:DG4_A 15 -7.389 0.434 -0.184 -0.315 -0.180 1 19 A 4 A 3 2.339 A_DG4:DC3_A 16 -7.389 -0.434 -0.184 -0.315 9.666 1 19 A 5 A 2 -1.629 A_DC5:DG2_A 17 -7.442 -0.175 -0.291 -0.418 -1.108 1 19 A 6 A 1 -3.407 A_DC6:DG1_A 18 5.423 0.423 -0.156 -0.470 3.566 35.037 B B 7 8 -2.187 C C 18 17 3.562 -1.316 -0.393 -0.313 BB_DG7DG8:DC17DC18_CC 1 0.380 -0.631 35.011 -0.304 0.715 3.317 36.537 B B 8 9 5.189 C C 17 16 3.266 3.245 1.057 -0.209 BB_DG8DC9:DG16DC17_CC 2 3.348 -5.354 36.249 -0.785 -1.220 3.507 32.505 B B 9 10 13.488 C C 16 15 3.510 7.482 -0.671 0.578 BB_DC9DG10:DC15DG16_CC 3 1.867 -3.366 31.601 -0.393 1.554 3.364 32.801 B B 10 11 5.512 C C 15 14 3.365 3.090 -0.502 -0.234 BB_DG10DC11:DG14DC15_CC 4 -6.285 11.212 32.064 -0.967 -0.235 3.203 34.468 B B 11 12 5.638 C C 14 13 3.261 3.336 0.866 -0.237 BB_DC11DC12:DG13DG14_CC 5 -0.836 1.413 34.301 -0.913 -1.590 3.389 -27.230 B E 12 25 -1.310 C D 13 24 3.392 0.616 -0.186 0.290 BE_DC12DG25:DC24DG13_DC 6 1.783 3.791 -27.166 -0.776 0.069 3.486 32.560 E E 25 26 -2.783 D D 24 23 3.416 -1.558 -0.622 -0.796 EE_DG25DG26:DC23DC24_DD 7 -2.406 4.296 32.437 -1.132 0.667 3.372 41.424 E E 26 27 3.453 D D 23 22 3.390 2.440 0.335 -0.481 EE_DG26DC27:DG22DC23_DD 8 2.699 -3.820 41.271 -0.950 -0.175 3.606 39.752 E E 27 28 5.899 D D 22 21 3.535 4.005 -0.113 0.886 EE_DC27DG28:DC21DG22_DD 9 -0.448 0.661 39.556 0.794 0.109 3.353 30.732 E E 28 29 -0.862 D D 21 20 3.335 -0.457 0.706 -1.253 EE_DG28DC29:DG20DC21_DD 10 -0.018 0.033 30.729 -2.273 -1.335 3.526 35.038 E E 29 30 2.181 D D 20 19 3.502 1.312 0.848 -0.160 EE_DC29DC30:DG19DG20_DD 11 1.482 -2.462 34.984 -0.478 -1.169 3.766 34.272 A A 1 2 1.935 A A 6 5 3.798 1.140 -0.552 -0.455 AA_DG1DG2:DC5DC6_AA 12 0.916 -1.555 34.241 -0.979 1.104 3.003 33.328 A A 2 3 8.762 A A 5 4 3.068 5.007 -0.598 -0.319 AA_DG2DC3:DG4DC5_AA 13 -0.873 1.528 32.949 -1.334 0.908 3.360 28.710 A A 3 4 18.073 A A 4 3 3.479 8.823 0.000 0.142 AA_DC3DG4:DC3DG4_AA 14 0.000 0.000 27.348 -1.842 0.000 3.003 33.328 A A 4 5 8.762 A A 3 2 3.068 5.007 0.598 -0.319 AA_DG4DC5:DG2DC3_AA 15 0.873 -1.528 32.949 -1.334 -0.908 3.766 34.272 A A 5 6 1.935 A A 2 1 3.798 1.140 0.552 -0.455 AA_DC5DC6:DG1DG2_AA 16 -0.916 1.555 34.241 -0.979 -1.104 chem_comp_atom chem_comp_bond database_2 pdbx_unobs_or_zero_occ_atoms struct_conn struct_site repository Initial release Version format compliance Version format compliance Advisory Data collection Database references Derived calculations 1 0 2000-08-28 1 1 2008-04-27 1 2 2011-07-13 1 3 2024-02-07 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id B-DNA HEXAMER GGCGCC WITH COBALT HEXAMINE A-DNA HEXAMER GGCGM5CC E-DNA HEXAMER GGCGM5CC E-DNA HEXAMER GGCGBR5CC NDB Y NDB 2000-06-21 REL REL SPM SPERMINE HOH water SPM 32 2 SPM SPM 32 B SPM 31 2 SPM SPM 31 D HOH 34 3 HOH HOH 34 A HOH 36 3 HOH HOH 36 A HOH 38 3 HOH HOH 38 A HOH 39 3 HOH HOH 39 A HOH 33 3 HOH HOH 33 B HOH 42 3 HOH HOH 42 B HOH 44 3 HOH HOH 44 B HOH 35 3 HOH HOH 35 C HOH 37 3 HOH HOH 37 C HOH 40 3 HOH HOH 40 C HOH 41 3 HOH HOH 41 C HOH 43 3 HOH HOH 43 C HOH 45 3 HOH HOH 45 C HOH 46 3 HOH HOH 46 C HOH 47 3 HOH HOH 47 C HOH 48 3 HOH HOH 48 C G 1 n 1 DG 1 A G 2 n 2 DG 2 A C 3 n 3 DC 3 A G 4 n 4 DG 4 A C 5 n 5 DC 5 A C 6 n 6 DC 6 A G 7 n 1 DG 7 B G 8 n 2 DG 8 B C 9 n 3 DC 9 B G 10 n 4 DG 10 B C 11 n 5 DC 11 B C 12 n 6 DC 12 B G 13 n 1 DG 13 C G 14 n 2 DG 14 C C 15 n 3 DC 15 C G 16 n 4 DG 16 C C 17 n 5 DC 17 C C 18 n 6 DC 18 C G 19 n 1 DG 19 D G 20 n 2 DG 20 D C 21 n 3 DC 21 D G 22 n 4 DG 22 D C 23 n 5 DC 23 D C 24 n 6 DC 24 D G 25 n 1 DG 25 E G 26 n 2 DG 26 E C 27 n 3 DC 27 E G 28 n 4 DG 28 E C 29 n 5 DC 29 E C 30 n 6 DC 30 E author_defined_assembly 2 dimeric author_defined_assembly 2 dimeric author_defined_assembly 2 dimeric 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 0.0000000000 1.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 7_556 y,x,-z+1 crystal symmetry operation 0.0000000000 0.0000000000 59.6300000000 -9.9024 0.0000 0.0000 -9.9024 0.0000 19.8048 ANISOTROPIC B VALUES WERE APPLIED TO FCALC DURING REFINEMENT IN ORDER TO SCALE FCALC TO FOBS 0.2880000 0.2260000 0.2330000 0.2320000 2.7 8.0 447 4316 4304 10.4 RANDOM 1 THROUGHOUT 2.0 MOLECULAR REPLACEMENT PARKINSON ET AL. 2.7 8.0 16 637 21 600 0 0.006 1.0 12.0 2.7 500 1F6C 4526 4526 0.0 0.0 0.0570000 1 18.7 7.0 98.8 0.3950000 2.7 2.82 6.8 96.7 phasing AMoRE refinement X-PLOR 3.851 data reduction d*TREK data scaling d*TREK CRYSTAL STRUCTURE OF THE B-DNA HEXAMER GGCGCC WITH SPERMINE 1 N N 1 N N 1 N N 1 N N 1 N N 2 N N 2 N N 3 N N 3 N N 3 N N covale 1.571 none B SPM 32 F C7 SPM 1_555 B SPM 32 F C7 SPM 7_466 hydrog WATSON-CRICK B DG 7 B N1 DG 1 1_555 C DC 18 C N3 DC 6 1_555 hydrog WATSON-CRICK B DG 7 B N2 DG 1 1_555 C DC 18 C O2 DC 6 1_555 hydrog WATSON-CRICK B DG 7 B O6 DG 1 1_555 C DC 18 C N4 DC 6 1_555 hydrog WATSON-CRICK B DG 8 B N1 DG 2 1_555 C DC 17 C N3 DC 5 1_555 hydrog WATSON-CRICK B DG 8 B N2 DG 2 1_555 C DC 17 C O2 DC 5 1_555 hydrog WATSON-CRICK B DG 8 B O6 DG 2 1_555 C DC 17 C N4 DC 5 1_555 hydrog WATSON-CRICK B DC 9 B N3 DC 3 1_555 C DG 16 C N1 DG 4 1_555 hydrog WATSON-CRICK B DC 9 B N4 DC 3 1_555 C DG 16 C O6 DG 4 1_555 hydrog WATSON-CRICK B DC 9 B O2 DC 3 1_555 C DG 16 C N2 DG 4 1_555 hydrog WATSON-CRICK B DG 10 B N1 DG 4 1_555 C DC 15 C N3 DC 3 1_555 hydrog WATSON-CRICK B DG 10 B N2 DG 4 1_555 C DC 15 C O2 DC 3 1_555 hydrog WATSON-CRICK B DG 10 B O6 DG 4 1_555 C DC 15 C N4 DC 3 1_555 hydrog WATSON-CRICK B DC 11 B N3 DC 5 1_555 C DG 14 C N1 DG 2 1_555 hydrog WATSON-CRICK B DC 11 B N4 DC 5 1_555 C DG 14 C O6 DG 2 1_555 hydrog WATSON-CRICK B DC 11 B O2 DC 5 1_555 C DG 14 C N2 DG 2 1_555 hydrog WATSON-CRICK B DC 12 B N3 DC 6 1_555 C DG 13 C N1 DG 1 1_555 hydrog WATSON-CRICK B DC 12 B N4 DC 6 1_555 C DG 13 C O6 DG 1 1_555 hydrog WATSON-CRICK B DC 12 B O2 DC 6 1_555 C DG 13 C N2 DG 1 1_555 hydrog WATSON-CRICK D DG 19 D N1 DG 1 1_555 E DC 30 E N3 DC 6 1_555 hydrog WATSON-CRICK D DG 19 D N2 DG 1 1_555 E DC 30 E O2 DC 6 1_555 hydrog WATSON-CRICK D DG 19 D O6 DG 1 1_555 E DC 30 E N4 DC 6 1_555 hydrog WATSON-CRICK D DG 20 D N1 DG 2 1_555 E DC 29 E N3 DC 5 1_555 hydrog WATSON-CRICK D DG 20 D N2 DG 2 1_555 E DC 29 E O2 DC 5 1_555 hydrog WATSON-CRICK D DG 20 D O6 DG 2 1_555 E DC 29 E N4 DC 5 1_555 hydrog WATSON-CRICK D DC 21 D N3 DC 3 1_555 E DG 28 E N1 DG 4 1_555 hydrog WATSON-CRICK D DC 21 D N4 DC 3 1_555 E DG 28 E O6 DG 4 1_555 hydrog WATSON-CRICK D DC 21 D O2 DC 3 1_555 E DG 28 E N2 DG 4 1_555 hydrog WATSON-CRICK D DG 22 D N1 DG 4 1_555 E DC 27 E N3 DC 3 1_555 hydrog WATSON-CRICK D DG 22 D N2 DG 4 1_555 E DC 27 E O2 DC 3 1_555 hydrog WATSON-CRICK D DG 22 D O6 DG 4 1_555 E DC 27 E N4 DC 3 1_555 hydrog WATSON-CRICK D DC 23 D N3 DC 5 1_555 E DG 26 E N1 DG 2 1_555 hydrog WATSON-CRICK D DC 23 D N4 DC 5 1_555 E DG 26 E O6 DG 2 1_555 hydrog WATSON-CRICK D DC 23 D O2 DC 5 1_555 E DG 26 E N2 DG 2 1_555 hydrog WATSON-CRICK D DC 24 D N3 DC 6 1_555 E DG 25 E N1 DG 1 1_555 hydrog WATSON-CRICK D DC 24 D N4 DC 6 1_555 E DG 25 E O6 DG 1 1_555 hydrog WATSON-CRICK D DC 24 D O2 DC 6 1_555 E DG 25 E N2 DG 1 1_555 hydrog WATSON-CRICK A DG 1 A N1 DG 1 1_555 A DC 6 A N3 DC 6 7_556 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 A DC 6 A O2 DC 6 7_556 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 A DC 6 A N4 DC 6 7_556 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 A DC 5 A N3 DC 5 7_556 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 A DC 5 A O2 DC 5 7_556 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 A DC 5 A N4 DC 5 7_556 hydrog WATSON-CRICK A DC 3 A N3 DC 3 1_555 A DG 4 A N1 DG 4 7_556 hydrog WATSON-CRICK A DC 3 A N4 DC 3 1_555 A DG 4 A O6 DG 4 7_556 hydrog WATSON-CRICK A DC 3 A O2 DC 3 1_555 A DG 4 A N2 DG 4 7_556 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 A DC 3 A N3 DC 3 7_556 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 A DC 3 A O2 DC 3 7_556 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 A DC 3 A N4 DC 3 7_556 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 A DG 2 A N1 DG 2 7_556 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 A DG 2 A O6 DG 2 7_556 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 A DG 2 A N2 DG 2 7_556 hydrog WATSON-CRICK A DC 6 A N3 DC 6 1_555 A DG 1 A N1 DG 1 7_556 hydrog WATSON-CRICK A DC 6 A N4 DC 6 1_555 A DG 1 A O6 DG 1 7_556 hydrog WATSON-CRICK A DC 6 A O2 DC 6 1_555 A DG 1 A N2 DG 1 7_556 DNA B-DNA, E-DNA, DOUBLE HELIX, DNA 1F6C PDB 1 1F6C 1 6 1F6C 1 6 1F6C A 1 1 6 7 12 1F6C 7 12 1F6C B 1 1 6 13 18 1F6C 13 18 1F6C C 1 1 6 19 24 1F6C 19 24 1F6C D 1 1 6 25 30 1F6C 25 30 1F6C E 1 1 6 BINDING SITE FOR RESIDUE SPM D 31 D SPM 31 Software 11 BINDING SITE FOR RESIDUE SPM B 32 B SPM 32 Software 8 A DG 1 A DG 1 11 7_556 A DG 2 A DG 2 11 7_556 A DC 3 A DC 3 11 1_555 A DC 3 A DC 3 11 7_556 A DG 4 A DG 4 11 1_555 A HOH 34 H HOH 11 1_555 B DG 7 B DG 1 11 4_454 B DG 8 B DG 2 11 4_454 D DG 19 D DG 1 11 1_555 E DC 29 E DC 5 11 1_555 E DC 30 E DC 6 11 1_555 A DC 3 A DC 3 8 3_555 A DG 4 A DG 4 8 3_555 B DG 7 B DG 1 8 7_466 B DG 7 B DG 1 8 1_555 B DG 8 B DG 2 8 1_555 B DC 9 B DC 3 8 1_555 B HOH 44 I HOH 8 1_555 C DG 16 C DG 4 8 1_555 92 tetragonal P 41 21 2