1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Chou, S.-H. Zhu, L. Gao, Z. Cheng, J.-W. Reid, B.R. 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 UK J.Mol.Biol. JMOBAK 0070 0022-2836 264 981 10.1006/jmbi.1996.0691 9000625 Hairpin loops consisting of single adenine residues closed by sheared A.A and G.G pairs formed by the DNA triplets AAA and GAG: solution structure of the d(GTACAAAGTAC) hairpin. 1996 10.2210/pdb1bjh/pdb pdb_00001bjh 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 3366.237 DNA (5'-D(*GP*TP*AP*CP*AP*AP*AP*GP*TP*AP*C)-3') 1 syn polymer no no (DG)(DT)(DA)(DC)(DA)(DA)(DA)(DG)(DT)(DA)(DC) GTACAAAGTAC A polydeoxyribonucleotide n n n n n n n n n n n 1.734 1 19 A 1 A 11 -2.675 A_DG1:DC11_A 1 -17.131 -0.893 0.321 -0.339 -0.563 1 20 A 2 A 10 2.918 A_DT2:DA10_A 2 -20.728 0.367 -0.026 -0.107 0.282 1 20 A 3 A 9 -1.388 A_DA3:DT9_A 3 0.821 -0.321 0.628 -0.145 16.363 1 19 A 4 A 8 1.395 A_DC4:DG8_A 4 9.323 0.851 0.247 -0.284 34.779 A 5 A 7 17.226 A_DA5:DA7_A 5 -6.966 6.800 1.271 -3.999 3.231 44.727 A A 1 2 -2.117 A A 11 10 3.234 -1.607 -0.016 -0.678 AA_DG1DT2:DA10DC11_AA 1 5.479 -7.218 44.379 -0.745 0.516 2.503 33.651 A A 2 3 15.560 A A 10 9 2.874 8.850 -0.094 -0.931 AA_DT2DA3:DT9DA10_AA 2 -6.611 11.624 31.836 -2.830 -0.751 2.976 36.149 A A 3 4 0.798 A A 9 8 2.966 0.495 0.353 -0.184 AA_DA3DC4:DG8DT9_AA 3 1.593 -2.568 36.111 -0.360 -0.364 3.138 56.735 A A 4 5 7.402 A A 8 7 2.947 7.015 0.896 1.436 AA_DC4DA5:DA7DG8_AA 4 3.574 -3.772 56.231 1.146 -0.757 database_2 pdbx_database_status pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Other 1 0 1997-12-03 1 1 2008-03-24 1 2 2011-07-13 1 3 2022-02-16 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site _pdbx_nmr_software.name Y BNL 1997-07-25 REL REL AMBER FORCE FIELD IS USED 16 BIOSYM TECHNOLOGIES refinement Discover G 1 n 1 DG 1 A T 2 n 2 DT 2 A A 3 n 3 DA 3 A C 4 n 4 DC 4 A A 5 n 5 DA 5 A A 6 n 6 DA 6 A A 7 n 7 DA 7 A G 8 n 8 DG 8 A T 9 n 9 DT 9 A A 10 n 10 DA 10 A C 11 n 11 DC 11 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 DT 2 0.066 SIDE CHAIN 1 A DA 3 0.053 SIDE CHAIN 1 A DA 7 0.095 SIDE CHAIN 2 A DT 2 0.067 SIDE CHAIN 2 A DA 3 0.056 SIDE CHAIN 2 A DA 7 0.096 SIDE CHAIN 3 A DT 2 0.065 SIDE CHAIN 3 A DA 3 0.053 SIDE CHAIN 3 A DA 7 0.095 SIDE CHAIN 4 A DT 2 0.066 SIDE CHAIN 4 A DA 3 0.054 SIDE CHAIN 4 A DA 7 0.095 SIDE CHAIN 5 A DT 2 0.065 SIDE CHAIN 5 A DA 3 0.054 SIDE CHAIN 5 A DA 7 0.095 SIDE CHAIN 6 A DT 2 0.065 SIDE CHAIN 6 A DA 3 0.054 SIDE CHAIN 6 A DA 7 0.095 SIDE CHAIN 7 A DT 2 0.066 SIDE CHAIN 7 A DA 3 0.056 SIDE CHAIN 7 A DA 7 0.096 SIDE CHAIN 8 A DT 2 0.066 SIDE CHAIN 8 A DA 3 0.053 SIDE CHAIN 8 A DA 7 0.095 SIDE CHAIN 9 A DT 2 0.067 SIDE CHAIN 9 A DA 3 0.054 SIDE CHAIN 9 A DA 7 0.096 SIDE CHAIN 10 A DT 2 0.064 SIDE CHAIN 10 A DA 7 0.094 SIDE CHAIN 10 A DA 10 0.069 SIDE CHAIN 11 A DT 2 0.066 SIDE CHAIN 11 A DA 3 0.053 SIDE CHAIN 11 A DA 7 0.095 SIDE CHAIN 12 A DT 2 0.067 SIDE CHAIN 12 A DA 3 0.053 SIDE CHAIN 12 A DA 7 0.094 SIDE CHAIN 13 A DT 2 0.065 SIDE CHAIN 13 A DA 3 0.053 SIDE CHAIN 13 A DA 7 0.095 SIDE CHAIN 14 A DT 2 0.065 SIDE CHAIN 14 A DA 3 0.051 SIDE CHAIN 14 A DA 7 0.095 SIDE CHAIN 15 A DT 2 0.064 SIDE CHAIN 15 A DA 3 0.053 SIDE CHAIN 15 A DA 7 0.095 SIDE CHAIN 16 A DT 2 0.066 SIDE CHAIN 16 A DA 3 0.055 SIDE CHAIN 16 A DA 7 0.096 SIDE CHAIN 1 3.09 0.30 108.30 111.39 A A A O4' C1' N9 DG DG DG 1 1 1 N 1 2.02 0.30 108.30 110.32 A A A O4' C1' N1 DT DT DT 2 2 2 N 1 2.24 0.30 108.30 110.54 A A A O4' C1' N1 DC DC DC 4 4 4 N 1 3.07 0.30 108.30 111.37 A A A O4' C1' N9 DA DA DA 5 5 5 N 1 4.19 0.30 108.30 112.49 A A A O4' C1' N9 DA DA DA 6 6 6 N 1 2.07 0.30 108.30 110.37 A A A O4' C1' N1 DT DT DT 9 9 9 N 1 2.00 0.30 108.30 110.30 A A A O4' C1' N9 DA DA DA 10 10 10 N 1 2.40 0.30 108.30 110.70 A A A O4' C1' N1 DC DC DC 11 11 11 N 2 3.54 0.30 108.30 111.84 A A A O4' C1' N9 DG DG DG 1 1 1 N 2 2.12 0.30 108.30 110.42 A A A O4' C1' N1 DT DT DT 2 2 2 N 2 2.24 0.30 108.30 110.54 A A A O4' C1' N1 DC DC DC 4 4 4 N 2 3.06 0.30 108.30 111.36 A A A O4' C1' N9 DA DA DA 5 5 5 N 2 4.14 0.30 108.30 112.44 A A A O4' C1' N9 DA DA DA 6 6 6 N 2 2.07 0.30 108.30 110.37 A A A O4' C1' N1 DT DT DT 9 9 9 N 2 -3.64 0.60 122.90 119.26 A A A C6 C5 C7 DT DT DT 9 9 9 N 2 2.18 0.30 108.30 110.48 A A A O4' C1' N9 DA DA DA 10 10 10 N 2 2.31 0.30 108.30 110.61 A A A O4' C1' N1 DC DC DC 11 11 11 N 3 3.02 0.30 108.30 111.32 A A A O4' C1' N9 DG DG DG 1 1 1 N 3 2.02 0.30 108.30 110.32 A A A O4' C1' N1 DT DT DT 2 2 2 N 3 2.30 0.30 108.30 110.60 A A A O4' C1' N1 DC DC DC 4 4 4 N 3 3.06 0.30 108.30 111.36 A A A O4' C1' N9 DA DA DA 5 5 5 N 3 4.14 0.30 108.30 112.44 A A A O4' C1' N9 DA DA DA 6 6 6 N 3 2.07 0.30 108.30 110.37 A A A O4' C1' N1 DT DT DT 9 9 9 N 3 2.02 0.30 108.30 110.32 A A A O4' C1' N9 DA DA DA 10 10 10 N 3 2.46 0.30 108.30 110.76 A A A O4' C1' N1 DC DC DC 11 11 11 N 4 3.03 0.30 108.30 111.33 A A A O4' C1' N9 DG DG DG 1 1 1 N 4 2.05 0.30 108.30 110.35 A A A O4' C1' N1 DT DT DT 2 2 2 N 4 2.22 0.30 108.30 110.52 A A A O4' C1' N1 DC DC DC 4 4 4 N 4 3.07 0.30 108.30 111.37 A A A O4' C1' N9 DA DA DA 5 5 5 N 4 4.15 0.30 108.30 112.45 A A A O4' C1' N9 DA DA DA 6 6 6 N 4 2.03 0.30 108.30 110.33 A A A O4' C1' N1 DT DT DT 9 9 9 N 4 -3.62 0.60 122.90 119.28 A A A C6 C5 C7 DT DT DT 9 9 9 N 4 2.04 0.30 108.30 110.34 A A A O4' C1' N9 DA DA DA 10 10 10 N 4 2.35 0.30 108.30 110.65 A A A O4' C1' N1 DC DC DC 11 11 11 N 5 3.13 0.30 108.30 111.43 A A A O4' C1' N9 DG DG DG 1 1 1 N 5 1.98 0.30 108.30 110.28 A A A O4' C1' N1 DT DT DT 2 2 2 N 5 2.23 0.30 108.30 110.53 A A A O4' C1' N1 DC DC DC 4 4 4 N 5 3.09 0.30 108.30 111.39 A A A O4' C1' N9 DA DA DA 5 5 5 N 5 4.14 0.30 108.30 112.44 A A A O4' C1' N9 DA DA DA 6 6 6 N 5 2.03 0.30 108.30 110.33 A A A O4' C1' N1 DT DT DT 9 9 9 N 5 -3.62 0.60 122.90 119.28 A A A C6 C5 C7 DT DT DT 9 9 9 N 5 2.15 0.30 108.30 110.45 A A A O4' C1' N9 DA DA DA 10 10 10 N 5 2.41 0.30 108.30 110.71 A A A O4' C1' N1 DC DC DC 11 11 11 N 6 3.13 0.30 108.30 111.43 A A A O4' C1' N9 DG DG DG 1 1 1 N 6 1.98 0.30 108.30 110.28 A A A O4' C1' N1 DT DT DT 2 2 2 N 6 2.23 0.30 108.30 110.53 A A A O4' C1' N1 DC DC DC 4 4 4 N 6 3.09 0.30 108.30 111.39 A A A O4' C1' N9 DA DA DA 5 5 5 N 6 4.14 0.30 108.30 112.44 A A A O4' C1' N9 DA DA DA 6 6 6 N 6 2.03 0.30 108.30 110.33 A A A O4' C1' N1 DT DT DT 9 9 9 N 6 -3.62 0.60 122.90 119.28 A A A C6 C5 C7 DT DT DT 9 9 9 N 6 2.15 0.30 108.30 110.45 A A A O4' C1' N9 DA DA DA 10 10 10 N 6 2.41 0.30 108.30 110.71 A A A O4' C1' N1 DC DC DC 11 11 11 N 7 3.47 0.30 108.30 111.77 A A A O4' C1' N9 DG DG DG 1 1 1 N 7 2.05 0.30 108.30 110.35 A A A O4' C1' N1 DT DT DT 2 2 2 N 7 2.23 0.30 108.30 110.53 A A A O4' C1' N1 DC DC DC 4 4 4 N 7 3.09 0.30 108.30 111.39 A A A O4' C1' N9 DA DA DA 5 5 5 N 7 4.17 0.30 108.30 112.47 A A A O4' C1' N9 DA DA DA 6 6 6 N 7 2.04 0.30 108.30 110.34 A A A O4' C1' N1 DT DT DT 9 9 9 N 7 -3.63 0.60 122.90 119.27 A A A C6 C5 C7 DT DT DT 9 9 9 N 7 2.16 0.30 108.30 110.46 A A A O4' C1' N9 DA DA DA 10 10 10 N 7 2.30 0.30 108.30 110.60 A A A O4' C1' N1 DC DC DC 11 11 11 N 8 3.32 0.30 108.30 111.62 A A A O4' C1' N9 DG DG DG 1 1 1 N 8 2.13 0.30 108.30 110.43 A A A O4' C1' N1 DT DT DT 2 2 2 N 8 2.20 0.30 108.30 110.50 A A A O4' C1' N1 DC DC DC 4 4 4 N 8 3.04 0.30 108.30 111.34 A A A O4' C1' N9 DA DA DA 5 5 5 N 8 4.15 0.30 108.30 112.45 A A A O4' C1' N9 DA DA DA 6 6 6 N 8 2.03 0.30 108.30 110.33 A A A O4' C1' N1 DT DT DT 9 9 9 N 8 -3.60 0.60 122.90 119.30 A A A C6 C5 C7 DT DT DT 9 9 9 N 8 1.94 0.30 108.30 110.24 A A A O4' C1' N9 DA DA DA 10 10 10 N 8 2.43 0.30 108.30 110.73 A A A O4' C1' N1 DC DC DC 11 11 11 N 9 3.21 0.30 108.30 111.51 A A A O4' C1' N9 DG DG DG 1 1 1 N 9 2.06 0.30 108.30 110.36 A A A O4' C1' N1 DT DT DT 2 2 2 N 9 2.28 0.30 108.30 110.58 A A A O4' C1' N1 DC DC DC 4 4 4 N 9 3.05 0.30 108.30 111.35 A A A O4' C1' N9 DA DA DA 5 5 5 N 9 4.13 0.30 108.30 112.43 A A A O4' C1' N9 DA DA DA 6 6 6 N 9 2.07 0.30 108.30 110.37 A A A O4' C1' N1 DT DT DT 9 9 9 N 9 2.01 0.30 108.30 110.31 A A A O4' C1' N9 DA DA DA 10 10 10 N 9 2.41 0.30 108.30 110.71 A A A O4' C1' N1 DC DC DC 11 11 11 N 10 1.96 0.30 108.30 110.26 A A A O4' C1' N9 DG DG DG 1 1 1 N 10 1.95 0.30 108.30 110.25 A A A O4' C1' N1 DT DT DT 2 2 2 N 10 2.23 0.30 108.30 110.53 A A A O4' C1' N1 DC DC DC 4 4 4 N 10 3.01 0.30 108.30 111.31 A A A O4' C1' N9 DA DA DA 5 5 5 N 10 4.21 0.30 108.30 112.51 A A A O4' C1' N9 DA DA DA 6 6 6 N 10 1.96 0.30 108.30 110.26 A A A O4' C1' N1 DT DT DT 9 9 9 N 10 4.97 0.30 108.30 113.27 A A A O4' C1' N1 DC DC DC 11 11 11 N 11 3.21 0.30 108.30 111.51 A A A O4' C1' N9 DG DG DG 1 1 1 N 11 2.10 0.30 108.30 110.40 A A A O4' C1' N1 DT DT DT 2 2 2 N 11 2.22 0.30 108.30 110.52 A A A O4' C1' N1 DC DC DC 4 4 4 N 11 3.04 0.30 108.30 111.34 A A A O4' C1' N9 DA DA DA 5 5 5 N 11 4.09 0.30 108.30 112.39 A A A O4' C1' N9 DA DA DA 6 6 6 N 11 2.02 0.30 108.30 110.32 A A A O4' C1' N1 DT DT DT 9 9 9 N 11 1.92 0.30 108.30 110.22 A A A O4' C1' N9 DA DA DA 10 10 10 N 11 2.39 0.30 108.30 110.69 A A A O4' C1' N1 DC DC DC 11 11 11 N 12 3.26 0.30 108.30 111.56 A A A O4' C1' N9 DG DG DG 1 1 1 N 12 2.11 0.30 108.30 110.41 A A A O4' C1' N1 DT DT DT 2 2 2 N 12 2.26 0.30 108.30 110.56 A A A O4' C1' N1 DC DC DC 4 4 4 N 12 3.04 0.30 108.30 111.34 A A A O4' C1' N9 DA DA DA 5 5 5 N 12 4.19 0.30 108.30 112.49 A A A O4' C1' N9 DA DA DA 6 6 6 N 12 2.01 0.30 108.30 110.31 A A A O4' C1' N1 DT DT DT 9 9 9 N 12 -3.65 0.60 122.90 119.25 A A A C6 C5 C7 DT DT DT 9 9 9 N 12 1.98 0.30 108.30 110.28 A A A O4' C1' N9 DA DA DA 10 10 10 N 12 2.45 0.30 108.30 110.75 A A A O4' C1' N1 DC DC DC 11 11 11 N 13 3.18 0.30 108.30 111.48 A A A O4' C1' N9 DG DG DG 1 1 1 N 13 2.01 0.30 108.30 110.31 A A A O4' C1' N1 DT DT DT 2 2 2 N 13 2.31 0.30 108.30 110.61 A A A O4' C1' N1 DC DC DC 4 4 4 N 13 3.10 0.30 108.30 111.40 A A A O4' C1' N9 DA DA DA 5 5 5 N 13 4.16 0.30 108.30 112.46 A A A O4' C1' N9 DA DA DA 6 6 6 N 13 2.02 0.30 108.30 110.32 A A A O4' C1' N1 DT DT DT 9 9 9 N 13 -3.61 0.60 122.90 119.29 A A A C6 C5 C7 DT DT DT 9 9 9 N 13 2.08 0.30 108.30 110.38 A A A O4' C1' N9 DA DA DA 10 10 10 N 13 2.37 0.30 108.30 110.67 A A A O4' C1' N1 DC DC DC 11 11 11 N 14 2.93 0.30 108.30 111.23 A A A O4' C1' N9 DG DG DG 1 1 1 N 14 2.06 0.30 108.30 110.36 A A A O4' C1' N1 DT DT DT 2 2 2 N 14 2.26 0.30 108.30 110.56 A A A O4' C1' N1 DC DC DC 4 4 4 N 14 3.06 0.30 108.30 111.36 A A A O4' C1' N9 DA DA DA 5 5 5 N 14 4.15 0.30 108.30 112.45 A A A O4' C1' N9 DA DA DA 6 6 6 N 14 2.01 0.30 108.30 110.31 A A A O4' C1' N1 DT DT DT 9 9 9 N 14 1.92 0.30 108.30 110.22 A A A O4' C1' N9 DA DA DA 10 10 10 N 14 2.41 0.30 108.30 110.71 A A A O4' C1' N1 DC DC DC 11 11 11 N 15 3.12 0.30 108.30 111.42 A A A O4' C1' N9 DG DG DG 1 1 1 N 15 2.01 0.30 108.30 110.31 A A A O4' C1' N1 DT DT DT 2 2 2 N 15 2.26 0.30 108.30 110.56 A A A O4' C1' N1 DC DC DC 4 4 4 N 15 3.09 0.30 108.30 111.39 A A A O4' C1' N9 DA DA DA 5 5 5 N 15 4.13 0.30 108.30 112.43 A A A O4' C1' N9 DA DA DA 6 6 6 N 15 2.04 0.30 108.30 110.34 A A A O4' C1' N1 DT DT DT 9 9 9 N 15 -3.61 0.60 122.90 119.29 A A A C6 C5 C7 DT DT DT 9 9 9 N 15 2.12 0.30 108.30 110.42 A A A O4' C1' N9 DA DA DA 10 10 10 N 15 2.40 0.30 108.30 110.70 A A A O4' C1' N1 DC DC DC 11 11 11 N 16 3.22 0.30 108.30 111.52 A A A O4' C1' N9 DG DG DG 1 1 1 N 16 2.03 0.30 108.30 110.33 A A A O4' C1' N1 DT DT DT 2 2 2 N 16 2.26 0.30 108.30 110.56 A A A O4' C1' N1 DC DC DC 4 4 4 N 16 3.03 0.30 108.30 111.33 A A A O4' C1' N9 DA DA DA 5 5 5 N 16 4.15 0.30 108.30 112.45 A A A O4' C1' N9 DA DA DA 6 6 6 N 16 2.05 0.30 108.30 110.35 A A A O4' C1' N1 DT DT DT 9 9 9 N 16 2.23 0.30 108.30 110.53 A A A O4' C1' N9 DA DA DA 10 10 10 N 16 2.33 0.30 108.30 110.63 A A A O4' C1' N1 DC DC DC 11 11 11 N refinement AMBER HAIRPIN LOOPS CONSISTING OF SINGLE ADENINE RESIDUES CLOSED BY SHEARED A(DOT)A AND G(DOT)G PAIRS FORMED BY THE DNA TRIPLETS AAA AND GAG: SOLUTION STRUCTURE OF THE D(GTACAAAGTAC) HAIRPIN, NMR, 16 STRUCTURES 1 N N hydrog WATSON-CRICK A DG 1 A N1 DG 1 1_555 A DC 11 A N3 DC 11 1_555 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 A DC 11 A O2 DC 11 1_555 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 A DC 11 A N4 DC 11 1_555 hydrog WATSON-CRICK A DT 2 A N3 DT 2 1_555 A DA 10 A N1 DA 10 1_555 hydrog WATSON-CRICK A DT 2 A O4 DT 2 1_555 A DA 10 A N6 DA 10 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 A DT 9 A N3 DT 9 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 A DT 9 A O4 DT 9 1_555 hydrog WATSON-CRICK A DC 4 A N3 DC 4 1_555 A DG 8 A N1 DG 8 1_555 hydrog WATSON-CRICK A DC 4 A N4 DC 4 1_555 A DG 8 A O6 DG 8 1_555 hydrog WATSON-CRICK A DC 4 A O2 DC 4 1_555 A DG 8 A N2 DG 8 1_555 hydrog DA-DA MISPAIR A DA 5 A N3 DA 5 1_555 A DA 7 A N6 DA 7 1_555 DNA DNA LOOP, SHEARED A:A, AAA LOOP, SINGLE RESIDUE LOOP, DEOXYRIBONUCLEIC ACID, DNA 1BJH PDB 1 1BJH 1 11 1BJH 1 11 1BJH A 1 1 11 1 P 1