1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Aramini, J.M. Mujeeb, A. Germann, M.W. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 C10 H15 N2 O8 P 322.208 n THYMIDINE-3'-PHOSPHATE DNA linking 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 Nucleic Acids Res. NARHAD 0389 0305-1048 26 5644 5654 10.1093/nar/26.24.5644 9837995 NMR solution structures of [d(GCGAAT-3'-3'-alphaT-5'-5'-CGC)2] and its unmodified control. 1998 10.2210/pdb1bx5/pdb pdb_00001bx5 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 ALPHA ANOMERIC THYMIDINES AT POSITION 7 3'-3' PHOSPHODIESTER LINKAGE BETWEEN T6 AND ALPHAT7 5'-5' PHOSPHODIESTER LINKAGE BETWEEN ALPHAT7 AND C8 3045.005 DNA (5'-D(*GP*CP*GP*AP*AP*TP*(ATD)P*CP*GP*C)-3') ALPHA ANOMERIC T, 3'-3' AND 5'-5' PHOSPHODIESTER LINKAGES 2 syn polymer no yes (DG)(DC)(DG)(DA)(DA)(DT)(ATD)(DC)(DG)(DC) GCGAATTCGC A,B polydeoxyribonucleotide n n n n n n n n n n 24.446 1 19 A 1 B 20 0.487 A_DG1:DC20_B 1 7.540 -0.439 0.204 -0.104 8.425 1 19 A 2 B 19 0.727 A_DC2:DG19_B 2 -13.345 0.144 -0.655 -0.267 10.251 1 19 A 3 B 18 0.171 A_DG3:DC18_B 3 0.902 0.068 -0.052 -0.108 3.441 1 20 A 4 B 17 -2.115 A_DA4:ATD17_B 4 -7.115 0.024 -0.097 -0.107 7.079 1 20 A 5 B 16 -2.353 A_DA5:DT16_B 5 -18.641 -0.056 0.120 -0.160 -5.272 1 20 A 6 B 15 -3.980 A_DT6:DA15_B 6 -19.563 -0.021 0.073 -0.148 -0.031 1 20 A 7 B 14 -1.685 A_ATD7:DA14_B 7 -6.696 -0.013 -0.244 -0.110 -4.941 1 19 A 8 B 13 0.413 A_DC8:DG13_B 8 -3.164 -0.142 -0.101 -0.113 3.622 1 19 A 9 B 12 -1.028 A_DG9:DC12_B 9 -4.972 -0.167 -0.269 -0.242 -14.946 1 19 A 10 B 11 -0.347 A_DC10:DG11_B 10 4.533 0.436 0.037 -0.168 3.353 36.858 A A 1 2 9.229 B B 20 19 3.599 5.795 -0.019 -1.121 AA_DG1DC2:DG19DC20_BB 1 5.011 -7.980 36.080 -2.617 0.759 2.415 35.579 A A 2 3 39.317 B B 19 18 3.422 22.322 -0.424 -0.473 AA_DC2DG3:DC18DG19_BB 2 -0.660 1.162 27.875 -4.058 0.597 3.284 37.856 A A 3 4 -10.312 B B 18 17 3.435 -6.656 -0.907 0.433 AA_DG3DA4:ATD17DC18_BB 3 1.155 -1.790 37.270 1.553 1.552 3.229 39.458 A A 4 5 -3.486 B B 17 16 3.188 -2.345 -0.528 -0.076 AA_DA4DA5:DT16ATD17_BB 4 -5.408 8.038 39.033 0.160 0.153 3.592 31.817 A A 5 6 -6.640 B B 16 15 3.533 -3.632 -0.164 -0.726 AA_DA5DT6:DA15DT16_BB 5 -0.116 0.211 31.614 -0.598 0.276 3.205 39.877 A A 6 7 -4.270 B B 15 14 3.141 -2.899 0.683 -0.086 AA_DT6ATD7:DA14DA15_BB 6 6.080 -8.955 39.327 0.201 -0.316 3.205 38.110 A A 7 8 -9.647 B B 14 13 3.364 -6.269 0.886 0.378 AA_ATD7DC8:DG13DA14_BB 7 -2.287 3.519 37.542 1.382 -1.650 2.138 34.465 A A 8 9 38.786 B B 13 12 3.160 21.324 -0.224 -0.610 AA_DC8DG9:DC12DG13_BB 8 -4.329 7.873 26.891 -4.071 -0.240 3.427 37.336 A A 9 10 9.089 B B 12 11 3.678 5.796 0.222 -1.348 AA_DG9DC10:DG11DC12_BB 9 -1.138 1.784 36.883 -2.942 -0.511 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list pdbx_validate_polymer_linkage struct_conn repository Initial release Version format compliance Version format compliance Advisory Data collection Database references Derived calculations 1 0 1999-01-06 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-16 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_conn.pdbx_leaving_atom_flag BNL Y RCSB 1998-09-28 REL REL MEAN STRUCTURE. THE STRUCTURE WAS DETERMINED USING DISTANCE AND TORSION ANGLE RESTRAINTS OBTAINED FROM HOMONUCLEAR NOESY (75, 150, 300 MS MIXING TIMES) AND DQF-COSY EXPERIMENTS. 9 1 NOESY DQF-COSY 50 mM NACL, 10 mM NAPHOSPHATE, 0.1 mM EDTA 6.5 1 atm 303 K REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE simulated annealing PEARLMAN ET AL., 1995 refinement Amber 4.1 structure solution RAMDMARDI structure solution Amber 4.1 600 Bruker AMX600 G 1 n 1 DG 1 A C 2 n 2 DC 2 A G 3 n 3 DG 3 A A 4 n 4 DA 4 A A 5 n 5 DA 5 A T 6 n 6 DT 6 A X 7 n 7 ATD 7 A C 8 n 8 DC 8 A G 9 n 9 DG 9 A C 10 n 10 DC 10 A G 11 n 1 DG 11 B C 12 n 2 DC 12 B G 13 n 3 DG 13 B A 14 n 4 DA 14 B A 15 n 5 DA 15 B T 16 n 6 DT 16 B X 17 n 7 ATD 17 B C 18 n 8 DC 18 B G 19 n 9 DG 19 B C 20 n 10 DC 20 B author_defined_assembly 2 dimeric A ATD 7 THYMIDINE-3'-PHOSPHATE A ATD 7 DT B ATD 17 THYMIDINE-3'-PHOSPHATE B ATD 7 DT 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 8 0.067 SIDE CHAIN 1 4.72 0.60 106.00 110.72 A A A O4' C4' C3' DC DC DC 2 2 2 N 1 5.23 0.30 108.30 113.53 A A A O4' C1' N1 DC DC DC 2 2 2 N 1 -3.68 0.60 119.90 116.22 A A A N1 C6 O6 DG DG DG 3 3 3 N 1 3.67 0.60 106.00 109.67 A A A O4' C4' C3' DA DA DA 4 4 4 N 1 3.92 0.60 106.00 109.92 A A A O4' C4' C3' DA DA DA 5 5 5 N 1 4.97 0.30 108.30 113.27 A A A O4' C1' N1 DT DT DT 6 6 6 N 1 4.45 0.60 119.00 123.45 A A A C4 C5 C7 DT DT DT 6 6 6 N 1 -6.80 0.60 122.90 116.10 A A A C6 C5 C7 DT DT DT 6 6 6 N 1 46.68 1.90 104.00 150.68 A A A O3' P O5' DT ATD ATD 6 7 7 Y 1 5.65 0.60 106.00 111.65 A A A O4' C4' C3' DC DC DC 8 8 8 N 1 10.55 1.20 102.50 113.05 A A A C3' C2' C1' DC DC DC 8 8 8 N 1 10.75 0.30 108.30 119.05 A A A O4' C1' N1 DC DC DC 8 8 8 N 1 4.08 0.30 108.30 112.38 A A A O4' C1' N1 DC DC DC 10 10 10 N 1 4.72 0.60 106.00 110.72 B B B O4' C4' C3' DC DC DC 12 12 12 N 1 3.91 0.30 108.30 112.21 B B B O4' C1' N1 DC DC DC 12 12 12 N 1 -3.63 0.60 119.90 116.27 B B B N1 C6 O6 DG DG DG 13 13 13 N 1 3.68 0.60 106.00 109.68 B B B O4' C4' C3' DA DA DA 15 15 15 N 1 5.97 0.30 108.30 114.27 B B B O4' C1' N1 DT DT DT 16 16 16 N 1 4.73 0.60 119.00 123.73 B B B C4 C5 C7 DT DT DT 16 16 16 N 1 -6.78 0.60 122.90 116.12 B B B C6 C5 C7 DT DT DT 16 16 16 N 1 46.65 1.90 104.00 150.65 B B B O3' P O5' DT ATD ATD 16 17 17 Y 1 5.59 0.60 106.00 111.59 B B B O4' C4' C3' DC DC DC 18 18 18 N 1 9.41 1.20 102.50 111.91 B B B C3' C2' C1' DC DC DC 18 18 18 N 1 9.90 0.30 108.30 118.20 B B B O4' C1' N1 DC DC DC 18 18 18 N 1 4.17 0.30 108.30 112.47 B B B O4' C1' N1 DC DC DC 20 20 20 N NMR SOLUTION STRUCTURE OF [D(GCGAAT-3'-3'-ALPHAT-5'-5'-CGC)2] 1 N N 1 N N covale 1.608 both A DT 6 A O3' DT 6 1_555 A ATD 7 A P ATD 7 1_555 covale 1.610 one A ATD 7 A O5' ATD 7 1_555 A DC 8 A P DC 8 1_555 covale 1.601 both B DT 16 B O3' DT 6 1_555 B ATD 17 B P ATD 7 1_555 covale 1.609 one B ATD 17 B O5' ATD 7 1_555 B DC 18 B P DC 8 1_555 hydrog WATSON-CRICK A DG 1 A N1 DG 1 1_555 B DC 20 B N3 DC 10 1_555 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 B DC 20 B O2 DC 10 1_555 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 B DC 20 B N4 DC 10 1_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 B DG 19 B N1 DG 9 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 B DG 19 B O6 DG 9 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 B DG 19 B N2 DG 9 1_555 hydrog WATSON-CRICK A DG 3 A N1 DG 3 1_555 B DC 18 B N3 DC 8 1_555 hydrog WATSON-CRICK A DG 3 A N2 DG 3 1_555 B DC 18 B O2 DC 8 1_555 hydrog WATSON-CRICK A DG 3 A O6 DG 3 1_555 B DC 18 B N4 DC 8 1_555 hydrog WATSON-CRICK A DA 4 A N1 DA 4 1_555 B ATD 17 B N3 ATD 7 1_555 hydrog WATSON-CRICK A DA 4 A N6 DA 4 1_555 B ATD 17 B O4 ATD 7 1_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 B DT 16 B N3 DT 6 1_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 B DT 16 B O4 DT 6 1_555 hydrog WATSON-CRICK A DT 6 A N3 DT 6 1_555 B DA 15 B N1 DA 5 1_555 hydrog WATSON-CRICK A DT 6 A O4 DT 6 1_555 B DA 15 B N6 DA 5 1_555 hydrog WATSON-CRICK A ATD 7 A N3 ATD 7 1_555 B DA 14 B N1 DA 4 1_555 hydrog WATSON-CRICK A ATD 7 A O4 ATD 7 1_555 B DA 14 B N6 DA 4 1_555 hydrog WATSON-CRICK A DC 8 A N3 DC 8 1_555 B DG 13 B N1 DG 3 1_555 hydrog WATSON-CRICK A DC 8 A N4 DC 8 1_555 B DG 13 B O6 DG 3 1_555 hydrog WATSON-CRICK A DC 8 A O2 DC 8 1_555 B DG 13 B N2 DG 3 1_555 hydrog WATSON-CRICK A DG 9 A N1 DG 9 1_555 B DC 12 B N3 DC 2 1_555 hydrog WATSON-CRICK A DG 9 A N2 DG 9 1_555 B DC 12 B O2 DC 2 1_555 hydrog WATSON-CRICK A DG 9 A O6 DG 9 1_555 B DC 12 B N4 DC 2 1_555 hydrog WATSON-CRICK A DC 10 A N3 DC 10 1_555 B DG 11 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 10 A N4 DC 10 1_555 B DG 11 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 10 A O2 DC 10 1_555 B DG 11 B N2 DG 1 1_555 DNA ALPHA ANOMERIC, POLARITY REVERSALS, DNA 1BX5 PDB 1 1BX5 1 10 1BX5 1 10 1BX5 A 1 1 10 11 20 1BX5 11 20 1BX5 B 1 1 10 1 P 1