0.023480 0.000000 0.000000 0.000000 0.023480 0.000000 0.000000 0.000000 0.015798 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 42.590 42.590 63.300 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 Mg 2 24.305 MAGNESIUM ION non-polymer Co H18 N6 3 161.116 COBALT HEXAMMINE(III) 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 MG N 76 N CO N 77 N N N 78 N N N 79 N N N 80 N N N 81 N N N 82 N N N 83 N H N 84 N H N 85 N H N 86 N H N 87 N H N 88 N H 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 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 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/pdb1f69/pdb pdb_00001f69 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 1999-01-27 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') 2 syn polymer 24.305 MAGNESIUM ION 1 syn non-polymer 161.116 COBALT HEXAMMINE(III) 1 syn non-polymer 18.015 water 18 nat water no no (DG)(DG)(DC)(DG)(DC)(DC) GGCGCC A,B polydeoxyribonucleotide n n n n n n 1 3.76 67.33 VAPOR DIFFUSION, SITTING DROP 6.0 MGCL2, CO(NH3)6, SPERMINE, SODIUM CACODYLATE, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K 298 MGCL2 1 CO(NH3)6 1 SPERMINE 1 SODIUM CACODYLATE 1 MGCL2 2 1.550 1 19 A 1 B 12 -0.671 A_DG1:DC12_B 1 -4.824 0.012 0.244 -0.407 3.872 1 19 A 2 B 11 -2.851 A_DG2:DC11_B 2 -1.000 0.323 0.254 -0.445 -0.524 1 19 A 3 B 10 -3.903 A_DC3:DG10_B 3 -14.341 -0.229 0.308 -0.320 1.145 1 19 A 4 B 9 -5.938 A_DG4:DC9_B 4 0.981 0.208 -0.262 -0.527 3.336 1 19 A 5 B 8 -0.854 A_DC5:DG8_B 5 -9.321 -0.223 0.108 -0.013 2.696 1 19 A 6 B 7 0.813 A_DC6:DG7_B 6 -6.631 0.643 0.109 -0.616 3.297 32.095 A A 1 2 9.767 B B 12 11 3.341 5.375 0.410 0.065 AA_DG1DG2:DC11DC12_BB 1 -0.737 1.339 31.645 -0.869 -0.877 3.562 33.943 A A 2 3 -6.541 B B 11 10 3.521 -3.809 -0.806 -0.196 AA_DG2DC3:DG10DC11_BB 2 -2.037 3.499 33.675 0.328 1.026 3.581 39.508 A A 3 4 3.390 B B 10 9 3.511 2.284 0.407 0.942 AA_DC3DG4:DC9DG10_BB 3 5.527 -8.205 39.071 1.101 0.107 3.352 31.216 A A 4 5 1.289 B B 9 8 3.333 0.692 -0.331 0.258 AA_DG4DC5:DG8DC9_BB 4 -4.231 7.886 30.928 0.345 -0.209 3.277 41.383 A A 5 6 9.109 B B 8 7 3.315 6.412 0.444 -0.109 AA_DC5DC6:DG7DG8_BB 5 1.674 -2.378 40.872 -0.850 -0.446 chem_comp_atom chem_comp_bond database_2 pdbx_struct_conn_angle struct_conn struct_site 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 _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.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _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.ptnr1_symmetry _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_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id B-DNA HEXAMER GGCGCC WITH SPERMINE A-DNA HEXAMER GGCGM5CC E-DNA HEXAMER GGCGM5CC E-DNA HEXAMER GGCGBR5CC RCSB Y RCSB 2000-06-20 REL REL MG MAGNESIUM ION NCO COBALT HEXAMMINE(III) HOH water MO6 13 2 MG MG 13 A NCO 14 3 NCO NCO 14 A HOH 15 4 HOH HOH 15 A HOH 20 4 HOH HOH 20 A HOH 22 4 HOH HOH 22 A HOH 24 4 HOH HOH 24 A HOH 25 4 HOH HOH 25 A HOH 26 4 HOH HOH 26 A MO6 13 4 HOH HOH 28 A MO6 13 4 HOH HOH 32 A HOH 16 4 HOH HOH 16 B HOH 17 4 HOH HOH 17 B HOH 18 4 HOH HOH 18 B HOH 19 4 HOH HOH 19 B HOH 21 4 HOH HOH 21 B HOH 23 4 HOH HOH 23 B MO6 13 4 HOH HOH 27 B MO6 13 4 HOH HOH 29 B MO6 13 4 HOH HOH 30 B MO6 13 4 HOH HOH 31 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 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 author_defined_assembly 2 dimeric A DG 1 A N7 DG 1 1_555 A NCO 14 D CO NCO 1_555 A NCO 14 D N1 NCO 1_555 164.8 A DG 1 A N7 DG 1 1_555 A NCO 14 D CO NCO 1_555 A NCO 14 D N2 NCO 1_555 90.5 A NCO 14 D N1 NCO 1_555 A NCO 14 D CO NCO 1_555 A NCO 14 D N2 NCO 1_555 85.0 A DG 1 A N7 DG 1 1_555 A NCO 14 D CO NCO 1_555 A DG 1 A N7 DG 1 7_554 108.7 A NCO 14 D N1 NCO 1_555 A NCO 14 D CO NCO 1_555 A DG 1 A N7 DG 1 7_554 86.4 A NCO 14 D N2 NCO 1_555 A NCO 14 D CO NCO 1_555 A DG 1 A N7 DG 1 7_554 103.4 A HOH 28 E O HOH 1_555 A MG 13 C MG MG 1_555 A HOH 32 E O HOH 1_555 89.7 A HOH 28 E O HOH 1_555 A MG 13 C MG MG 1_555 B HOH 27 F O HOH 1_555 179.6 A HOH 32 E O HOH 1_555 A MG 13 C MG MG 1_555 B HOH 27 F O HOH 1_555 89.9 A HOH 28 E O HOH 1_555 A MG 13 C MG MG 1_555 B HOH 29 F O HOH 1_555 89.8 A HOH 32 E O HOH 1_555 A MG 13 C MG MG 1_555 B HOH 29 F O HOH 1_555 90.5 B HOH 27 F O HOH 1_555 A MG 13 C MG MG 1_555 B HOH 29 F O HOH 1_555 90.3 A HOH 28 E O HOH 1_555 A MG 13 C MG MG 1_555 B HOH 30 F O HOH 1_555 90.2 A HOH 32 E O HOH 1_555 A MG 13 C MG MG 1_555 B HOH 30 F O HOH 1_555 89.8 B HOH 27 F O HOH 1_555 A MG 13 C MG MG 1_555 B HOH 30 F O HOH 1_555 89.6 B HOH 29 F O HOH 1_555 A MG 13 C MG MG 1_555 B HOH 30 F O HOH 1_555 179.7 A HOH 28 E O HOH 1_555 A MG 13 C MG MG 1_555 B HOH 31 F O HOH 1_555 90.2 A HOH 32 E O HOH 1_555 A MG 13 C MG MG 1_555 B HOH 31 F O HOH 1_555 179.8 B HOH 27 F O HOH 1_555 A MG 13 C MG MG 1_555 B HOH 31 F O HOH 1_555 90.2 B HOH 29 F O HOH 1_555 A MG 13 C MG MG 1_555 B HOH 31 F O HOH 1_555 89.7 B HOH 30 F O HOH 1_555 A MG 13 C MG MG 1_555 B HOH 31 F O HOH 1_555 90.0 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 NCO 14 D NCO 1 A HOH 15 E HOH 1 B HOH 21 F HOH 0.2790000 0.2050000 0.2136000 0.2134000 2.6 8.0 214 1938 1937 11. RANDOM 1 THROUGHOUT 2.0 MOLECULAR REPLACEMENT, REAL SPACE TRANSLATION/ROTATION/RIGID BODY SEARCH USING A CUSTOM X-PLOR 3.851 SCRIPT PARKINSON ET AL. 2.6 8.0 12 262 10 240 0 0.005 1.1 42.5 2.6 500 1F69 2026 2026 0.0 0.0 0.0610000 1 27.0 9.5 99.9 0.2510000 2.60 2.72 9.7 99.9 model building X-PLOR refinement X-PLOR 3.851 data reduction d*TREK data scaling d*TREK phasing X-PLOR CRYSTAL STRUCTURE OF THE B-DNA HEXAMER GGCGCC WITH COBALT HEXAMINE 1 N N 1 N N 2 N N 3 N N 4 N N 4 N N metalc 1.944 A DG 1 A N7 DG 1 1_555 A NCO 14 D CO NCO 1_555 metalc 1.947 A DG 1 A N7 DG 1 7_554 A NCO 14 D CO NCO 1_555 metalc 2.022 A MG 13 C MG MG 1_555 A HOH 28 E O HOH 1_555 metalc 2.017 A MG 13 C MG MG 1_555 A HOH 32 E O HOH 1_555 metalc 2.021 A MG 13 C MG MG 1_555 B HOH 27 F O HOH 1_555 metalc 2.025 A MG 13 C MG MG 1_555 B HOH 29 F O HOH 1_555 metalc 2.012 A MG 13 C MG MG 1_555 B HOH 30 F O HOH 1_555 metalc 2.012 A MG 13 C MG MG 1_555 B HOH 31 F O HOH 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 DC 11 B N3 DC 5 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 11 B O2 DC 5 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 11 B N4 DC 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 DC 5 A N3 DC 5 1_555 B DG 8 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 B DG 8 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 5 A O2 DC 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 B-DNA, E-DNA, DOUBLE HELIX, DNA 1F69 PDB 1 1F69 1 6 1F69 1 6 1F69 A 1 1 6 7 12 1F69 7 12 1F69 B 1 1 6 BINDING SITE FOR RESIDUE MG A 13 A MG 13 Software 7 BINDING SITE FOR RESIDUE NCO A 14 A NCO 14 Software 4 A DG 4 A DG 4 7 1_555 A HOH 28 E HOH 7 1_555 A HOH 32 E HOH 7 1_555 B HOH 27 F HOH 7 1_555 B HOH 29 F HOH 7 1_555 B HOH 30 F HOH 7 1_555 B HOH 31 F HOH 7 1_555 A DG 1 A DG 1 4 7_554 A DG 1 A DG 1 4 1_555 A DG 2 A DG 2 4 1_555 B DC 11 B DC 5 4 1_555 91 tetragonal P 41 2 2