1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Chin, K.H. Chou, S.H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 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 UK J.Mol.Biol. JMOBAK 0070 0022-2836 329 351 361 10.1016/S0022-2836(03)00440-6 12758081 Sheared-type G(anti).C(syn) Base-pair: A Unique d(GXC) Loop Closure Motif. 2003 10.2210/pdb1p0u/pdb pdb_00001p0u 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M 1 1.0 3976.599 5'-D(*GP*CP*AP*TP*CP*GP*AP*CP*GP*AP*TP*GP*C)-3' 1 syn polymer no no (DG)(DC)(DA)(DT)(DC)(DG)(DA)(DC)(DG)(DA)(DT)(DG)(DC) GCATCGACGATGC A polydeoxyribonucleotide n n n n n n n n n n n n n -14.624 1 19 A 1 A 13 1.321 A_DG1:DC13_A 1 -20.536 -0.882 -0.613 -0.313 -18.201 1 19 A 2 A 12 -2.945 A_DC2:DG12_A 2 -9.250 0.893 0.175 -0.307 -8.530 1 20 A 3 A 11 -4.093 A_DA3:DT11_A 3 -13.156 -0.210 0.458 -0.173 -4.198 1 20 A 4 A 10 -2.539 A_DT4:DA10_A 4 -6.157 0.235 0.398 -0.081 -1.483 1 19 A 5 A 9 -0.925 A_DC5:DG9_A 5 -6.473 0.967 0.233 -0.325 13.615 6 A 6 A 8 -76.039 A_DG6:DC8_A 6 -29.079 2.232 0.379 -2.686 3.332 38.398 A A 1 2 3.452 A A 13 12 3.313 2.260 -0.757 -0.937 AA_DG1DC2:DG12DC13_AA 1 -6.175 9.432 37.852 -1.713 0.363 2.340 32.011 A A 2 3 20.048 A A 12 11 2.711 10.847 0.402 -0.672 AA_DC2DA3:DT11DG12_AA 2 0.315 -0.583 30.161 -2.778 -0.684 3.152 32.132 A A 3 4 1.465 A A 11 10 3.169 0.811 0.319 -1.026 AA_DA3DT4:DA10DT11_AA 3 1.229 -2.222 32.099 -1.995 -0.364 2.949 33.351 A A 4 5 4.405 A A 10 9 3.057 2.525 0.055 -1.342 AA_DT4DC5:DG9DA10_AA 4 1.580 -2.757 33.221 -2.725 0.145 3.044 93.772 A A 5 6 4.436 A A 9 8 3.122 6.472 1.413 -0.375 AA_DC5DG6:DC8DG9_AA 5 -4.476 3.068 93.518 -0.369 -1.045 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 2003-06-03 1 1 2008-04-29 1 2 2011-07-13 1 3 2022-02-23 1 4 2024-05-29 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name RCSB Y PDBJ 2003-04-11 REL This structure was determined using standard 2D homonuclear techniques. 10 2D NOESY DQF-COSY P-COSY 2D TOCSY 6.8 ambient 278 K distance geometry, simulated annealing, molecular dynamics lowest energy 20mM NaCl, 10mM phosphate buffer 90% H2O, 10% D2O; 100% D2O processing Felix refinement Discover structure solution DGII 600 Varian G5' 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 C 5 n 5 DC 5 A G 6 n 6 DG 6 A A 7 n 7 DA 7 A C 8 n 8 DC 8 A G 9 n 9 DG 9 A A 10 n 10 DA 10 A T 11 n 11 DT 11 A G 12 n 12 DG 12 A C3' 13 n 13 DC 13 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 DC 5 0.057 SIDE CHAIN 1 A DG 9 0.096 SIDE CHAIN 1 A DA 10 0.064 SIDE CHAIN 2 A DG 9 0.087 SIDE CHAIN 3 A DC 8 0.076 SIDE CHAIN 3 A DG 9 0.101 SIDE CHAIN 3 A DG 12 0.079 SIDE CHAIN 3 A DC 13 0.076 SIDE CHAIN 4 A DA 3 0.066 SIDE CHAIN 4 A DC 8 0.075 SIDE CHAIN 4 A DG 9 0.123 SIDE CHAIN 4 A DG 12 0.068 SIDE CHAIN 4 A DC 13 0.084 SIDE CHAIN 5 A DC 8 0.083 SIDE CHAIN 5 A DG 9 0.114 SIDE CHAIN 6 A DC 8 0.075 SIDE CHAIN 6 A DG 9 0.108 SIDE CHAIN 7 A DC 8 0.075 SIDE CHAIN 7 A DG 9 0.089 SIDE CHAIN 8 A DC 8 0.074 SIDE CHAIN 8 A DG 9 0.088 SIDE CHAIN 8 A DG 12 0.068 SIDE CHAIN 9 A DA 3 0.063 SIDE CHAIN 9 A DG 9 0.091 SIDE CHAIN 9 A DG 12 0.072 SIDE CHAIN 10 A DC 8 0.072 SIDE CHAIN 10 A DG 9 0.103 SIDE CHAIN 1 2.19 0.30 108.30 110.49 A A A O4' C1' N9 DG DG DG 1 1 1 N 1 2.04 0.30 108.30 110.34 A A A O4' C1' N1 DC DC DC 2 2 2 N 1 2.40 0.30 108.30 110.70 A A A O4' C1' N9 DA DA DA 3 3 3 N 1 2.55 0.30 108.30 110.85 A A A O4' C1' N1 DT DT DT 4 4 4 N 1 4.27 0.30 108.30 112.57 A A A O4' C1' N1 DC DC DC 5 5 5 N 1 2.83 0.30 108.30 111.13 A A A O4' C1' N1 DC DC DC 8 8 8 N 1 3.62 0.60 118.90 122.52 A A A N1 C2 O2 DC DC DC 8 8 8 N 1 4.60 0.30 108.30 112.90 A A A O4' C1' N9 DG DG DG 9 9 9 N 1 2.77 0.30 108.30 111.07 A A A O4' C1' N1 DT DT DT 11 11 11 N 1 3.21 0.30 108.30 111.51 A A A O4' C1' N1 DC DC DC 13 13 13 N 2 2.82 0.30 108.30 111.12 A A A O4' C1' N9 DG DG DG 1 1 1 N 2 2.49 0.30 108.30 110.79 A A A O4' C1' N1 DC DC DC 2 2 2 N 2 3.18 0.30 108.30 111.48 A A A O4' C1' N9 DA DA DA 3 3 3 N 2 1.94 0.30 108.30 110.24 A A A O4' C1' N1 DT DT DT 4 4 4 N 2 4.88 0.30 108.30 113.18 A A A O4' C1' N1 DC DC DC 5 5 5 N 2 2.80 0.30 108.30 111.10 A A A O4' C1' N1 DC DC DC 8 8 8 N 2 4.47 0.30 108.30 112.77 A A A O4' C1' N9 DG DG DG 9 9 9 N 2 2.81 0.30 108.30 111.11 A A A O4' C1' N9 DA DA DA 10 10 10 N 2 2.64 0.30 108.30 110.94 A A A O4' C1' N9 DG DG DG 12 12 12 N 2 3.26 0.30 108.30 111.56 A A A O4' C1' N1 DC DC DC 13 13 13 N 3 2.41 0.30 108.30 110.71 A A A O4' C1' N9 DG DG DG 1 1 1 N 3 4.26 0.30 108.30 112.56 A A A O4' C1' N1 DC DC DC 5 5 5 N 3 2.38 0.30 108.30 110.68 A A A O4' C1' N1 DC DC DC 8 8 8 N 3 3.86 0.60 118.90 122.76 A A A N1 C2 O2 DC DC DC 8 8 8 N 3 3.79 0.30 108.30 112.09 A A A O4' C1' N9 DG DG DG 9 9 9 N 3 2.11 0.30 108.30 110.41 A A A O4' C1' N9 DA DA DA 10 10 10 N 3 2.87 0.30 108.30 111.17 A A A O4' C1' N1 DT DT DT 11 11 11 N 4 1.94 0.30 108.30 110.24 A A A O4' C1' N9 DG DG DG 1 1 1 N 4 4.16 0.30 108.30 112.46 A A A O4' C1' N1 DC DC DC 5 5 5 N 4 2.28 0.30 108.30 110.58 A A A O4' C1' N9 DG DG DG 6 6 6 N 4 2.05 0.30 108.30 110.35 A A A O4' C1' N9 DA DA DA 7 7 7 N 4 1.82 0.30 108.30 110.12 A A A O4' C1' N1 DC DC DC 8 8 8 N 4 3.78 0.60 118.90 122.68 A A A N1 C2 O2 DC DC DC 8 8 8 N 4 3.68 0.30 108.30 111.98 A A A O4' C1' N9 DG DG DG 9 9 9 N 4 2.08 0.30 108.30 110.38 A A A O4' C1' N9 DA DA DA 10 10 10 N 4 2.23 0.30 108.30 110.53 A A A O4' C1' N1 DT DT DT 11 11 11 N 5 3.00 0.30 108.30 111.30 A A A O4' C1' N9 DG DG DG 1 1 1 N 5 3.21 0.30 108.30 111.51 A A A O4' C1' N1 DC DC DC 2 2 2 N 5 1.88 0.30 108.30 110.18 A A A O4' C1' N9 DA DA DA 3 3 3 N 5 3.91 0.30 108.30 112.21 A A A O4' C1' N1 DC DC DC 5 5 5 N 5 1.92 0.30 108.30 110.22 A A A O4' C1' N9 DG DG DG 6 6 6 N 5 1.87 0.30 108.30 110.17 A A A O4' C1' N1 DC DC DC 8 8 8 N 5 3.85 0.60 118.90 122.75 A A A N1 C2 O2 DC DC DC 8 8 8 N 5 2.88 0.30 108.30 111.18 A A A O4' C1' N9 DG DG DG 9 9 9 N 5 2.10 0.30 108.30 110.40 A A A O4' C1' N9 DA DA DA 10 10 10 N 5 1.88 0.30 108.30 110.18 A A A O4' C1' N9 DG DG DG 12 12 12 N 5 3.40 0.30 108.30 111.70 A A A O4' C1' N1 DC DC DC 13 13 13 N 6 2.59 0.30 108.30 110.89 A A A O4' C1' N9 DG DG DG 1 1 1 N 6 3.33 0.30 108.30 111.63 A A A O4' C1' N1 DC DC DC 2 2 2 N 6 2.23 0.30 108.30 110.53 A A A O4' C1' N9 DA DA DA 3 3 3 N 6 4.74 0.30 108.30 113.04 A A A O4' C1' N1 DC DC DC 5 5 5 N 6 1.86 0.30 108.30 110.16 A A A O4' C1' N9 DG DG DG 6 6 6 N 6 2.26 0.30 108.30 110.56 A A A O4' C1' N1 DC DC DC 8 8 8 N 6 3.83 0.60 118.90 122.73 A A A N1 C2 O2 DC DC DC 8 8 8 N 6 4.36 0.30 108.30 112.66 A A A O4' C1' N9 DG DG DG 9 9 9 N 6 2.81 0.30 108.30 111.11 A A A O4' C1' N9 DA DA DA 10 10 10 N 6 2.16 0.30 108.30 110.46 A A A O4' C1' N1 DT DT DT 11 11 11 N 6 2.77 0.30 108.30 111.07 A A A O4' C1' N9 DG DG DG 12 12 12 N 6 2.99 0.30 108.30 111.29 A A A O4' C1' N1 DC DC DC 13 13 13 N 7 2.98 0.30 108.30 111.28 A A A O4' C1' N9 DG DG DG 1 1 1 N 7 3.14 0.30 108.30 111.44 A A A O4' C1' N1 DC DC DC 2 2 2 N 7 2.85 0.30 108.30 111.15 A A A O4' C1' N9 DA DA DA 3 3 3 N 7 3.87 0.30 108.30 112.17 A A A O4' C1' N1 DC DC DC 5 5 5 N 7 2.11 0.30 108.30 110.41 A A A O4' C1' N1 DC DC DC 8 8 8 N 7 3.78 0.60 118.90 122.68 A A A N1 C2 O2 DC DC DC 8 8 8 N 7 4.42 0.30 108.30 112.72 A A A O4' C1' N9 DG DG DG 9 9 9 N 7 2.42 0.30 108.30 110.72 A A A O4' C1' N9 DA DA DA 10 10 10 N 7 1.92 0.30 108.30 110.22 A A A O4' C1' N1 DT DT DT 11 11 11 N 7 2.52 0.30 108.30 110.82 A A A O4' C1' N9 DG DG DG 12 12 12 N 7 4.13 0.30 108.30 112.43 A A A O4' C1' N1 DC DC DC 13 13 13 N 8 2.85 0.30 108.30 111.15 A A A O4' C1' N9 DG DG DG 1 1 1 N 8 3.15 0.30 108.30 111.45 A A A O4' C1' N1 DC DC DC 2 2 2 N 8 4.86 0.30 108.30 113.16 A A A O4' C1' N1 DC DC DC 5 5 5 N 8 2.39 0.30 108.30 110.69 A A A O4' C1' N1 DC DC DC 8 8 8 N 8 3.61 0.60 118.90 122.51 A A A N1 C2 O2 DC DC DC 8 8 8 N 8 4.86 0.30 108.30 113.16 A A A O4' C1' N9 DG DG DG 9 9 9 N 8 2.95 0.30 108.30 111.25 A A A O4' C1' N9 DA DA DA 10 10 10 N 8 2.77 0.30 108.30 111.07 A A A O4' C1' N1 DT DT DT 11 11 11 N 8 2.54 0.30 108.30 110.84 A A A O4' C1' N1 DC DC DC 13 13 13 N 9 2.28 0.30 108.30 110.58 A A A O4' C1' N9 DG DG DG 1 1 1 N 9 2.62 0.30 108.30 110.92 A A A O4' C1' N1 DC DC DC 2 2 2 N 9 2.23 0.30 108.30 110.53 A A A O4' C1' N1 DT DT DT 4 4 4 N 9 4.57 0.30 108.30 112.87 A A A O4' C1' N1 DC DC DC 5 5 5 N 9 1.95 0.30 108.30 110.25 A A A O4' C1' N9 DG DG DG 6 6 6 N 9 2.16 0.30 108.30 110.46 A A A O4' C1' N1 DC DC DC 8 8 8 N 9 3.68 0.60 118.90 122.58 A A A N1 C2 O2 DC DC DC 8 8 8 N 9 5.08 0.30 108.30 113.38 A A A O4' C1' N9 DG DG DG 9 9 9 N 9 2.53 0.30 108.30 110.83 A A A O4' C1' N9 DA DA DA 10 10 10 N 9 2.17 0.30 108.30 110.47 A A A O4' C1' N1 DT DT DT 11 11 11 N 9 2.92 0.30 108.30 111.22 A A A O4' C1' N1 DC DC DC 13 13 13 N 10 3.16 0.30 108.30 111.46 A A A O4' C1' N9 DG DG DG 1 1 1 N 10 2.39 0.30 108.30 110.69 A A A O4' C1' N1 DC DC DC 2 2 2 N 10 1.94 0.30 108.30 110.24 A A A O4' C1' N1 DT DT DT 4 4 4 N 10 5.14 0.30 108.30 113.44 A A A O4' C1' N1 DC DC DC 5 5 5 N 10 2.04 0.30 108.30 110.34 A A A O4' C1' N1 DC DC DC 8 8 8 N 10 3.82 0.60 118.90 122.72 A A A N1 C2 O2 DC DC DC 8 8 8 N 10 3.61 0.30 108.30 111.91 A A A O4' C1' N9 DG DG DG 9 9 9 N 10 2.46 0.30 108.30 110.76 A A A O4' C1' N9 DA DA DA 10 10 10 N 10 2.19 0.30 108.30 110.49 A A A O4' C1' N1 DT DT DT 11 11 11 N 10 2.77 0.30 108.30 111.07 A A A O4' C1' N9 DG DG DG 12 12 12 N 10 2.90 0.30 108.30 111.20 A A A O4' C1' N1 DC DC DC 13 13 13 N Sheared G/C Base Pair 1 N N hydrog WATSON-CRICK A DG 1 A N1 DG 1 1_555 A DC 13 A N3 DC 13 1_555 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 A DC 13 A O2 DC 13 1_555 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 A DC 13 A N4 DC 13 1_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 A DG 12 A N1 DG 12 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 A DG 12 A O6 DG 12 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 A DG 12 A N2 DG 12 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 A DT 11 A N3 DT 11 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 A DT 11 A O4 DT 11 1_555 hydrog WATSON-CRICK A DT 4 A N3 DT 4 1_555 A DA 10 A N1 DA 10 1_555 hydrog WATSON-CRICK A DT 4 A O4 DT 4 1_555 A DA 10 A N6 DA 10 1_555 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 A DG 9 A N1 DG 9 1_555 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 A DG 9 A O6 DG 9 1_555 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 A DG 9 A N2 DG 9 1_555 hydrog DG-DC PAIR A DG 6 A N2 DG 6 1_555 A DC 8 A N3 DC 8 1_555 DNA Sheared GC base pair, single-residue loop, syn cytidine, DNA 1P0U PDB 1 1P0U 1 13 1P0U 1 13 1P0U A 1 1 13