1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Znosko, B.M. Barnes III, T.W. Krugh, T.R. Turner, D.H. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C12 H16 N3 O7 P 345.245 n 5(1-PROPYNYL)-2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA linking C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking C12 H15 N2 O8 P 346.230 5(1-PROPYNYL)-2'-DEOXYURIDINE-5-MONOPHOSPHATE DNA linking US J.Am.Chem.Soc. JACSAT 0004 0002-7863 125 6090 6097 10.1021/ja021285d 12785839 NMR Studies of DNA Single Strands and DNA:RNA Hybrids With and Without 1-Propynylation at C5 of Oligopyrimidines 2003 US J.Am.Chem.Soc. JACSAT 0004 0002-7863 123 4107 4118 10.1021/ja003208t Long-Range Cooperativity in Molecular Recognition of RNA by Oligodeoxynucleotides with Multiple C5-(1-Propynyl) Pyrimidines 2001 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 2981.895 5'-R(*AP*AP*AP*GP*GP*AP*GP*GP*A)-3' 1 syn polymer 2210.558 5'-D(*CP*(5PC)P*(PDU)P*(5PC)P*(5PC)P*(PDU)P*(PDU))-3' 1 syn polymer no no AAAGGAGGA AAAGGAGGA A polyribonucleotide no yes (DC)(5PC)(PDU)(5PC)(5PC)(PDU)(PDU) CCXCCXX B polydeoxyribonucleotide n n n n n n n n n n n n n n n n -9.980 1 20 A 3 B 7 1.980 A_A3:PDU7_B 1 -13.535 -0.090 -0.242 0.279 0.482 1 20 A 4 B 6 3.526 A_A4:PDU6_B 2 -16.681 -0.297 0.524 0.261 4.032 1 19 A 5 B 5 1.148 A_G5:5PC5_B 3 -17.768 -1.383 0.352 -0.061 -2.769 1 19 A 6 B 4 -6.331 A_G6:5PC4_B 4 -14.332 -0.479 -0.305 0.132 3.255 1 20 A 7 B 3 -0.149 A_A7:PDU3_B 5 -14.110 -0.594 0.094 0.222 5.741 1 19 A 8 B 2 3.110 A_G8:5PC2_B 6 -16.352 -1.355 0.252 -0.032 -4.324 1 19 A 9 B 1 -0.610 A_G9:DC1_B 7 -22.792 -0.675 -0.460 0.057 2.980 30.203 A A 3 4 3.740 B B 7 6 3.130 1.942 0.428 -0.948 AA_A3A4:PDU6PDU7_BB 1 -4.077 7.853 29.871 -2.189 -1.599 3.242 29.327 A A 4 5 1.322 B B 6 5 3.293 0.668 -0.128 -1.084 AA_A4G5:5PC5PDU6_BB 2 2.786 -5.511 29.190 -2.285 0.853 3.489 36.443 A A 5 6 4.991 B B 5 4 3.658 3.113 -0.580 -0.960 AA_G5G6:5PC45PC5_BB 3 3.778 -6.058 36.124 -2.008 1.502 3.157 32.579 A A 6 7 4.491 B B 4 3 3.279 2.516 0.695 -0.947 AA_G6A7:PDU35PC4_BB 4 -1.779 3.176 32.437 -2.120 -1.544 3.083 28.518 A A 7 8 7.146 B B 3 2 3.306 3.509 0.278 -1.415 AA_A7G8:5PC2PDU3_BB 5 -2.091 4.259 28.230 -3.657 -1.032 3.430 40.137 A A 8 9 11.671 B B 2 1 3.698 7.959 -0.496 -0.964 AA_G8G9:DC15PC2_BB 6 1.221 -1.790 39.353 -2.403 0.876 atom_site chem_comp entity entity_poly pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_conn repository Initial release Version format compliance Version format compliance Atomic model Data collection Derived calculations Non-polymer description Polymer sequence Structure summary 1 0 2003-06-10 1 1 2008-04-29 1 2 2011-07-13 2 0 2021-07-28 _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_atom_id _atom_site.label_atom_id _chem_comp.formula _chem_comp.formula_weight _chem_comp.mon_nstd_flag _entity.formula_weight _entity_poly.pdbx_seq_one_letter_code_can _pdbx_nmr_software.name _struct_conn.pdbx_leaving_atom_flag DNA:RNA hybrid with same sequence DNA:RNA hybrid with propynylated bases 1-7 in DNA strand RCSB Y RCSB 2003-01-30 REL REL 1 2D NOESY 80 mM NaCl 7.0 ambient 273 K 80 mM NaCl 7.0 ambient 303 K The structure is based on a total of 160 interproton distance restraints, 18 hydrogen bond restraints, and 59 dihedral angle restraints. simulated annealing, energy minimization 1 minimized average structure ~1mM hybrid, 80 mM NaCl, 10 mM phosphate buffer, 0.5 mM EDTA, 90% H2O, 10% D2O 90% H2O/10% D2O ~2.5 mM hybrid, 80 mM NaCl, 10 mM phosphate, 0.5 mM EDTA, 99.996% D2O 99.996% D2O Varian collection VNMR 5.2 MSI data analysis Felix 2000 MSI structure solution Discover 95.0 MSI refinement Discover 95.0 500 Varian INOVA A 2 n 1 A 2 A A 3 n 2 A 3 A A 4 n 3 A 4 A G 5 n 4 G 5 A G 6 n 5 G 6 A A 7 n 6 A 7 A G 8 n 7 G 8 A G 9 n 8 G 9 A A 10 n 9 A 10 A C 1 n 1 DC 1 B 5PC 2 n 2 5PC 2 B PDU 3 n 3 PDU 3 B 5PC 4 n 4 5PC 4 B 5PC 5 n 5 5PC 5 B PDU 6 n 6 PDU 6 B PDU 7 n 7 PDU 7 B author_defined_assembly 2 dimeric B 5PC 2 B 5PC 2 DC B PDU 3 B PDU 3 DU B 5PC 4 B 5PC 4 DC B 5PC 5 B 5PC 5 DC B PDU 6 B PDU 6 DU B PDU 7 B PDU 7 DU 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 identity operation 0.0000000000 0.0000000000 0.0000000000 1 A A 2 0.063 SIDE CHAIN 1 5.20 0.50 110.60 115.80 A A A C2 N3 C4 A A A 2 2 2 N 1 -9.41 0.70 126.80 117.39 A A A N3 C4 C5 A A A 2 2 2 N 1 -6.44 0.50 103.90 97.46 A A A C5 N7 C8 A A A 2 2 2 N 1 8.60 0.50 113.80 122.40 A A A N7 C8 N9 A A A 2 2 2 N 1 -6.38 0.40 105.80 99.42 A A A C8 N9 C4 A A A 2 2 2 N 1 7.03 0.80 127.40 134.43 A A A N3 C4 N9 A A A 2 2 2 N 1 -10.07 1.50 119.60 109.53 A A A OP1 P OP2 A A A 3 3 3 N 1 5.06 0.50 110.60 115.66 A A A C2 N3 C4 A A A 3 3 3 N 1 -9.16 0.70 126.80 117.64 A A A N3 C4 C5 A A A 3 3 3 N 1 -6.57 0.50 103.90 97.33 A A A C5 N7 C8 A A A 3 3 3 N 1 8.42 0.50 113.80 122.22 A A A N7 C8 N9 A A A 3 3 3 N 1 -6.09 0.40 105.80 99.71 A A A C8 N9 C4 A A A 3 3 3 N 1 6.86 0.80 127.40 134.26 A A A N3 C4 N9 A A A 3 3 3 N 1 -10.05 1.50 119.60 109.55 A A A OP1 P OP2 A A A 4 4 4 N 1 5.11 0.50 110.60 115.71 A A A C2 N3 C4 A A A 4 4 4 N 1 -9.20 0.70 126.80 117.60 A A A N3 C4 C5 A A A 4 4 4 N 1 -6.36 0.50 103.90 97.54 A A A C5 N7 C8 A A A 4 4 4 N 1 8.25 0.50 113.80 122.05 A A A N7 C8 N9 A A A 4 4 4 N 1 -6.03 0.40 105.80 99.77 A A A C8 N9 C4 A A A 4 4 4 N 1 6.83 0.80 127.40 134.23 A A A N3 C4 N9 A A A 4 4 4 N 1 -10.04 1.50 119.60 109.56 A A A OP1 P OP2 G G G 5 5 5 N 1 11.22 0.50 111.90 123.12 A A A C2 N3 C4 G G G 5 5 5 N 1 -10.85 0.50 128.60 117.75 A A A N3 C4 C5 G G G 5 5 5 N 1 3.66 0.50 111.50 115.16 A A A C5 C6 N1 G G G 5 5 5 N 1 2.53 0.40 110.80 113.33 A A A C4 C5 N7 G G G 5 5 5 N 1 -7.30 0.50 104.30 97.00 A A A C5 N7 C8 G G G 5 5 5 N 1 8.80 0.50 113.10 121.90 A A A N7 C8 N9 G G G 5 5 5 N 1 -6.78 0.40 106.40 99.62 A A A C8 N9 C4 G G G 5 5 5 N 1 2.68 0.40 105.40 108.08 A A A N9 C4 C5 G G G 5 5 5 N 1 8.15 0.60 126.00 134.15 A A A N3 C4 N9 G G G 5 5 5 N 1 -4.81 0.60 128.60 123.79 A A A C5 C6 O6 G G G 5 5 5 N 1 -10.04 1.50 119.60 109.56 A A A OP1 P OP2 G G G 6 6 6 N 1 11.22 0.50 111.90 123.12 A A A C2 N3 C4 G G G 6 6 6 N 1 -10.91 0.50 128.60 117.69 A A A N3 C4 C5 G G G 6 6 6 N 1 3.82 0.50 111.50 115.32 A A A C5 C6 N1 G G G 6 6 6 N 1 2.71 0.40 110.80 113.51 A A A C4 C5 N7 G G G 6 6 6 N 1 -7.24 0.50 104.30 97.06 A A A C5 N7 C8 G G G 6 6 6 N 1 8.72 0.50 113.10 121.82 A A A N7 C8 N9 G G G 6 6 6 N 1 -6.85 0.40 106.40 99.55 A A A C8 N9 C4 G G G 6 6 6 N 1 2.63 0.40 105.40 108.03 A A A N9 C4 C5 G G G 6 6 6 N 1 8.27 0.60 126.00 134.27 A A A N3 C4 N9 G G G 6 6 6 N 1 -3.61 0.60 130.40 126.79 A A A C6 C5 N7 G G G 6 6 6 N 1 -5.22 0.60 128.60 123.38 A A A C5 C6 O6 G G G 6 6 6 N 1 -10.06 1.50 119.60 109.54 A A A OP1 P OP2 A A A 7 7 7 N 1 5.14 0.50 110.60 115.74 A A A C2 N3 C4 A A A 7 7 7 N 1 -9.26 0.70 126.80 117.54 A A A N3 C4 C5 A A A 7 7 7 N 1 -6.37 0.50 103.90 97.53 A A A C5 N7 C8 A A A 7 7 7 N 1 8.26 0.50 113.80 122.06 A A A N7 C8 N9 A A A 7 7 7 N 1 -6.05 0.40 105.80 99.75 A A A C8 N9 C4 A A A 7 7 7 N 1 6.97 0.80 127.40 134.37 A A A N3 C4 N9 A A A 7 7 7 N 1 -10.13 1.50 119.60 109.47 A A A OP1 P OP2 G G G 8 8 8 N 1 11.16 0.50 111.90 123.06 A A A C2 N3 C4 G G G 8 8 8 N 1 -10.72 0.50 128.60 117.88 A A A N3 C4 C5 G G G 8 8 8 N 1 3.64 0.50 111.50 115.14 A A A C5 C6 N1 G G G 8 8 8 N 1 2.48 0.40 110.80 113.28 A A A C4 C5 N7 G G G 8 8 8 N 1 -7.12 0.50 104.30 97.18 A A A C5 N7 C8 G G G 8 8 8 N 1 8.66 0.50 113.10 121.76 A A A N7 C8 N9 G G G 8 8 8 N 1 -6.90 0.40 106.40 99.50 A A A C8 N9 C4 G G G 8 8 8 N 1 2.85 0.40 105.40 108.25 A A A N9 C4 C5 G G G 8 8 8 N 1 7.84 0.60 126.00 133.84 A A A N3 C4 N9 G G G 8 8 8 N 1 -4.67 0.60 128.60 123.93 A A A C5 C6 O6 G G G 8 8 8 N 1 -10.14 1.50 119.60 109.46 A A A OP1 P OP2 G G G 9 9 9 N 1 11.09 0.50 111.90 122.99 A A A C2 N3 C4 G G G 9 9 9 N 1 -10.72 0.50 128.60 117.88 A A A N3 C4 C5 G G G 9 9 9 N 1 3.65 0.50 111.50 115.15 A A A C5 C6 N1 G G G 9 9 9 N 1 2.53 0.40 110.80 113.33 A A A C4 C5 N7 G G G 9 9 9 N 1 -7.38 0.50 104.30 96.92 A A A C5 N7 C8 G G G 9 9 9 N 1 8.78 0.50 113.10 121.88 A A A N7 C8 N9 G G G 9 9 9 N 1 -6.58 0.40 106.40 99.82 A A A C8 N9 C4 G G G 9 9 9 N 1 2.54 0.40 105.40 107.94 A A A N9 C4 C5 G G G 9 9 9 N 1 8.16 0.60 126.00 134.16 A A A N3 C4 N9 G G G 9 9 9 N 1 -4.80 0.60 128.60 123.80 A A A C5 C6 O6 G G G 9 9 9 N 1 -10.18 1.50 119.60 109.42 A A A OP1 P OP2 A A A 10 10 10 N 1 5.12 0.50 110.60 115.72 A A A C2 N3 C4 A A A 10 10 10 N 1 -9.27 0.70 126.80 117.53 A A A N3 C4 C5 A A A 10 10 10 N 1 -6.35 0.50 103.90 97.55 A A A C5 N7 C8 A A A 10 10 10 N 1 8.26 0.50 113.80 122.06 A A A N7 C8 N9 A A A 10 10 10 N 1 -6.08 0.40 105.80 99.72 A A A C8 N9 C4 A A A 10 10 10 N 1 6.95 0.80 127.40 134.35 A A A N3 C4 N9 A A A 10 10 10 N 1 3.57 0.30 108.30 111.87 B B B O4' C1' N1 DC DC DC 1 1 1 N 1 -3.04 0.40 120.30 117.26 B B B C6 N1 C2 DC DC DC 1 1 1 N 1 3.63 0.50 117.40 121.03 B B B C4 C5 C6 DC DC DC 1 1 1 N 1 8.62 1.20 119.70 128.32 B B B C3' O3' P 5PC 5PC PDU 2 2 3 Y 1 A A N3 C4 A A 2 2 0.122 0.006 1.344 1.466 N 1 A A C4 C5 A A 2 2 0.077 0.007 1.383 1.460 N 1 A A N7 C8 A A 2 2 0.067 0.007 1.311 1.378 N 1 A A N3 C4 A A 3 3 0.121 0.006 1.344 1.465 N 1 A A C4 C5 A A 3 3 0.076 0.007 1.383 1.459 N 1 A A N7 C8 A A 3 3 0.067 0.007 1.311 1.378 N 1 A A N3 C4 A A 4 4 0.122 0.006 1.344 1.466 N 1 A A C4 C5 A A 4 4 0.076 0.007 1.383 1.459 N 1 A A N7 C8 A A 4 4 0.069 0.007 1.311 1.380 N 1 A A N1 C2 G G 5 5 0.094 0.008 1.373 1.467 N 1 A A N3 C4 G G 5 5 0.095 0.007 1.350 1.445 N 1 A A C4 C5 G G 5 5 0.058 0.007 1.379 1.437 N 1 A A C5 C6 G G 5 5 0.132 0.010 1.419 1.551 N 1 A A N7 C8 G G 5 5 0.072 0.006 1.305 1.377 N 1 A A N1 C2 G G 6 6 0.093 0.008 1.373 1.466 N 1 A A N3 C4 G G 6 6 0.098 0.007 1.350 1.448 N 1 A A C4 C5 G G 6 6 0.056 0.007 1.379 1.435 N 1 A A C5 C6 G G 6 6 0.130 0.010 1.419 1.549 N 1 A A N7 C8 G G 6 6 0.070 0.006 1.305 1.375 N 1 A A N3 C4 A A 7 7 0.122 0.006 1.344 1.466 N 1 A A C4 C5 A A 7 7 0.076 0.007 1.383 1.459 N 1 A A N7 C8 A A 7 7 0.067 0.007 1.311 1.378 N 1 A A N1 C2 G G 8 8 0.094 0.008 1.373 1.467 N 1 A A N3 C4 G G 8 8 0.094 0.007 1.350 1.444 N 1 A A C4 C5 G G 8 8 0.058 0.007 1.379 1.437 N 1 A A C5 C6 G G 8 8 0.133 0.010 1.419 1.552 N 1 A A N7 C8 G G 8 8 0.073 0.006 1.305 1.378 N 1 A A N1 C2 G G 9 9 0.093 0.008 1.373 1.466 N 1 A A N3 C4 G G 9 9 0.096 0.007 1.350 1.446 N 1 A A C4 C5 G G 9 9 0.058 0.007 1.379 1.437 N 1 A A C5 C6 G G 9 9 0.131 0.010 1.419 1.550 N 1 A A N7 C8 G G 9 9 0.072 0.006 1.305 1.377 N 1 A A N3 C4 A A 10 10 0.122 0.006 1.344 1.466 N 1 A A C4 C5 A A 10 10 0.075 0.007 1.383 1.458 N 1 A A N7 C8 A A 10 10 0.067 0.007 1.311 1.378 N 1 B B C4 N4 DC DC 1 1 0.072 0.009 1.335 1.407 N 1 B B N1 C6 DC DC 1 1 0.131 0.006 1.367 1.498 N 1 B B C2 N3 DC DC 1 1 0.117 0.008 1.353 1.470 N 1 B B C4 C5 DC DC 1 1 -0.056 0.008 1.425 1.369 N minimized average 5'(dCPCPUPCPCPUPUP)3':(rAGGAGGAAA)5', where P=propynyl 1 N N 2 N N covale 1.616 both B DC 1 B O3' DC 1 1_555 B 5PC 2 B P 5PC 2 1_555 covale 1.636 both B 5PC 2 B O3' 5PC 2 1_555 B PDU 3 B P PDU 3 1_555 covale 1.631 one B PDU 3 B O3' PDU 3 1_555 B 5PC 4 B P 5PC 4 1_555 covale 1.623 both B 5PC 4 B O3' 5PC 4 1_555 B 5PC 5 B P 5PC 5 1_555 covale 1.627 both B 5PC 5 B O3' 5PC 5 1_555 B PDU 6 B P PDU 6 1_555 covale 1.625 one B PDU 6 B O3' PDU 6 1_555 B PDU 7 B P PDU 7 1_555 hydrog WATSON-CRICK A A 3 A N1 A 2 1_555 B PDU 7 B N3 PDU 7 1_555 hydrog WATSON-CRICK A A 3 A N6 A 2 1_555 B PDU 7 B O4 PDU 7 1_555 hydrog WATSON-CRICK A A 4 A N1 A 3 1_555 B PDU 6 B N3 PDU 6 1_555 hydrog WATSON-CRICK A A 4 A N6 A 3 1_555 B PDU 6 B O4 PDU 6 1_555 hydrog WATSON-CRICK A G 5 A N1 G 4 1_555 B 5PC 5 B N3 5PC 5 1_555 hydrog WATSON-CRICK A G 5 A N2 G 4 1_555 B 5PC 5 B O2 5PC 5 1_555 hydrog WATSON-CRICK A G 5 A O6 G 4 1_555 B 5PC 5 B N4 5PC 5 1_555 hydrog WATSON-CRICK A G 6 A N1 G 5 1_555 B 5PC 4 B N3 5PC 4 1_555 hydrog WATSON-CRICK A G 6 A N2 G 5 1_555 B 5PC 4 B O2 5PC 4 1_555 hydrog WATSON-CRICK A G 6 A O6 G 5 1_555 B 5PC 4 B N4 5PC 4 1_555 hydrog WATSON-CRICK A A 7 A N1 A 6 1_555 B PDU 3 B N3 PDU 3 1_555 hydrog WATSON-CRICK A A 7 A N6 A 6 1_555 B PDU 3 B O4 PDU 3 1_555 hydrog WATSON-CRICK A G 8 A N1 G 7 1_555 B 5PC 2 B N3 5PC 2 1_555 hydrog WATSON-CRICK A G 8 A N2 G 7 1_555 B 5PC 2 B O2 5PC 2 1_555 hydrog WATSON-CRICK A G 8 A O6 G 7 1_555 B 5PC 2 B N4 5PC 2 1_555 hydrog WATSON-CRICK A G 9 A N1 G 8 1_555 B DC 1 B N3 DC 1 1_555 hydrog WATSON-CRICK A G 9 A N2 G 8 1_555 B DC 1 B O2 DC 1 1_555 hydrog WATSON-CRICK A G 9 A O6 G 8 1_555 B DC 1 B N4 DC 1 1_555 RNA/DNA DNA, RNA, hybrid, propynyl, RNA-DNA COMPLEX 1NTT PDB 1 1NTT 1NTT PDB 2 1NTT 2 10 1NTT 2 10 1NTT A 1 1 9 1 7 1NTT 1 7 1NTT B 2 1 7