0.016556 0.000000 0.000000 0.000000 0.016556 0.000000 0.000000 0.000000 0.040479 0.00000 0.00000 0.00000 Vargason, J.M. Eichman, B.F. Ho, P.S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 16 90.00 90.00 90.00 60.400 60.400 24.704 C9 H13 Br N3 O7 P 386.093 n 5-BROMO-2'-DEOXY-CYTIDINE-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 H2 O 18.015 WATER non-polymer N 1 N BR N 2 N P N 3 N O N 4 N O N 5 N O N 6 N N N 7 N C N 8 N C N 9 N O N 10 N N N 11 N C N 12 N N N 13 N C N 14 N C N 15 N C N 16 R C N 17 N O N 18 R C N 19 S C N 20 N O N 21 N O 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 N 47 N N N 48 N C N 49 N O N 50 N N N 51 N C N 52 N N N 53 N C N 54 N C N 55 N H N 56 N H N 57 N H 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 O N 70 N P N 71 N O N 72 N O N 73 N O N 74 N C N 75 R C N 76 N O N 77 S C N 78 N O N 79 N C N 80 R C Y 81 N N Y 82 N C Y 83 N N Y 84 N C N 85 N C N 86 N O N 87 N N N 88 N C N 89 N N N 90 N N Y 91 N C 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 O N 107 N H N 108 N H N 1 N sing N 2 N doub N 3 N sing 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 doub N 12 N sing N 13 N doub N 14 N sing N 15 N doub 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 sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N sing 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 N 59 N sing N 60 N sing N 61 N doub N 62 N sing N 63 N doub N 64 N sing N 65 N sing N 66 N sing N 67 N sing N 68 N doub N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N doub 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 Y 94 N sing Y 95 N sing Y 96 N doub N 97 N sing Y 98 N sing N 99 N sing Y 100 N doub N 101 N doub N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N doub N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 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/pdb1f6j/pdb pdb_00001f6j 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 1999-03-05 RIGAKU RAXIS IV SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU RU300 1889.101 DNA (5'-D(*GP*GP*CP*GP*(CBR)P*C)-3') 2 syn polymer 18.015 water 28 nat water no yes (DG)(DG)(DC)(DG)(CBR)(DC) GGCGCC A,B polydeoxyribonucleotide n n n n n n 1 2.95 58.37 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 -4.408 1 19 A 1 B 12 3.260 A_DG1:DC12_B 1 5.668 -0.471 0.229 -0.230 -2.126 1 19 A 2 B 11 5.060 A_DG2:CBR11_B 2 -8.479 -0.297 -0.018 -0.255 -0.340 1 19 A 3 B 10 4.883 A_DC3:DG10_B 3 0.916 0.022 -0.101 -0.222 -7.327 1 19 A 4 B 9 8.181 A_DG4:DC9_B 4 -7.305 -0.685 -0.075 -0.018 -2.194 1 19 A 5 B 8 2.770 A_CBR5:DG8_B 5 -11.728 0.216 0.156 -0.237 7.425 1 19 A 6 B 7 2.396 A_DC6:DG7_B 6 -7.452 0.570 -0.133 -0.418 2.952 32.849 A A 1 2 10.298 B B 12 11 3.314 5.793 -0.197 -1.762 AA_DG1DG2:CBR11DC12_BB 1 1.314 -2.335 32.322 -4.075 0.566 3.230 32.722 A A 2 3 2.552 B B 11 10 3.316 1.437 0.636 -1.970 AA_DG2DC3:DG10CBR11_BB 2 0.080 -0.143 32.691 -3.745 -1.115 3.854 22.802 A A 3 4 -5.579 B B 10 9 3.661 -2.202 -0.229 -2.176 AA_DC3DG4:DC9DG10_BB 3 -0.278 0.704 22.695 -4.596 0.466 3.404 36.627 A A 4 5 0.453 B B 9 8 3.311 0.284 -1.323 -1.990 AA_DG4CBR5:DG8DC9_BB 4 -3.524 5.616 36.462 -3.207 1.607 2.618 28.721 A A 5 6 13.504 B B 8 7 3.014 6.609 0.708 -1.744 AA_CBR5DC6:DG7DG8_BB 5 4.865 -9.941 27.547 -4.823 -0.465 chem_comp_atom chem_comp_bond database_2 struct_conn repository Initial release Version format compliance Version format compliance 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 B-DNA HEXAMER GGCGCC WITH COBALT HEXAMINE B-DNA HEXAMER GGCGCC WITH SPERMINE A-DNA HEXAMER GGCGM5CC E-DNA HEXAMER GGCGM5CC NDB Y NDB 2000-06-21 REL REL HOH water HOH 23 2 HOH HOH 23 A HOH 24 2 HOH HOH 24 A HOH 26 2 HOH HOH 26 A HOH 35 2 HOH HOH 35 A HOH 38 2 HOH HOH 38 A HOH 40 2 HOH HOH 40 A HOH 13 2 HOH HOH 13 B HOH 14 2 HOH HOH 14 B HOH 15 2 HOH HOH 15 B HOH 16 2 HOH HOH 16 B HOH 17 2 HOH HOH 17 B HOH 18 2 HOH HOH 18 B HOH 19 2 HOH HOH 19 B HOH 20 2 HOH HOH 20 B HOH 21 2 HOH HOH 21 B HOH 22 2 HOH HOH 22 B HOH 25 2 HOH HOH 25 B HOH 27 2 HOH HOH 27 B HOH 28 2 HOH HOH 28 B HOH 29 2 HOH HOH 29 B HOH 30 2 HOH HOH 30 B HOH 31 2 HOH HOH 31 B HOH 32 2 HOH HOH 32 B HOH 33 2 HOH HOH 33 B HOH 34 2 HOH HOH 34 B HOH 36 2 HOH HOH 36 B HOH 37 2 HOH HOH 37 B HOH 39 2 HOH HOH 39 B 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 BRO 5 n 5 CBR 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 BRO 11 n 5 CBR 11 B C 12 n 6 DC 12 B author_defined_assembly 2 dimeric A CBR 5 A CBR 5 DC B CBR 11 B CBR 5 DC 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 0.256 0.193 0.2 0.2 2.25 8.0 226 2324 2324 9.7 RANDOM 1 THROUGHOUT 0.0 0.0 MOLECULAR REPLACEMENT PARKINSON ET AL. 2.25 8.0 28 270 2 240 0 0.004 0.9 36.3 2.25 500 1F6J 2393 2393 0.0 0.0 0.05 1 39.3 12.9 99.9 0.347 2.25 2.33 12.0 99.9 phasing AMoRE refinement X-PLOR 3.851 data reduction d*TREK data scaling d*TREK CRYSTAL STRUCTURE OF THE E-DNA HEXAMER GGCGBR5CC 1 N N 1 N N 2 N N 2 N N covale 1.605 both A DG 4 A O3' DG 4 1_555 A CBR 5 A P CBR 5 1_555 covale 1.604 both A CBR 5 A O3' CBR 5 1_555 A DC 6 A P DC 6 1_555 covale 1.603 both B DG 10 B O3' DG 4 1_555 B CBR 11 B P CBR 5 1_555 covale 1.597 both B CBR 11 B O3' CBR 5 1_555 B DC 12 B P DC 6 1_555 hydrog WATSON-CRICK A DG 1 A N1 DG 1 1_555 B DC 12 B N3 DC 6 1_555 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 B DC 12 B O2 DC 6 1_555 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 B DC 12 B N4 DC 6 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B CBR 11 B N3 CBR 5 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B CBR 11 B O2 CBR 5 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B CBR 11 B N4 CBR 5 1_555 hydrog WATSON-CRICK A DC 3 A N3 DC 3 1_555 B DG 10 B N1 DG 4 1_555 hydrog WATSON-CRICK A DC 3 A N4 DC 3 1_555 B DG 10 B O6 DG 4 1_555 hydrog WATSON-CRICK A DC 3 A O2 DC 3 1_555 B DG 10 B N2 DG 4 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B DC 9 B N3 DC 3 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 9 B O2 DC 3 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B DC 9 B N4 DC 3 1_555 hydrog WATSON-CRICK A CBR 5 A N3 CBR 5 1_555 B DG 8 B N1 DG 2 1_555 hydrog WATSON-CRICK A CBR 5 A N4 CBR 5 1_555 B DG 8 B O6 DG 2 1_555 hydrog WATSON-CRICK A CBR 5 A O2 CBR 5 1_555 B DG 8 B N2 DG 2 1_555 hydrog WATSON-CRICK A DC 6 A N3 DC 6 1_555 B DG 7 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 6 A N4 DC 6 1_555 B DG 7 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 6 A O2 DC 6 1_555 B DG 7 B N2 DG 1 1_555 DNA E-DNA, DOUBLE HELIX, METHYLATION, DNA 1F6J PDB 1 1F6J 1 6 1F6J 1 6 1F6J A 1 1 6 7 12 1F6J 7 12 1F6J B 1 1 6 96 tetragonal P 43 21 2