1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Wu, J.H. Chang, C. Pei, J.M. Xiao, Q. Shi, Y.Y. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 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 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 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 to be published 0353 Solution structure of E2F binding DNA fragment GCGCGAAAC-T-GTTTCGCGC studied by Molecular Dynamics Simulation and Two Dimensional NMR experiment 2000 10.2210/pdb1ecu/pdb pdb_00001ecu 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 5821.759 DNA (5'-D(*GP*CP*GP*CP*GP*AP*AP*AP*CP*TP*GP*TP*TP*TP*CP*GP*CP*GP*C)-3') FRAGMENT OF E2F BINDING DNA 1 syn polymer no no (DG)(DC)(DG)(DC)(DG)(DA)(DA)(DA)(DC)(DT)(DG)(DT)(DT)(DT)(DC)(DG)(DC)(DG)(DC) GCGCGAAACTGTTTCGCGC A polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n 5.238 1 19 A 1 A 19 -6.006 A_DG1:DC19_A 1 -7.554 -0.758 0.220 -0.249 3.072 1 19 A 2 A 18 -3.093 A_DC2:DG18_A 2 -8.776 0.641 -0.003 -0.277 -1.478 1 19 A 3 A 17 -0.191 A_DG3:DC17_A 3 -4.859 -0.588 -0.043 -0.222 2.854 1 19 A 4 A 16 -7.261 A_DC4:DG16_A 4 -9.912 0.767 -0.114 -0.348 -8.564 1 19 A 5 A 15 -3.826 A_DG5:DC15_A 5 -18.588 -0.479 -0.560 -0.247 -7.996 1 20 A 6 A 14 -11.096 A_DA6:DT14_A 6 -6.855 0.144 -0.457 -0.074 7.210 1 20 A 7 A 13 -4.413 A_DA7:DT13_A 7 0.589 -0.098 0.083 -0.073 23.936 1 20 A 8 A 12 -6.626 A_DA8:DT12_A 8 4.781 0.778 0.141 0.113 33.435 A 9 A 11 74.812 A_DC9:DG11_A 9 6.401 4.513 1.474 -0.414 3.443 42.159 A A 1 2 2.187 A A 19 18 3.456 1.573 0.152 -0.415 AA_DG1DC2:DG18DC19_AA 1 1.764 -2.453 42.096 -0.747 -0.020 2.455 26.532 A A 2 3 30.759 A A 18 17 3.282 13.477 0.189 -0.777 AA_DC2DG3:DC17DG18_AA 2 0.863 -1.969 22.892 -5.051 -0.197 3.217 41.255 A A 3 4 1.035 A A 17 16 3.210 0.729 0.223 0.080 AA_DG3DC4:DG16DC17_AA 3 1.507 -2.140 41.223 0.037 -0.157 1.990 37.125 A A 4 5 44.053 A A 16 15 3.470 25.462 0.434 -0.875 AA_DC4DG5:DC15DG16_AA 4 5.496 -9.508 26.685 -4.722 0.040 3.240 38.647 A A 5 6 3.327 A A 15 14 3.271 2.201 -0.026 -0.477 AA_DG5DA6:DT14DC15_AA 5 -0.494 0.746 38.583 -0.991 -0.021 2.916 35.529 A A 6 7 -3.765 A A 14 13 2.947 -2.291 0.633 -1.003 AA_DA6DA7:DT13DT14_AA 6 -4.058 6.668 35.232 -1.343 -1.572 2.809 28.589 A A 7 8 6.272 A A 13 12 2.929 3.085 -0.633 -1.474 AA_DA7DA8:DT12DT13_AA 7 -3.279 6.667 28.239 -3.602 0.626 1.932 37.280 A A 8 9 21.793 A A 12 11 3.276 13.405 3.003 -0.191 AA_DA8DC9:DG11DT12_AA 8 -11.582 18.830 32.934 -1.809 -6.001 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list chem_comp_atom chem_comp_bond repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Data collection 1 0 2000-02-02 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-16 1 4 2024-05-22 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name RCSB Y RCSB 2000-01-26 REL The sequence is formed by adding CTG loop to ends of ds(GCGCGAAA:TTTCGCGC), which occurs naturally in humans. sample Solvent suppression was realized by WATERGATE method. all calculated structures submitted 2 2 2D NOESY 2D NOESY 150mM NaCl 7.0 ambient 300 K Initial structure for model 1 is A-DNA, while that for model 2 is B-DNA. First we applied 640ps free MD with 18 Na+ counterions and 2789 waters for A-DNA and 2303 waters for B-DNA. Then we applied 4 cycles of IRMA with 174 NOE restraints and 19 hydrogen bond restraints Molecular Dynamics with Particle-Particle Particle-Mesh method; Iterative Relaxation Matrix Approach with generalized order parameters 3.5mM DNA fragment; 50mM phosphate buffer, pH 7.0; 150mM NaCl; 1mM EDTA; 1mM NaN3; 90% H2O, 10% D2O 90% H2O/10% D2O same as 1 except in D2O 99.96% D2O Bruker collection XwinNMR 1.1 Alexandre Bonvin iterative matrix relaxation IRMA 0.1 W.F.van Gunsteren refinement GROMOS 96 500 Bruker DMX G 1 n 1 DG 1 A C 2 n 2 DC 2 A G 3 n 3 DG 3 A C 4 n 4 DC 4 A G 5 n 5 DG 5 A A 6 n 6 DA 6 A A 7 n 7 DA 7 A A 8 n 8 DA 8 A C 9 n 9 DC 9 A T 10 n 10 DT 10 A G 11 n 11 DG 11 A T 12 n 12 DT 12 A T 13 n 13 DT 13 A T 14 n 14 DT 14 A C 15 n 15 DC 15 A G 16 n 16 DG 16 A C 17 n 17 DC 17 A G 18 n 18 DG 18 A C 19 n 19 DC 19 A author_defined_assembly 1 monomeric 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 DG 5 0.060 SIDE CHAIN 1 A DA 6 0.059 SIDE CHAIN 1 A DA 8 0.118 SIDE CHAIN 1 A DC 9 0.157 SIDE CHAIN 1 A DG 11 0.187 SIDE CHAIN 1 A DT 12 0.092 SIDE CHAIN 1 A DC 19 0.107 SIDE CHAIN 2 A DA 6 0.082 SIDE CHAIN 2 A DC 9 0.185 SIDE CHAIN 2 A DG 11 0.080 SIDE CHAIN 2 A DT 12 0.086 SIDE CHAIN 2 A DC 17 0.063 SIDE CHAIN 2 A DC 19 0.080 SIDE CHAIN 1 -6.46 0.60 125.10 118.64 A A A C6 N1 C2 DG DG DG 1 1 1 N 1 9.53 0.50 111.90 121.43 A A A C2 N3 C4 DG DG DG 1 1 1 N 1 -9.13 0.50 128.60 119.47 A A A N3 C4 C5 DG DG DG 1 1 1 N 1 6.52 0.50 111.50 118.02 A A A C5 C6 N1 DG DG DG 1 1 1 N 1 -3.23 0.40 110.80 107.57 A A A C4 C5 N7 DG DG DG 1 1 1 N 1 6.98 0.60 126.00 132.98 A A A N3 C4 N9 DG DG DG 1 1 1 N 1 7.41 0.90 116.20 123.61 A A A N1 C2 N2 DG DG DG 1 1 1 N 1 -4.85 0.70 119.90 115.05 A A A N3 C2 N2 DG DG DG 1 1 1 N 1 -9.48 0.60 128.60 119.12 A A A C5 C6 O6 DG DG DG 1 1 1 N 1 10.36 1.20 119.70 130.06 A A A C3' O3' P DG DG DC 1 1 2 Y 1 -2.69 0.40 120.30 117.61 A A A C6 N1 C2 DC DC DC 2 2 2 N 1 3.18 0.50 119.90 123.08 A A A C2 N3 C4 DC DC DC 2 2 2 N 1 2.50 0.30 108.30 110.80 A A A O4' C1' N9 DG DG DG 3 3 3 N 1 -5.80 0.60 125.10 119.30 A A A C6 N1 C2 DG DG DG 3 3 3 N 1 9.29 0.50 111.90 121.19 A A A C2 N3 C4 DG DG DG 3 3 3 N 1 -8.43 0.50 128.60 120.17 A A A N3 C4 C5 DG DG DG 3 3 3 N 1 6.27 0.50 111.50 117.77 A A A C5 C6 N1 DG DG DG 3 3 3 N 1 -3.52 0.40 110.80 107.28 A A A C4 C5 N7 DG DG DG 3 3 3 N 1 3.37 0.50 104.30 107.67 A A A C5 N7 C8 DG DG DG 3 3 3 N 1 6.53 0.60 126.00 132.53 A A A N3 C4 N9 DG DG DG 3 3 3 N 1 7.31 0.90 116.20 123.51 A A A N1 C2 N2 DG DG DG 3 3 3 N 1 -4.30 0.70 119.90 115.60 A A A N3 C2 N2 DG DG DG 3 3 3 N 1 -9.04 0.60 128.60 119.56 A A A C5 C6 O6 DG DG DG 3 3 3 N 1 10.36 1.20 119.70 130.06 A A A C3' O3' P DG DG DC 3 3 4 Y 1 7.58 1.10 109.80 117.38 A A A C5' C4' O4' DC DC DC 4 4 4 N 1 -6.99 1.00 110.10 103.11 A A A C1' O4' C4' DC DC DC 4 4 4 N 1 3.55 0.30 108.30 111.85 A A A O4' C1' N1 DC DC DC 4 4 4 N 1 3.09 0.50 119.90 122.99 A A A C2 N3 C4 DC DC DC 4 4 4 N 1 -2.61 0.40 121.90 119.29 A A A N3 C4 C5 DC DC DC 4 4 4 N 1 -5.77 0.60 125.10 119.33 A A A C6 N1 C2 DG DG DG 5 5 5 N 1 9.48 0.50 111.90 121.38 A A A C2 N3 C4 DG DG DG 5 5 5 N 1 -8.30 0.50 128.60 120.30 A A A N3 C4 C5 DG DG DG 5 5 5 N 1 6.50 0.50 111.50 118.00 A A A C5 C6 N1 DG DG DG 5 5 5 N 1 -3.05 0.40 110.80 107.75 A A A C4 C5 N7 DG DG DG 5 5 5 N 1 3.06 0.50 104.30 107.36 A A A C5 N7 C8 DG DG DG 5 5 5 N 1 6.87 0.60 126.00 132.87 A A A N3 C4 N9 DG DG DG 5 5 5 N 1 6.12 0.90 116.20 122.32 A A A N1 C2 N2 DG DG DG 5 5 5 N 1 -8.29 0.60 128.60 120.31 A A A C5 C6 O6 DG DG DG 5 5 5 N 1 -6.44 0.50 129.30 122.86 A A A N1 C2 N3 DA DA DA 6 6 6 N 1 9.89 0.50 110.60 120.49 A A A C2 N3 C4 DA DA DA 6 6 6 N 1 -8.56 0.70 126.80 118.24 A A A N3 C4 C5 DA DA DA 6 6 6 N 1 8.10 0.80 127.40 135.50 A A A N3 C4 N9 DA DA DA 6 6 6 N 1 4.85 0.60 118.60 123.45 A A A N1 C6 N6 DA DA DA 6 6 6 N 1 -5.66 0.80 123.70 118.04 A A A C5 C6 N6 DA DA DA 6 6 6 N 1 -6.53 0.50 129.30 122.77 A A A N1 C2 N3 DA DA DA 7 7 7 N 1 9.57 0.50 110.60 120.17 A A A C2 N3 C4 DA DA DA 7 7 7 N 1 -8.20 0.70 126.80 118.60 A A A N3 C4 C5 DA DA DA 7 7 7 N 1 7.27 0.80 127.40 134.67 A A A N3 C4 N9 DA DA DA 7 7 7 N 1 3.88 0.60 118.60 122.48 A A A N1 C6 N6 DA DA DA 7 7 7 N 1 -6.60 0.50 129.30 122.70 A A A N1 C2 N3 DA DA DA 8 8 8 N 1 9.60 0.50 110.60 120.20 A A A C2 N3 C4 DA DA DA 8 8 8 N 1 -8.08 0.70 126.80 118.72 A A A N3 C4 C5 DA DA DA 8 8 8 N 1 -3.10 0.50 113.80 110.70 A A A N7 C8 N9 DA DA DA 8 8 8 N 1 7.00 0.80 127.40 134.40 A A A N3 C4 N9 DA DA DA 8 8 8 N 1 5.34 0.30 108.30 113.64 A A A O4' C1' N1 DC DC DC 9 9 9 N 1 -5.42 0.70 121.90 116.48 A A A N3 C2 O2 DC DC DC 9 9 9 N 1 8.76 0.30 108.30 117.06 A A A O4' C1' N1 DT DT DT 10 10 10 N 1 5.48 0.60 114.60 120.08 A A A N1 C2 N3 DT DT DT 10 10 10 N 1 -6.63 0.60 127.20 120.57 A A A C2 N3 C4 DT DT DT 10 10 10 N 1 4.26 0.60 115.20 119.46 A A A N3 C4 C5 DT DT DT 10 10 10 N 1 -5.53 0.70 124.90 119.37 A A A C5 C4 O4 DT DT DT 10 10 10 N 1 -6.46 0.60 125.10 118.64 A A A C6 N1 C2 DG DG DG 11 11 11 N 1 8.94 0.50 111.90 120.84 A A A C2 N3 C4 DG DG DG 11 11 11 N 1 -8.92 0.50 128.60 119.68 A A A N3 C4 C5 DG DG DG 11 11 11 N 1 6.14 0.50 111.50 117.64 A A A C5 C6 N1 DG DG DG 11 11 11 N 1 -3.39 0.40 110.80 107.41 A A A C4 C5 N7 DG DG DG 11 11 11 N 1 5.80 0.60 126.00 131.80 A A A N3 C4 N9 DG DG DG 11 11 11 N 1 7.75 0.90 116.20 123.95 A A A N1 C2 N2 DG DG DG 11 11 11 N 1 -5.58 0.70 119.90 114.32 A A A N3 C2 N2 DG DG DG 11 11 11 N 1 -9.72 0.60 128.60 118.88 A A A C5 C6 O6 DG DG DG 11 11 11 N 1 3.90 0.30 108.30 112.20 A A A O4' C1' N1 DT DT DT 12 12 12 N 1 5.22 0.60 114.60 119.82 A A A N1 C2 N3 DT DT DT 12 12 12 N 1 -6.63 0.60 127.20 120.57 A A A C2 N3 C4 DT DT DT 12 12 12 N 1 4.47 0.60 115.20 119.67 A A A N3 C4 C5 DT DT DT 12 12 12 N 1 -5.07 0.70 124.90 119.83 A A A C5 C4 O4 DT DT DT 12 12 12 N 1 4.35 0.30 108.30 112.65 A A A O4' C1' N1 DT DT DT 13 13 13 N 1 5.55 0.60 114.60 120.15 A A A N1 C2 N3 DT DT DT 13 13 13 N 1 -6.59 0.60 127.20 120.61 A A A C2 N3 C4 DT DT DT 13 13 13 N 1 3.91 0.60 115.20 119.11 A A A N3 C4 C5 DT DT DT 13 13 13 N 1 -3.65 0.60 122.90 119.25 A A A C6 C5 C7 DT DT DT 13 13 13 N 1 5.55 0.60 114.60 120.15 A A A N1 C2 N3 DT DT DT 14 14 14 N 1 -6.95 0.60 127.20 120.25 A A A C2 N3 C4 DT DT DT 14 14 14 N 1 4.29 0.60 115.20 119.49 A A A N3 C4 C5 DT DT DT 14 14 14 N 1 -5.39 0.70 124.90 119.51 A A A C5 C4 O4 DT DT DT 14 14 14 N 1 -2.54 0.40 121.90 119.36 A A A N3 C4 C5 DC DC DC 15 15 15 N 1 -6.23 0.60 125.10 118.87 A A A C6 N1 C2 DG DG DG 16 16 16 N 1 9.54 0.50 111.90 121.44 A A A C2 N3 C4 DG DG DG 16 16 16 N 1 -8.68 0.50 128.60 119.92 A A A N3 C4 C5 DG DG DG 16 16 16 N 1 6.68 0.50 111.50 118.18 A A A C5 C6 N1 DG DG DG 16 16 16 N 1 -2.93 0.40 110.80 107.87 A A A C4 C5 N7 DG DG DG 16 16 16 N 1 7.16 0.60 126.00 133.16 A A A N3 C4 N9 DG DG DG 16 16 16 N 1 7.34 0.90 116.20 123.54 A A A N1 C2 N2 DG DG DG 16 16 16 N 1 -4.47 0.70 119.90 115.43 A A A N3 C2 N2 DG DG DG 16 16 16 N 1 -10.20 0.60 128.60 118.40 A A A C5 C6 O6 DG DG DG 16 16 16 N 1 2.09 0.30 108.30 110.39 A A A O4' C1' N9 DG DG DG 18 18 18 N 1 -5.86 0.60 125.10 119.24 A A A C6 N1 C2 DG DG DG 18 18 18 N 1 9.02 0.50 111.90 120.92 A A A C2 N3 C4 DG DG DG 18 18 18 N 1 -8.54 0.50 128.60 120.06 A A A N3 C4 C5 DG DG DG 18 18 18 N 1 6.01 0.50 111.50 117.51 A A A C5 C6 N1 DG DG DG 18 18 18 N 1 -3.46 0.40 110.80 107.34 A A A C4 C5 N7 DG DG DG 18 18 18 N 1 3.11 0.50 104.30 107.41 A A A C5 N7 C8 DG DG DG 18 18 18 N 1 6.57 0.60 126.00 132.57 A A A N3 C4 N9 DG DG DG 18 18 18 N 1 6.76 0.90 116.20 122.96 A A A N1 C2 N2 DG DG DG 18 18 18 N 1 -8.79 0.60 128.60 119.81 A A A C5 C6 O6 DG DG DG 18 18 18 N 1 5.20 0.30 108.30 113.50 A A A O4' C1' N1 DC DC DC 19 19 19 N 1 -2.62 0.40 121.90 119.28 A A A N3 C4 C5 DC DC DC 19 19 19 N 1 -4.26 0.70 121.90 117.64 A A A N3 C2 O2 DC DC DC 19 19 19 N 2 -5.84 0.60 125.10 119.26 A A A C6 N1 C2 DG DG DG 1 1 1 N 2 9.27 0.50 111.90 121.17 A A A C2 N3 C4 DG DG DG 1 1 1 N 2 -8.51 0.50 128.60 120.09 A A A N3 C4 C5 DG DG DG 1 1 1 N 2 6.17 0.50 111.50 117.67 A A A C5 C6 N1 DG DG DG 1 1 1 N 2 -3.20 0.40 110.80 107.60 A A A C4 C5 N7 DG DG DG 1 1 1 N 2 6.71 0.60 126.00 132.71 A A A N3 C4 N9 DG DG DG 1 1 1 N 2 7.48 0.90 116.20 123.68 A A A N1 C2 N2 DG DG DG 1 1 1 N 2 -4.56 0.70 119.90 115.34 A A A N3 C2 N2 DG DG DG 1 1 1 N 2 -9.43 0.60 128.60 119.17 A A A C5 C6 O6 DG DG DG 1 1 1 N 2 -2.84 0.40 120.30 117.46 A A A C6 N1 C2 DC DC DC 2 2 2 N 2 -5.83 0.60 125.10 119.27 A A A C6 N1 C2 DG DG DG 3 3 3 N 2 9.28 0.50 111.90 121.18 A A A C2 N3 C4 DG DG DG 3 3 3 N 2 -8.53 0.50 128.60 120.07 A A A N3 C4 C5 DG DG DG 3 3 3 N 2 6.22 0.50 111.50 117.72 A A A C5 C6 N1 DG DG DG 3 3 3 N 2 -3.24 0.40 110.80 107.56 A A A C4 C5 N7 DG DG DG 3 3 3 N 2 6.62 0.60 126.00 132.62 A A A N3 C4 N9 DG DG DG 3 3 3 N 2 7.03 0.90 116.20 123.23 A A A N1 C2 N2 DG DG DG 3 3 3 N 2 -9.17 0.60 128.60 119.43 A A A C5 C6 O6 DG DG DG 3 3 3 N 2 9.92 1.20 119.70 129.62 A A A C3' O3' P DG DG DC 3 3 4 Y 2 -2.70 0.40 120.30 117.60 A A A C6 N1 C2 DC DC DC 4 4 4 N 2 -2.58 0.40 121.90 119.32 A A A N3 C4 C5 DC DC DC 4 4 4 N 2 -4.45 0.70 121.90 117.45 A A A N3 C2 O2 DC DC DC 4 4 4 N 2 12.58 1.60 120.90 133.48 A A A P O5' C5' DG DG DG 5 5 5 N 2 -5.60 0.60 125.10 119.50 A A A C6 N1 C2 DG DG DG 5 5 5 N 2 9.34 0.50 111.90 121.24 A A A C2 N3 C4 DG DG DG 5 5 5 N 2 -8.31 0.50 128.60 120.29 A A A N3 C4 C5 DG DG DG 5 5 5 N 2 6.26 0.50 111.50 117.76 A A A C5 C6 N1 DG DG DG 5 5 5 N 2 -2.89 0.40 110.80 107.91 A A A C4 C5 N7 DG DG DG 5 5 5 N 2 6.82 0.60 126.00 132.82 A A A N3 C4 N9 DG DG DG 5 5 5 N 2 6.90 0.90 116.20 123.10 A A A N1 C2 N2 DG DG DG 5 5 5 N 2 -9.24 0.60 128.60 119.36 A A A C5 C6 O6 DG DG DG 5 5 5 N 2 7.49 1.20 119.70 127.19 A A A C3' O3' P DG DG DA 5 5 6 Y 2 -5.85 0.50 129.30 123.45 A A A N1 C2 N3 DA DA DA 6 6 6 N 2 9.72 0.50 110.60 120.32 A A A C2 N3 C4 DA DA DA 6 6 6 N 2 -8.78 0.70 126.80 118.02 A A A N3 C4 C5 DA DA DA 6 6 6 N 2 8.36 0.80 127.40 135.76 A A A N3 C4 N9 DA DA DA 6 6 6 N 2 5.37 0.60 118.60 123.97 A A A N1 C6 N6 DA DA DA 6 6 6 N 2 -6.39 0.80 123.70 117.31 A A A C5 C6 N6 DA DA DA 6 6 6 N 2 -6.32 0.50 129.30 122.98 A A A N1 C2 N3 DA DA DA 7 7 7 N 2 9.88 0.50 110.60 120.48 A A A C2 N3 C4 DA DA DA 7 7 7 N 2 -8.65 0.70 126.80 118.15 A A A N3 C4 C5 DA DA DA 7 7 7 N 2 7.88 0.80 127.40 135.28 A A A N3 C4 N9 DA DA DA 7 7 7 N 2 4.59 0.60 118.60 123.19 A A A N1 C6 N6 DA DA DA 7 7 7 N 2 -5.25 0.80 123.70 118.45 A A A C5 C6 N6 DA DA DA 7 7 7 N 2 -6.52 0.50 129.30 122.78 A A A N1 C2 N3 DA DA DA 8 8 8 N 2 9.74 0.50 110.60 120.34 A A A C2 N3 C4 DA DA DA 8 8 8 N 2 -8.29 0.70 126.80 118.51 A A A N3 C4 C5 DA DA DA 8 8 8 N 2 7.59 0.80 127.40 134.99 A A A N3 C4 N9 DA DA DA 8 8 8 N 2 3.71 0.60 118.60 122.31 A A A N1 C6 N6 DA DA DA 8 8 8 N 2 6.88 1.10 109.80 116.68 A A A C5' C4' O4' DT DT DT 10 10 10 N 2 -6.84 1.00 110.10 103.26 A A A C1' O4' C4' DT DT DT 10 10 10 N 2 9.99 0.30 108.30 118.29 A A A O4' C1' N1 DT DT DT 10 10 10 N 2 -3.23 0.50 121.30 118.07 A A A C6 N1 C2 DT DT DT 10 10 10 N 2 5.26 0.60 114.60 119.86 A A A N1 C2 N3 DT DT DT 10 10 10 N 2 -6.14 0.60 127.20 121.06 A A A C2 N3 C4 DT DT DT 10 10 10 N 2 4.28 0.60 115.20 119.48 A A A N3 C4 C5 DT DT DT 10 10 10 N 2 -5.63 0.60 122.30 116.67 A A A N3 C2 O2 DT DT DT 10 10 10 N 2 -6.31 0.70 124.90 118.59 A A A C5 C4 O4 DT DT DT 10 10 10 N 2 8.17 1.20 119.70 127.87 A A A C3' O3' P DT DT DG 10 10 11 Y 2 -5.05 0.60 125.10 120.05 A A A C6 N1 C2 DG DG DG 11 11 11 N 2 8.76 0.50 111.90 120.66 A A A C2 N3 C4 DG DG DG 11 11 11 N 2 -8.06 0.50 128.60 120.54 A A A N3 C4 C5 DG DG DG 11 11 11 N 2 5.48 0.50 111.50 116.98 A A A C5 C6 N1 DG DG DG 11 11 11 N 2 -2.41 0.40 110.80 108.39 A A A C4 C5 N7 DG DG DG 11 11 11 N 2 6.06 0.60 126.00 132.06 A A A N3 C4 N9 DG DG DG 11 11 11 N 2 8.24 0.90 116.20 124.44 A A A N1 C2 N2 DG DG DG 11 11 11 N 2 -5.14 0.70 119.90 114.76 A A A N3 C2 N2 DG DG DG 11 11 11 N 2 3.96 0.60 119.90 123.86 A A A N1 C6 O6 DG DG DG 11 11 11 N 2 -9.53 0.60 128.60 119.07 A A A C5 C6 O6 DG DG DG 11 11 11 N 2 -6.11 1.00 110.10 103.99 A A A C1' O4' C4' DT DT DT 12 12 12 N 2 4.29 0.30 108.30 112.59 A A A O4' C1' N1 DT DT DT 12 12 12 N 2 5.67 0.60 114.60 120.27 A A A N1 C2 N3 DT DT DT 12 12 12 N 2 -7.03 0.60 127.20 120.17 A A A C2 N3 C4 DT DT DT 12 12 12 N 2 4.38 0.60 115.20 119.58 A A A N3 C4 C5 DT DT DT 12 12 12 N 2 -4.53 0.70 124.90 120.37 A A A C5 C4 O4 DT DT DT 12 12 12 N 2 10.42 1.20 119.70 130.12 A A A C3' O3' P DT DT DT 12 12 13 Y 2 3.58 0.30 108.30 111.88 A A A O4' C1' N1 DT DT DT 13 13 13 N 2 5.47 0.60 114.60 120.07 A A A N1 C2 N3 DT DT DT 13 13 13 N 2 -6.84 0.60 127.20 120.36 A A A C2 N3 C4 DT DT DT 13 13 13 N 2 4.34 0.60 115.20 119.54 A A A N3 C4 C5 DT DT DT 13 13 13 N 2 -5.61 0.70 124.90 119.29 A A A C5 C4 O4 DT DT DT 13 13 13 N 2 8.82 1.20 119.70 128.52 A A A C3' O3' P DT DT DT 13 13 14 Y 2 5.45 0.60 114.60 120.05 A A A N1 C2 N3 DT DT DT 14 14 14 N 2 -7.39 0.60 127.20 119.81 A A A C2 N3 C4 DT DT DT 14 14 14 N 2 4.87 0.60 115.20 120.07 A A A N3 C4 C5 DT DT DT 14 14 14 N 2 -5.99 0.70 124.90 118.91 A A A C5 C4 O4 DT DT DT 14 14 14 N 2 3.10 0.30 108.30 111.40 A A A O4' C1' N1 DC DC DC 15 15 15 N 2 -2.55 0.40 120.30 117.75 A A A C6 N1 C2 DC DC DC 15 15 15 N 2 -2.76 0.40 121.90 119.14 A A A N3 C4 C5 DC DC DC 15 15 15 N 2 9.40 1.20 119.70 129.10 A A A C3' O3' P DC DC DG 15 15 16 Y 2 -6.30 0.60 125.10 118.80 A A A C6 N1 C2 DG DG DG 16 16 16 N 2 9.69 0.50 111.90 121.59 A A A C2 N3 C4 DG DG DG 16 16 16 N 2 -9.03 0.50 128.60 119.57 A A A N3 C4 C5 DG DG DG 16 16 16 N 2 6.64 0.50 111.50 118.14 A A A C5 C6 N1 DG DG DG 16 16 16 N 2 -2.99 0.40 110.80 107.81 A A A C4 C5 N7 DG DG DG 16 16 16 N 2 7.27 0.60 126.00 133.27 A A A N3 C4 N9 DG DG DG 16 16 16 N 2 6.29 0.90 116.20 122.49 A A A N1 C2 N2 DG DG DG 16 16 16 N 2 -9.95 0.60 128.60 118.65 A A A C5 C6 O6 DG DG DG 16 16 16 N 2 -2.67 0.40 120.30 117.63 A A A C6 N1 C2 DC DC DC 17 17 17 N 2 -6.06 0.60 125.10 119.04 A A A C6 N1 C2 DG DG DG 18 18 18 N 2 9.37 0.50 111.90 121.27 A A A C2 N3 C4 DG DG DG 18 18 18 N 2 -8.69 0.50 128.60 119.91 A A A N3 C4 C5 DG DG DG 18 18 18 N 2 6.32 0.50 111.50 117.82 A A A C5 C6 N1 DG DG DG 18 18 18 N 2 -3.06 0.40 110.80 107.74 A A A C4 C5 N7 DG DG DG 18 18 18 N 2 7.02 0.60 126.00 133.02 A A A N3 C4 N9 DG DG DG 18 18 18 N 2 6.27 0.90 116.20 122.47 A A A N1 C2 N2 DG DG DG 18 18 18 N 2 -9.21 0.60 128.60 119.39 A A A C5 C6 O6 DG DG DG 18 18 18 N 2 4.71 0.30 108.30 113.01 A A A O4' C1' N1 DC DC DC 19 19 19 N 2 -2.58 0.40 121.90 119.32 A A A N3 C4 C5 DC DC DC 19 19 19 N 1 A A C5 N7 DG DG 1 1 -0.076 0.006 1.388 1.312 N 1 A A C8 N9 DG DG 1 1 -0.061 0.007 1.374 1.313 N 1 A A N9 C4 DG DG 1 1 -0.060 0.008 1.375 1.315 N 1 A A C5 N7 DG DG 3 3 -0.068 0.006 1.388 1.320 N 1 A A C8 N9 DG DG 3 3 -0.053 0.007 1.374 1.321 N 1 A A N9 C4 DG DG 3 3 -0.054 0.008 1.375 1.321 N 1 A A O3' P DG DC 3 4 -0.090 0.012 1.607 1.517 Y 1 A A P OP1 DC DC 4 4 -0.109 0.017 1.485 1.376 N 1 A A C5 N7 DG DG 5 5 -0.066 0.006 1.388 1.322 N 1 A A C8 N9 DG DG 5 5 -0.053 0.007 1.374 1.321 N 1 A A N9 C4 DG DG 5 5 -0.052 0.008 1.375 1.323 N 1 A A C5 N7 DA DA 6 6 -0.069 0.006 1.388 1.319 N 1 A A C8 N9 DA DA 6 6 -0.053 0.008 1.373 1.320 N 1 A A N9 C4 DA DA 6 6 -0.054 0.006 1.374 1.320 N 1 A A C5 N7 DA DA 7 7 -0.069 0.006 1.388 1.319 N 1 A A C8 N9 DA DA 7 7 -0.051 0.008 1.373 1.322 N 1 A A N9 C4 DA DA 7 7 -0.053 0.006 1.374 1.321 N 1 A A C5 N7 DA DA 8 8 -0.067 0.006 1.388 1.321 N 1 A A C8 N9 DA DA 8 8 -0.051 0.008 1.373 1.322 N 1 A A N9 C4 DA DA 8 8 -0.051 0.006 1.374 1.323 N 1 A A C4 C5 DT DT 10 10 -0.072 0.009 1.445 1.373 N 1 A A C5 N7 DG DG 11 11 -0.070 0.006 1.388 1.318 N 1 A A C8 N9 DG DG 11 11 -0.053 0.007 1.374 1.321 N 1 A A N9 C4 DG DG 11 11 -0.058 0.008 1.375 1.317 N 1 A A C4 C5 DT DT 12 12 -0.070 0.009 1.445 1.375 N 1 A A C4 C5 DT DT 13 13 -0.069 0.009 1.445 1.376 N 1 A A C4 C5 DT DT 14 14 -0.066 0.009 1.445 1.379 N 1 A A C4 C5 DC DC 15 15 -0.051 0.008 1.425 1.374 N 1 A A C5 N7 DG DG 16 16 -0.070 0.006 1.388 1.318 N 1 A A C8 N9 DG DG 16 16 -0.058 0.007 1.374 1.316 N 1 A A N9 C4 DG DG 16 16 -0.055 0.008 1.375 1.320 N 1 A A C5 N7 DG DG 18 18 -0.072 0.006 1.388 1.316 N 1 A A C8 N9 DG DG 18 18 -0.057 0.007 1.374 1.317 N 1 A A N9 C4 DG DG 18 18 -0.059 0.008 1.375 1.316 N 1 A A C4 C5 DC DC 19 19 -0.055 0.008 1.425 1.370 N 2 A A C5 N7 DG DG 1 1 -0.072 0.006 1.388 1.316 N 2 A A C8 N9 DG DG 1 1 -0.057 0.007 1.374 1.317 N 2 A A N9 C4 DG DG 1 1 -0.058 0.008 1.375 1.317 N 2 A A C4 C5 DC DC 2 2 -0.049 0.008 1.425 1.376 N 2 A A C5 N7 DG DG 3 3 -0.069 0.006 1.388 1.319 N 2 A A C8 N9 DG DG 3 3 -0.054 0.007 1.374 1.320 N 2 A A N9 C4 DG DG 3 3 -0.054 0.008 1.375 1.321 N 2 A A O3' P DG DC 3 4 -0.096 0.012 1.607 1.511 Y 2 A A P OP1 DG DG 5 5 -0.125 0.017 1.485 1.360 N 2 A A P OP2 DG DG 5 5 -0.118 0.017 1.485 1.367 N 2 A A P O5' DG DG 5 5 -0.127 0.010 1.593 1.466 N 2 A A C5 N7 DG DG 5 5 -0.068 0.006 1.388 1.320 N 2 A A C8 N9 DG DG 5 5 -0.053 0.007 1.374 1.321 N 2 A A N9 C4 DG DG 5 5 -0.052 0.008 1.375 1.323 N 2 A A C5 N7 DA DA 6 6 -0.068 0.006 1.388 1.320 N 2 A A C8 N9 DA DA 6 6 -0.052 0.008 1.373 1.321 N 2 A A N9 C4 DA DA 6 6 -0.054 0.006 1.374 1.320 N 2 A A C5 N7 DA DA 7 7 -0.071 0.006 1.388 1.317 N 2 A A C8 N9 DA DA 7 7 -0.054 0.008 1.373 1.319 N 2 A A N9 C4 DA DA 7 7 -0.058 0.006 1.374 1.316 N 2 A A C5 N7 DA DA 8 8 -0.068 0.006 1.388 1.320 N 2 A A C8 N9 DA DA 8 8 -0.050 0.008 1.373 1.323 N 2 A A N9 C4 DA DA 8 8 -0.053 0.006 1.374 1.321 N 2 A A C4 C5 DC DC 9 9 -0.052 0.008 1.425 1.373 N 2 A A C4 C5 DT DT 10 10 -0.082 0.009 1.445 1.363 N 2 A A C5' C4' DG DG 11 11 -0.085 0.011 1.509 1.424 N 2 A A O4' C4' DG DG 11 11 -0.090 0.010 1.446 1.356 N 2 A A C5 N7 DG DG 11 11 -0.072 0.006 1.388 1.316 N 2 A A C8 N9 DG DG 11 11 -0.056 0.007 1.374 1.318 N 2 A A N9 C4 DG DG 11 11 -0.058 0.008 1.375 1.317 N 2 A A C4 C5 DT DT 12 12 -0.065 0.009 1.445 1.380 N 2 A A C4 C5 DT DT 13 13 -0.073 0.009 1.445 1.372 N 2 A A C4 C5 DT DT 14 14 -0.067 0.009 1.445 1.378 N 2 A A C4 C5 DC DC 15 15 -0.050 0.008 1.425 1.375 N 2 A A O3' P DC DG 15 16 -0.085 0.012 1.607 1.522 Y 2 A A C5 N7 DG DG 16 16 -0.068 0.006 1.388 1.320 N 2 A A C8 N9 DG DG 16 16 -0.055 0.007 1.374 1.319 N 2 A A N9 C4 DG DG 16 16 -0.056 0.008 1.375 1.319 N 2 A A C5 N7 DG DG 18 18 -0.072 0.006 1.388 1.316 N 2 A A C8 N9 DG DG 18 18 -0.056 0.007 1.374 1.318 N 2 A A N9 C4 DG DG 18 18 -0.057 0.008 1.375 1.318 N 2 A A C4 C5 DC DC 19 19 -0.049 0.008 1.425 1.376 N SOLUTION STRUCTURE OF E2F BINDING DNA FRAGMENT GCGCGAAAC-T-GTTTCGCGC 1 N N hydrog WATSON-CRICK A DG 1 A N1 DG 1 1_555 A DC 19 A N3 DC 19 1_555 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 A DC 19 A O2 DC 19 1_555 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 A DC 19 A N4 DC 19 1_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 A DG 18 A N1 DG 18 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 A DG 18 A O6 DG 18 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 A DG 18 A N2 DG 18 1_555 hydrog WATSON-CRICK A DG 3 A N1 DG 3 1_555 A DC 17 A N3 DC 17 1_555 hydrog WATSON-CRICK A DG 3 A N2 DG 3 1_555 A DC 17 A O2 DC 17 1_555 hydrog WATSON-CRICK A DG 3 A O6 DG 3 1_555 A DC 17 A N4 DC 17 1_555 hydrog WATSON-CRICK A DC 4 A N3 DC 4 1_555 A DG 16 A N1 DG 16 1_555 hydrog WATSON-CRICK A DC 4 A N4 DC 4 1_555 A DG 16 A O6 DG 16 1_555 hydrog WATSON-CRICK A DC 4 A O2 DC 4 1_555 A DG 16 A N2 DG 16 1_555 hydrog WATSON-CRICK A DG 5 A N1 DG 5 1_555 A DC 15 A N3 DC 15 1_555 hydrog WATSON-CRICK A DG 5 A N2 DG 5 1_555 A DC 15 A O2 DC 15 1_555 hydrog WATSON-CRICK A DG 5 A O6 DG 5 1_555 A DC 15 A N4 DC 15 1_555 hydrog WATSON-CRICK A DA 6 A N1 DA 6 1_555 A DT 14 A N3 DT 14 1_555 hydrog WATSON-CRICK A DA 6 A N6 DA 6 1_555 A DT 14 A O4 DT 14 1_555 hydrog WATSON-CRICK A DA 7 A N1 DA 7 1_555 A DT 13 A N3 DT 13 1_555 hydrog WATSON-CRICK A DA 7 A N6 DA 7 1_555 A DT 13 A O4 DT 13 1_555 hydrog WATSON-CRICK A DA 8 A N1 DA 8 1_555 A DT 12 A N3 DT 12 1_555 hydrog WATSON-CRICK A DA 8 A N6 DA 8 1_555 A DT 12 A O4 DT 12 1_555 hydrog DC-DG PAIR A DC 9 A O2 DC 9 1_555 A DG 11 A N1 DG 11 1_555 DNA double strands, loop, DNA 1ECU PDB 1 1ECU 1 19 1ECU 1 19 1ECU A 1 1 19 1 P 1