0.045192 0.000000 0.000000 0.000000 0.016888 0.000000 0.000000 0.000000 0.021842 0.00000 0.00000 0.00000 Thorpe, J.H. Teixeira, S.C.M. Gale, B.C. Cardin, C.J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 16 90.00 90.00 90.00 22.128 59.215 45.784 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 H2 O 18.015 WATER 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 Y 13 N N Y 14 N C Y 15 N N Y 16 N C Y 17 N C N 18 N N Y 19 N N Y 20 N C Y 21 N N Y 22 N C 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 H N 36 N H N 37 N O N 38 N P N 39 N O N 40 N O N 41 N O N 42 N C N 43 R C N 44 N O N 45 S C N 46 N O N 47 N C N 48 R C N 49 N N N 50 N C N 51 N O N 52 N N N 53 N C N 54 N N N 55 N C N 56 N C 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 H N 70 N H N 71 N O N 72 N P N 73 N O N 74 N O N 75 N O N 76 N C N 77 R C N 78 N O N 79 S C N 80 N O N 81 N C N 82 R C Y 83 N N Y 84 N C Y 85 N N Y 86 N C N 87 N C N 88 N O N 89 N N N 90 N C N 91 N N N 92 N N Y 93 N C 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 O N 109 N P N 110 N O N 111 N O N 112 N O N 113 N C N 114 R C N 115 N O N 116 S C N 117 N O N 118 N C N 119 R C N 120 N N N 121 N C N 122 N O N 123 N N N 124 N C N 125 N O N 126 N C N 127 N C N 128 N C N 129 N H 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 O N 145 N H N 146 N H N 147 N CO N 148 N N N 149 N N N 150 N N N 151 N N N 152 N N N 153 N N N 154 N H N 155 N H N 156 N H N 157 N H N 158 N H N 159 N H N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N H N 169 N H N 170 N H N 171 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 sing 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 N 173 N sing N 174 N sing N 175 N sing UK Nucleic Acids Res. NARHAD 0389 0305-1048 31 844 849 10.1093/nar/gkg168 12560479 Crystal structure of the complementary quadruplex formed by d(GCATGCT) at atomic resolution 2003 10.2210/pdb1mf5/pdb pdb_00001mf5 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 100 1 CCD 2002-05-19 MARRESEARCH SINGLE WAVELENGTH M x-ray 1 0.811 1.0 X11 EMBL/DESY, HAMBURG 0.811 0.811 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 2113.410 5'-D(*GP*CP*AP*TP*GP*CP*T)-3' 2 syn polymer 161.116 COBALT HEXAMMINE(III) 1 syn non-polymer 18.015 water 38 nat water no no (DG)(DC)(DA)(DT)(DG)(DC)(DT) GCATGCT A,B polydeoxyribonucleotide n n n n n n n 1 1.77 30.67 VAPOR DIFFUSION, SITTING DROP 6.6 Cobalt Hexammine, Cacodylate, MPD, NaCl, KCl, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K 293 Cobalt Hexammine 1 Cacodylate 1 MPD 1 NaCl 1 KCl 1 -2.155 A 1 A 6 176.744 A_DG1:DC6_A 1 40.830 -3.252 -0.379 8.800 11.055 A 2 A 5 176.174 A_DC2:DG5_A 2 36.495 3.258 -0.286 8.403 -11.727 B 8 B 13 173.995 B_DG8:DC13_B 3 32.550 -2.907 -0.458 8.518 9.392 B 9 B 12 176.510 B_DC9:DG12_B 4 34.642 3.791 -0.003 8.222 2.837 29.282 A A 1 2 14.254 A A 6 5 2.822 7.136 0.268 0.421 AA_DG1DC2:DG5DC6_AA 1 -0.363 0.726 28.416 -0.522 -0.598 3.045 32.521 B B 8 9 9.059 B B 13 12 3.028 5.050 0.149 0.453 BB_DG8DC9:DG12DC13_BB 2 -2.237 4.014 32.061 -0.017 -0.631 chem_comp_atom chem_comp_bond database_2 diffrn_source struct_site pdbx_initial_refinement_model repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Refinement description 1 0 2003-02-11 1 1 2008-04-28 1 2 2011-07-13 1 3 2024-02-14 1 4 2024-04-03 _database_2.pdbx_DOI _database_2.pdbx_database_accession _diffrn_source.pdbx_synchrotron_site _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id GCATGCT With Different Ion Content RCSB Y RCSB 2002-08-09 REL REL NCO COBALT HEXAMMINE(III) HOH water 184D UDG028 PDB experimental model NCO 15 2 NCO NCO 15 B HOH 101 3 HOH HOH 101 A HOH 102 3 HOH HOH 102 A HOH 106 3 HOH HOH 106 A HOH 107 3 HOH HOH 107 A HOH 110 3 HOH HOH 110 A HOH 116 3 HOH HOH 116 A HOH 119 3 HOH HOH 119 A HOH 126 3 HOH HOH 126 A HOH 127 3 HOH HOH 127 A HOH 129 3 HOH HOH 129 A HOH 130 3 HOH HOH 130 A HOH 131 3 HOH HOH 131 A HOH 132 3 HOH HOH 132 A HOH 134 3 HOH HOH 134 A HOH 135 3 HOH HOH 135 A HOH 137 3 HOH HOH 137 A HOH 100 3 HOH HOH 100 B HOH 103 3 HOH HOH 103 B HOH 104 3 HOH HOH 104 B HOH 105 3 HOH HOH 105 B HOH 108 3 HOH HOH 108 B HOH 109 3 HOH HOH 109 B HOH 111 3 HOH HOH 111 B HOH 112 3 HOH HOH 112 B HOH 113 3 HOH HOH 113 B HOH 114 3 HOH HOH 114 B HOH 115 3 HOH HOH 115 B HOH 117 3 HOH HOH 117 B HOH 118 3 HOH HOH 118 B HOH 120 3 HOH HOH 120 B HOH 121 3 HOH HOH 121 B HOH 122 3 HOH HOH 122 B HOH 123 3 HOH HOH 123 B HOH 124 3 HOH HOH 124 B HOH 125 3 HOH HOH 125 B HOH 128 3 HOH HOH 128 B HOH 133 3 HOH HOH 133 B HOH 136 3 HOH HOH 136 B G 1 n 1 DG 1 A C 2 n 2 DC 2 A A 3 n 3 DA 3 A T 4 n 4 DT 4 A G 5 n 5 DG 5 A C 6 n 6 DC 6 A T 7 n 7 DT 7 A G 8 n 1 DG 8 B C 9 n 2 DC 9 B A 10 n 3 DA 10 B T 11 n 4 DT 11 B G 12 n 5 DG 12 B C 13 n 6 DC 13 B T 14 n 7 DT 14 B 0.2164 0.2163 0.2126 0.2126 0.2295 0.224 563 625 4.49 4.99 11296 author_defined_assembly 4 tetrameric 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 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 3_654 -x+1,y,-z-1/2 crystal symmetry operation 22.1280000000 0.0000000000 -22.8920000000 1 A HOH 126 D HOH 1 B HOH 128 E HOH 1 -4.96 0.70 108.00 103.04 A A A O4' C1' N9 DG DG DG 1 1 1 N 1 4.04 0.60 118.90 122.94 A A A N1 C2 O2 DC DC DC 2 2 2 N 1 3.68 0.60 106.00 109.68 A A A O4' C4' C3' DA DA DA 3 3 3 N 1 -3.35 0.50 129.30 125.95 A A A N1 C2 N3 DA DA DA 3 3 3 N 1 3.45 0.50 110.60 114.05 A A A C2 N3 C4 DA DA DA 3 3 3 N 1 -5.20 0.80 102.40 97.20 A A A C3' C2' C1' DT DT DT 4 4 4 N 1 3.66 0.60 119.00 122.66 A A A C4 C5 C7 DT DT DT 4 4 4 N 1 -5.21 0.80 109.40 104.19 A A A O5' C5' C4' DG DG DG 5 5 5 N 1 -5.05 0.70 108.00 102.95 A A A O4' C1' N1 DC DC DC 6 6 6 N 1 4.39 0.30 108.30 112.69 A A A O4' C1' N1 DT DT DT 7 7 7 N 1 -5.15 0.80 123.10 117.95 A A A N1 C2 O2 DT DT DT 7 7 7 N 1 -5.70 0.70 108.00 102.30 B B B O4' C1' N9 DG DG DG 8 8 8 N 1 -3.37 0.50 117.40 114.03 B B B C4 C5 C6 DC DC DC 9 9 9 N 1 4.10 0.50 121.00 125.10 B B B C5 C6 N1 DC DC DC 9 9 9 N 1 -3.46 0.50 129.30 125.84 B B B N1 C2 N3 DA DA DA 10 10 10 N 1 3.17 0.50 110.60 113.77 B B B C2 N3 C4 DA DA DA 10 10 10 N 1 4.86 0.30 108.30 113.16 B B B O4' C1' N1 DT DT DT 11 11 11 N 1 -4.13 0.60 127.20 123.07 B B B C2 N3 C4 DT DT DT 11 11 11 N 1 -8.98 0.80 109.40 100.42 B B B O5' C5' C4' DC DC DC 13 13 13 N 1 2.08 0.30 108.30 110.38 B B B O4' C1' N1 DC DC DC 13 13 13 N 1 -5.45 0.60 127.20 121.75 B B B C2 N3 C4 DT DT DT 14 14 14 N 1 4.70 0.60 115.20 119.90 B B B N3 C4 C5 DT DT DT 14 14 14 N 1 -5.29 0.60 122.30 117.01 B B B N3 C2 O2 DT DT DT 14 14 14 N 1 -4.24 0.60 119.90 115.66 B B B N3 C4 O4 DT DT DT 14 14 14 N 1 A A O3' P DA DT 3 4 0.098 0.012 1.607 1.705 Y 1 A A O4' C4' DT DT 7 7 -0.060 0.010 1.446 1.386 N ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) 0.224 0.2126 0.216 0.216 1.10 20 2924 625 12514 12514 2847 4.99 97.5 RANDOM 1 FREE R 0.0 MOLECULAR REPLACEMENT UDG028 ENGH AND HUBER 0 175.00 322.00 1.10 20 38 325 7 280 0 0.018 0.035 0.000 0.0018 0.000 0.000 0.013 0.000 0.034 0.000 18.213 1.10 29.62 1MF5 12514 0.11 1 10.96 7.7 99.3 0.37 1.10 1.20 5.24 2803 6.59 99.4 data scaling XDS data scaling XSCALE model building SHELX refinement SHELXL-97 data reduction XDS phasing SHELX GCATGCT Quadruplex 1 N N 1 N N 2 N N 3 N N 3 N N hydrog DG-DC PAIR A DG 1 A N2 DG 1 1_555 A DC 6 A O2 DC 6 1_555 hydrog DC-DG PAIR A DC 2 A O2 DC 2 1_555 A DG 5 A N2 DG 5 1_555 hydrog DG-DC PAIR B DG 8 B N2 DG 1 1_555 B DC 13 B O2 DC 6 1_555 hydrog DC-DG PAIR B DC 9 B O2 DC 2 1_555 B DG 12 B N2 DG 5 1_555 DNA QUADRUPLEX, ATOMIC RESOLUTION, DNA 1MF5 PDB 1 1MF5 1 7 1MF5 1 7 1MF5 A 1 1 7 8 14 1MF5 8 14 1MF5 B 1 1 7 BINDING SITE FOR RESIDUE NCO B 15 B NCO 15 Software 11 A DA 3 A DA 3 11 2_655 B DG 8 B DG 1 11 1_555 B DC 9 B DC 2 11 1_555 B DC 9 B DC 2 11 4_555 B DA 10 B DA 3 11 4_555 B DG 12 B DG 5 11 1_555 B DC 13 B DC 6 11 1_555 B HOH 103 E HOH 11 4_555 B HOH 104 E HOH 11 4_555 B HOH 111 E HOH 11 1_555 B HOH 112 E HOH 11 4_555 20 C 2 2 21