1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Volk, D.E. Yang, X. Fennewald, S.M. King, D.J. Bassett, S.E. Venkitachalam, S. Herzog, N. Luxon, B.A. Gorenstein, D.G. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C9 H14 N3 O5 P S2 339.328 n CYTIDINE-5'-DITHIOPHOSPHORATE 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 US Bioorg.Chem. BOCMBM 0368 0045-2068 30 396 419 10.1016/S0045-2068(02)00510-2 12642125 Solution structure and design of dithiophosphate backbone aptamers targeting transcription factor NF-kappaB 2002 10.2210/pdb1k8n/pdb pdb_00001k8n 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 CK14 IS A SUBUNIT OF THE NF-KB BINDING SITE CK1 4249.781 FIRST STRAND OF CK14 DNA DUPLEX 1 syn polymer CK14 IS A SUBUNIT OF THE NF-KB BINDING SITE CK1 4376.063 SECOND STRAND OF CK14 DNA DUPLEX DITHIOATED AT C22 and C24 DITHIOATED AT C22 and C24 1 syn polymer no no (DC)(DC)(DA)(DG)(DG)(DA)(DG)(DA)(DT)(DT)(DC)(DC)(DA)(DC) CCAGGAGATTCCAC A polydeoxyribonucleotide no yes (DG)(DT)(DG)(DG)(DA)(DA)(DT)(C2S)(DT)(C2S)(DC)(DT)(DG)(DG) GTGGAATCTCCTGG B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n n n n n n 33.540 1 19 A 1 B 28 1.266 A_DC1:DG28_B 1 -17.943 0.650 -0.607 -0.140 3.532 1 19 A 2 B 27 -1.320 A_DC2:DG27_B 2 8.410 0.386 -0.315 -0.226 -2.377 1 20 A 3 B 26 -5.926 A_DA3:DT26_B 3 -1.949 0.412 -0.282 -0.015 11.403 1 19 A 4 B 25 0.826 A_DG4:DC25_B 4 0.047 -0.447 -0.063 -0.211 17.891 1 19 A 5 B 24 -0.719 A_DG5:C2S24_B 5 4.489 -0.302 0.291 -0.145 17.601 1 20 A 6 B 23 1.959 A_DA6:DT23_B 6 -13.297 0.043 -0.219 -0.143 2.674 1 19 A 7 B 22 -0.823 A_DG7:C2S22_B 7 -4.831 -0.294 -0.138 -0.197 4.209 1 20 A 8 B 21 -2.042 A_DA8:DT21_B 8 -11.873 0.073 0.083 -0.109 -1.331 1 20 A 9 B 20 -4.791 A_DT9:DA20_B 9 -12.268 -0.166 0.039 -0.094 -0.607 1 20 A 10 B 19 -2.865 A_DT10:DA19_B 10 -12.855 -0.183 -0.198 -0.099 -8.160 1 19 A 11 B 18 -0.723 A_DC11:DG18_B 11 -3.718 0.338 -0.055 -0.211 -6.008 1 19 A 12 B 17 -0.014 A_DC12:DG17_B 12 -1.402 0.384 0.175 -0.206 4.726 1 20 A 13 B 16 -1.609 A_DA13:DT16_B 13 -6.327 0.108 0.058 -0.115 0.610 1 19 A 14 B 15 -0.040 A_DC14:DG15_B 14 -4.148 0.507 0.207 -0.240 6.124 38.049 A A 1 2 -3.331 B B 28 27 6.281 -2.156 0.473 -1.336 AA_DC1DC2:DG27DG28_BB 1 -7.874 12.165 37.194 -1.523 -2.645 3.700 33.783 A A 2 3 -5.661 B B 27 26 3.597 -3.284 -1.595 -0.560 AA_DC2DA3:DT26DG27_BB 2 -1.511 2.604 33.594 -0.369 2.472 3.037 23.744 A A 3 4 -9.200 B B 26 25 3.144 -3.753 1.125 -1.021 AA_DA3DG4:DC25DT26_BB 3 -3.947 9.678 23.119 -1.296 -3.981 3.442 39.073 A A 4 5 -8.822 B B 25 24 3.252 -5.857 -1.076 -0.684 AA_DG4DG5:C2S24DC25_BB 4 -6.157 9.274 38.174 -0.293 0.841 2.832 28.352 A A 5 6 17.758 B B 24 23 3.356 8.565 -0.025 -1.246 AA_DG5DA6:DT23C2S24_BB 5 1.298 -2.692 27.023 -4.460 0.342 3.472 40.603 A A 6 7 20.122 B B 23 22 3.398 13.604 -1.883 -0.182 AA_DA6DG7:C2S22DT23_BB 6 -8.820 13.045 37.351 -1.926 1.636 3.132 35.313 A A 7 8 11.408 B B 22 21 3.265 6.870 0.099 -0.284 AA_DG7DA8:DT21C2S22_BB 7 -3.151 5.232 34.520 -1.474 -0.625 3.298 29.797 A A 8 9 4.912 B B 21 20 3.384 2.522 -0.750 -1.136 AA_DA8DT9:DA20DT21_BB 8 -0.880 1.714 29.680 -2.747 1.270 3.136 37.675 A A 9 10 1.717 B B 20 19 3.154 1.108 0.018 -0.373 AA_DT9DT10:DA19DA20_BB 9 2.734 -4.238 37.563 -0.715 0.313 3.426 46.620 A A 10 11 2.956 B B 19 18 3.410 2.338 0.611 0.257 AA_DT10DC11:DG18DA19_BB 10 0.596 -0.753 46.561 0.120 -0.720 3.227 25.442 A A 11 12 1.687 B B 18 17 3.256 0.742 -0.118 -1.014 AA_DC11DC12:DG17DG18_BB 11 -1.519 3.451 25.386 -2.515 -0.166 3.035 39.145 A A 12 13 2.344 B B 17 16 2.993 1.565 0.444 0.294 AA_DC12DA13:DT16DG17_BB 12 5.649 -8.461 38.721 0.264 -0.036 3.537 42.471 A A 13 14 -7.170 B B 16 15 3.482 -5.175 0.214 -0.949 AA_DA13DC14:DG15DT16_BB 13 -3.851 5.335 42.001 -0.744 -0.717 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_conn repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2003-04-15 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_conn.pdbx_leaving_atom_flag NMR Structure of CK14, the non-thioated analog of XBY6 NMR Structure of CK14, an analog with 6 phosphorodithioates RCSB Y RCSB 2001-10-24 REL REL SYNTHESIZED WITH NORMAL PHOSPHOROAMIDITE CHEMISTRY sample SYNTHESIZED WITH BOTH NORMAL PHOSPHOROAMIDITE CHEMISTRY AND THIOPHOSPHORAMIDITE CHEMISTRY sample Standard 2D homonuclear methods were used structures with the lowest energy 10 1 2D NOESY 2D NOESY DQF-COSY 100 mM 6.7 ambient 278 K 100 mM 6.7 ambient 288 K Distance restraints were derived by MORASS 2.5 using a total relaxation matrix method. The deposited structure represents the average of 10 final structures molecular dynamics 1 minimized average structure 1 mM duplex, 12 mM Na2HPO4, 8 mM NaH2PO4, 56 mM NaCl, 50 uM NaN3 90% H2O/10% D2O 1 mM duplex, 12 mM Na2HPO4,8 mM NaH2PO4, 56 mM NaCl, 50 uM NaN3 99.96% D2O Gorenstein iterative matrix relaxation MORASS 2.5 Case and Kollman structure solution Amber 5 Case and Kollman refinement Amber 5 750 Varian UNITYPLUS 600 Varian UNITYPLUS C 1 n 1 DC 1 A C 2 n 2 DC 2 A A 3 n 3 DA 3 A G 4 n 4 DG 4 A G 5 n 5 DG 5 A A 6 n 6 DA 6 A G 7 n 7 DG 7 A A 8 n 8 DA 8 A T 9 n 9 DT 9 A T 10 n 10 DT 10 A C 11 n 11 DC 11 A C 12 n 12 DC 12 A A 13 n 13 DA 13 A C 14 n 14 DC 14 A G 15 n 1 DG 15 B T 16 n 2 DT 16 B G 17 n 3 DG 17 B G 18 n 4 DG 18 B A 19 n 5 DA 19 B A 20 n 6 DA 20 B T 21 n 7 DT 21 B C2S 22 n 8 C2S 22 B T 23 n 9 DT 23 B C2S 24 n 10 C2S 24 B C 25 n 11 DC 25 B T 26 n 12 DT 26 B G 27 n 13 DG 27 B G 28 n 14 DG 28 B author_defined_assembly 2 dimeric B C2S 22 CYTIDINE-5'-DITHIOPHOSPHORATE B C2S 8 DC B C2S 24 CYTIDINE-5'-DITHIOPHOSPHORATE B C2S 10 DC 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 A HO5' OP2 DC DC 1 2 1.33 1 A DC 1 0.063 SIDE CHAIN 1 A DC 2 0.067 SIDE CHAIN 1 A DG 4 0.059 SIDE CHAIN 1 5.50 0.30 108.30 113.80 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 4.16 0.30 108.30 112.46 A A A O4' C1' N1 DC DC DC 2 2 2 N 1 3.35 0.50 117.70 121.05 A A A C5 C6 N1 DA DA DA 3 3 3 N 1 5.45 0.30 108.30 113.75 A A A O4' C1' N9 DG DG DG 4 4 4 N 1 4.05 0.30 108.30 112.35 A A A O4' C1' N9 DA DA DA 6 6 6 N 1 -3.64 0.60 118.60 114.96 A A A N1 C6 N6 DA DA DA 6 6 6 N 1 3.99 0.30 108.30 112.29 A A A O4' C1' N1 DC DC DC 12 12 12 N 1 3.21 0.30 108.30 111.51 B B B O4' C1' N9 DG DG DG 15 15 15 N 1 4.92 0.30 108.30 113.22 B B B O4' C1' N9 DG DG DG 18 18 18 N 1 4.41 0.30 108.30 112.71 B B B O4' C1' N1 DT DT DT 21 21 21 N 1 -3.76 0.60 122.90 119.14 B B B C6 C5 C7 DT DT DT 21 21 21 N 1 2.64 0.30 108.30 110.94 B B B O4' C1' N1 DT DT DT 23 23 23 N 1 -3.87 0.60 122.90 119.03 B B B C6 C5 C7 DT DT DT 23 23 23 N 1 3.83 0.30 108.30 112.13 B B B O4' C1' N1 DC DC DC 25 25 25 N 1 1.90 0.30 108.30 110.20 B B B O4' C1' N1 DT DT DT 26 26 26 N 1 6.17 0.30 108.30 114.47 B B B O4' C1' N9 DG DG DG 27 27 27 N 1 2.52 0.30 108.30 110.82 B B B O4' C1' N9 DG DG DG 28 28 28 N minimized average NMR structure of the XBY2 DNA duplex, an analog of CK14 containing phosphorodithioate groups at C22 and C24 1 N N 2 N N covale 1.620 both B DT 21 B O3' DT 7 1_555 B C2S 22 B P C2S 8 1_555 covale 1.616 both B C2S 22 B O3' C2S 8 1_555 B DT 23 B P DT 9 1_555 covale 1.618 both B DT 23 B O3' DT 9 1_555 B C2S 24 B P C2S 10 1_555 covale 1.619 both B C2S 24 B O3' C2S 10 1_555 B DC 25 B P DC 11 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 28 B N1 DG 14 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 28 B O6 DG 14 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 28 B N2 DG 14 1_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 B DG 27 B N1 DG 13 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 B DG 27 B O6 DG 13 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 B DG 27 B N2 DG 13 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 B DT 26 B N3 DT 12 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 B DT 26 B O4 DT 12 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B DC 25 B N3 DC 11 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 25 B O2 DC 11 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B DC 25 B N4 DC 11 1_555 hydrog WATSON-CRICK A DG 5 A N1 DG 5 1_555 B C2S 24 B N3 C2S 10 1_555 hydrog WATSON-CRICK A DG 5 A N2 DG 5 1_555 B C2S 24 B O2 C2S 10 1_555 hydrog WATSON-CRICK A DG 5 A O6 DG 5 1_555 B C2S 24 B N4 C2S 10 1_555 hydrog WATSON-CRICK A DA 6 A N1 DA 6 1_555 B DT 23 B N3 DT 9 1_555 hydrog WATSON-CRICK A DA 6 A N6 DA 6 1_555 B DT 23 B O4 DT 9 1_555 hydrog WATSON-CRICK A DG 7 A N1 DG 7 1_555 B C2S 22 B N3 C2S 8 1_555 hydrog WATSON-CRICK A DG 7 A N2 DG 7 1_555 B C2S 22 B O2 C2S 8 1_555 hydrog WATSON-CRICK A DG 7 A O6 DG 7 1_555 B C2S 22 B N4 C2S 8 1_555 hydrog WATSON-CRICK A DA 8 A N1 DA 8 1_555 B DT 21 B N3 DT 7 1_555 hydrog WATSON-CRICK A DA 8 A N6 DA 8 1_555 B DT 21 B O4 DT 7 1_555 hydrog WATSON-CRICK A DT 9 A N3 DT 9 1_555 B DA 20 B N1 DA 6 1_555 hydrog WATSON-CRICK A DT 9 A O4 DT 9 1_555 B DA 20 B N6 DA 6 1_555 hydrog WATSON-CRICK A DT 10 A N3 DT 10 1_555 B DA 19 B N1 DA 5 1_555 hydrog WATSON-CRICK A DT 10 A O4 DT 10 1_555 B DA 19 B N6 DA 5 1_555 hydrog WATSON-CRICK A DC 11 A N3 DC 11 1_555 B DG 18 B N1 DG 4 1_555 hydrog WATSON-CRICK A DC 11 A N4 DC 11 1_555 B DG 18 B O6 DG 4 1_555 hydrog WATSON-CRICK A DC 11 A O2 DC 11 1_555 B DG 18 B N2 DG 4 1_555 hydrog WATSON-CRICK A DC 12 A N3 DC 12 1_555 B DG 17 B N1 DG 3 1_555 hydrog WATSON-CRICK A DC 12 A N4 DC 12 1_555 B DG 17 B O6 DG 3 1_555 hydrog WATSON-CRICK A DC 12 A O2 DC 12 1_555 B DG 17 B N2 DG 3 1_555 hydrog WATSON-CRICK A DA 13 A N1 DA 13 1_555 B DT 16 B N3 DT 2 1_555 hydrog WATSON-CRICK A DA 13 A N6 DA 13 1_555 B DT 16 B O4 DT 2 1_555 hydrog WATSON-CRICK A DC 14 A N3 DC 14 1_555 B DG 15 B N1 DG 1 1_555 hydrog WATSON-CRICK A DC 14 A N4 DC 14 1_555 B DG 15 B O6 DG 1 1_555 hydrog WATSON-CRICK A DC 14 A O2 DC 14 1_555 B DG 15 B N2 DG 1 1_555 DNA phosphorodithioate, CK14, CK1, NF-kB, XBY6, XBY2, thiophosphate, DNA 1K8N PDB 1 1K8N 1K8N PDB 2 1K8N 1 14 1K8N 1 14 1K8N A 1 1 14 15 28 1K8N 15 28 1K8N B 2 1 14