1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Gyi, J.I. Gao, D. Conn, G.L. Trent, J.O. Brown, T. Lane, A.N. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 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 O8 P 323.197 y CYTIDINE-5'-MONOPHOSPHATE RNA 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 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 UK Nucleic Acids Res. NARHAD 0389 0305-1048 31 2683 2693 10.1093/nar/gkg356 12736318 The solution structure of a DNA*RNA duplex containing 5-propynyl U and C; comparison with 5-Me modifications 2003 US Biochemistry BICHAW 0033 0006-2960 37 73 80 10.1021/bi9719713 Solution Structures of DNA.RNA Hybrids with Purine-Rich and Pyrimidine-Rich Strands: Comparison with the Homologous DNA and RNA Duplexes 1998 US Biochemistry BICHAW 0033 0006-2960 35 12538 12548 10.1021/bi960948z Comparison of the Thermodynamic Stabilities and Solution Conformations of DNA.RNA Hybrids Containing Purine-Rich and Pyrimidine-Rich Strands with DNA and RNA Duplexes 1996 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 3287.076 5'-R(*GP*AP*AP*GP*AP*GP*AP*AP*GP*C)-3' 1 syn polymer 3196.194 5'-D(*GP*(5PC)P*(PDU)P*(PDU)P*(5PC)P*(PDU)P*(5PC)P*(PDU)P*(PDU)P*C)-3' 1 syn polymer no no GAAGAGAAGC GAAGAGAAGC A polyribonucleotide no yes (DG)(5PC)(PDU)(PDU)(5PC)(PDU)(5PC)(PDU)(PDU)(DC) GCXXCXCXXC B polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n -5.969 1 19 A 1 B 10 1.464 A_G1:DC10_B 1 -5.374 -0.878 0.000 -0.165 -4.838 1 20 A 2 B 9 0.925 A_A2:PDU9_B 2 -7.219 0.141 -0.142 0.087 -4.809 1 20 A 3 B 8 0.765 A_A3:PDU8_B 3 -7.620 0.053 -0.121 0.105 -1.907 1 19 A 4 B 7 -0.137 A_G4:5PC7_B 4 -6.815 -0.666 0.087 -0.184 -5.851 1 20 A 5 B 6 1.419 A_A5:PDU6_B 5 -5.749 -0.024 -0.171 0.081 -2.322 1 19 A 6 B 5 -0.466 A_G6:5PC5_B 6 -6.410 -0.683 0.132 -0.199 -9.577 1 20 A 7 B 4 0.461 A_A7:PDU4_B 7 -6.146 0.017 -0.284 0.080 -13.134 1 20 A 8 B 3 0.990 A_A8:PDU3_B 8 -6.598 0.027 -0.362 0.101 -10.837 1 19 A 9 B 2 0.528 A_G9:5PC2_B 9 -10.455 -0.702 -0.212 -0.179 -15.058 1 19 A 10 B 1 0.728 A_C10:DG1_B 10 5.091 1.148 0.070 -0.275 3.235 39.855 A A 1 2 5.771 B B 10 9 3.348 3.927 0.052 -1.032 AA_G1A2:PDU9DC10_BB 1 1.755 -2.580 39.632 -1.972 0.128 2.968 30.631 A A 2 3 10.337 B B 9 8 3.277 5.431 0.087 -1.501 AA_A2A3:PDU8PDU9_BB 2 1.502 -2.858 30.120 -3.873 0.120 2.684 27.629 A A 3 4 13.160 B B 8 7 3.135 6.232 0.229 -1.680 AA_A3G4:5PC7PDU8_BB 3 -0.202 0.427 26.929 -4.885 -0.523 3.229 35.563 A A 4 5 6.522 B B 7 6 3.386 3.964 0.338 -1.413 AA_G4A5:PDU65PC7_BB 4 4.784 -7.870 35.033 -2.902 0.157 2.799 26.780 A A 5 6 9.360 B B 6 5 3.138 4.317 0.374 -1.880 AA_A5G6:5PC5PDU6_BB 5 -0.139 0.301 26.436 -5.079 -0.840 3.390 36.995 A A 6 7 5.437 B B 5 4 3.512 3.428 0.428 -1.443 AA_G6A7:PDU45PC5_BB 6 6.664 -10.570 36.254 -2.765 0.282 3.154 31.130 A A 7 8 10.392 B B 4 3 3.474 5.537 0.186 -1.529 AA_A7A8:PDU3PDU4_BB 7 3.565 -6.691 30.442 -3.934 0.351 3.094 28.672 A A 8 9 9.268 B B 3 2 3.335 4.568 0.237 -1.331 AA_A8G9:5PC2PDU3_BB 8 1.864 -3.783 28.253 -3.707 -0.061 3.381 41.265 A A 9 10 4.102 B B 2 1 3.473 2.888 0.394 -1.175 AA_G9C10:DG15PC2_BB 9 -0.561 0.797 41.165 -1.994 -0.622 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 2003-11-11 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 Duplex Containing A Purine-Rich DNA Strand, NMR, 10 Structures DNA/RNA Hybrid Duplex Containing A Purine-Rich RNA Strand, NMR, 10 Structures RCSB Y RCSB 2003-03-03 REL REL THE STRUCTURE WAS DETERMINED FROM 2D HOMONUCLEAR NMR EXPERIMENTS USING UNLABELLED SAMPLE all calculated structures submitted 4 4 NOESY COSY 100 mM KCL 7.0 1 atm 303 K DISTANCE CONSTRAINTS FOR GLYCOSIDIC TORSION ANGLES, PENTOSE PSEUDOROTATIONAL PHASE ANGLES/AMPLITUDES AND FRACTION OF SOUTH STATE SUGARS CALCULATED FROM NOE BUILD-UP CURVES AND COUPLING CONSTANTS BY A LEAST-SQUARES/GRID SEARCH METHOD IMPLEMENTED IN NUCFIT AND PFIT (A.N. LANE, NIMR, UK). TEN DIFFERENT SETS OF UNIQUE RESTRAINTS GENERATED 10 STRUCTURES, THE AVERAGE OF WHICH SATISFIED THE EXPERIMENTALLY DERIVED FRACTION OF SOUTH STATE SUGARS BETTER THAN STRUCTURES GENERATED FROM A SINGLE SET OF RESTRAINTS. INTERNUCLEOTIDE DISTANCE CONSTRAINTS CALCULATED FROM NOE-BUILD-UP CURVES. STRUCTURES CALCULATED BY SIMULATED ANNEALING/RMD PROTOCOL WITHIN DISCOVER 95.0 USING AN AMBER FORCE FIELD AND A DISTANCE DIELECTRIC CONSTANT. MULTIPLE STARTING CONFORMATIONS 1 minimized average structure 100% D2O OR 90% H2O, 10% D2O CORNELL, W.D., ET AL. refinement Amber 7.0 Biosym processing Felix 95.0 Lane, A.N. data analysis NUCFIT Conte, M.R., Bauer, C.J., Lane, A.N. data analysis pfit 500 Varian UNITY 600 Varian UNITYPLUS G 1 n 1 G 1 A A 2 n 2 A 2 A A 3 n 3 A 3 A G 4 n 4 G 4 A A 5 n 5 A 5 A G 6 n 6 G 6 A A 7 n 7 A 7 A A 8 n 8 A 8 A G 9 n 9 G 9 A C 10 n 10 C 10 A G 1 n 1 DG 1 B 5PC 2 n 2 5PC 2 B PDU 3 n 3 PDU 3 B PDU 4 n 4 PDU 4 B 5PC 5 n 5 5PC 5 B PDU 6 n 6 PDU 6 B 5PC 7 n 7 5PC 7 B PDU 8 n 8 PDU 8 B PDU 9 n 9 PDU 9 B C 10 n 10 DC 10 B author_defined_assembly 2 dimeric B 5PC 2 B 5PC 2 DC B PDU 3 B PDU 3 DU B PDU 4 B PDU 4 DU B 5PC 5 B 5PC 5 DC B PDU 6 B PDU 6 DU B 5PC 7 B 5PC 7 DC B PDU 8 B PDU 8 DU B PDU 9 B PDU 9 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 G 1 0.060 SIDE CHAIN 2 B DG 1 0.064 SIDE CHAIN 4 B DG 1 0.071 SIDE CHAIN 1 -5.15 0.70 119.90 114.75 A A A N3 C2 N2 G G G 1 1 1 N 1 3.66 0.50 117.70 121.36 A A A C5 C6 N1 A A A 2 2 2 N 1 3.75 0.50 117.70 121.45 A A A C5 C6 N1 A A A 3 3 3 N 1 4.48 0.70 108.50 112.98 A A A O4' C1' N9 G G G 4 4 4 N 1 -4.45 0.70 119.90 115.45 A A A N3 C2 N2 G G G 4 4 4 N 1 -3.72 0.60 119.90 116.18 A A A N1 C6 O6 G G G 4 4 4 N 1 3.56 0.50 117.70 121.26 A A A C5 C6 N1 A A A 5 5 5 N 1 -3.74 0.60 118.60 114.86 A A A N1 C6 N6 A A A 5 5 5 N 1 4.58 0.70 108.50 113.08 A A A O4' C1' N9 G G G 6 6 6 N 1 -4.63 0.70 119.90 115.27 A A A N3 C2 N2 G G G 6 6 6 N 1 3.77 0.50 117.70 121.47 A A A C5 C6 N1 A A A 7 7 7 N 1 3.74 0.50 117.70 121.44 A A A C5 C6 N1 A A A 8 8 8 N 1 -3.69 0.60 118.60 114.91 A A A N1 C6 N6 A A A 8 8 8 N 1 5.67 0.70 108.50 114.17 A A A O4' C1' N9 G G G 9 9 9 N 1 4.98 0.70 108.50 113.48 A A A O4' C1' N1 C C C 10 10 10 N 1 -4.29 0.70 121.90 117.61 A A A N3 C2 O2 C C C 10 10 10 N 1 -4.34 0.70 119.90 115.56 B B B N3 C2 N2 DG DG DG 1 1 1 N 2 -5.16 0.70 119.90 114.74 A A A N3 C2 N2 G G G 1 1 1 N 2 3.59 0.50 117.70 121.29 A A A C5 C6 N1 A A A 2 2 2 N 2 3.71 0.50 117.70 121.41 A A A C5 C6 N1 A A A 3 3 3 N 2 5.96 0.70 108.50 114.46 A A A O4' C1' N9 G G G 4 4 4 N 2 -4.45 0.70 119.90 115.45 A A A N3 C2 N2 G G G 4 4 4 N 2 -3.62 0.60 119.90 116.28 A A A N1 C6 O6 G G G 4 4 4 N 2 3.46 0.50 117.70 121.16 A A A C5 C6 N1 A A A 5 5 5 N 2 -3.92 0.60 118.60 114.68 A A A N1 C6 N6 A A A 5 5 5 N 2 5.12 0.70 108.50 113.62 A A A O4' C1' N9 G G G 6 6 6 N 2 -5.02 0.70 119.90 114.88 A A A N3 C2 N2 G G G 6 6 6 N 2 -3.76 0.60 119.90 116.14 A A A N1 C6 O6 G G G 6 6 6 N 2 3.48 0.50 117.70 121.18 A A A C5 C6 N1 A A A 7 7 7 N 2 -4.10 0.60 118.60 114.50 A A A N1 C6 N6 A A A 7 7 7 N 2 3.47 0.50 117.70 121.17 A A A C5 C6 N1 A A A 8 8 8 N 2 -3.92 0.60 118.60 114.68 A A A N1 C6 N6 A A A 8 8 8 N 2 5.02 0.70 108.50 113.52 A A A O4' C1' N9 G G G 9 9 9 N 2 -4.50 0.70 119.90 115.40 A A A N3 C2 N2 G G G 9 9 9 N 2 -3.61 0.60 119.90 116.29 A A A N1 C6 O6 G G G 9 9 9 N 2 5.52 0.70 108.50 114.02 A A A O4' C1' N1 C C C 10 10 10 N 2 -4.28 0.70 121.90 117.62 A A A N3 C2 O2 C C C 10 10 10 N 2 -5.00 0.70 119.90 114.90 B B B N3 C2 N2 DG DG DG 1 1 1 N 2 2.16 0.30 108.30 110.46 B B B O4' C1' N1 DC DC DC 10 10 10 N 3 -4.99 0.70 119.90 114.91 A A A N3 C2 N2 G G G 1 1 1 N 3 3.71 0.50 117.70 121.41 A A A C5 C6 N1 A A A 2 2 2 N 3 3.82 0.50 117.70 121.52 A A A C5 C6 N1 A A A 3 3 3 N 3 -3.65 0.60 118.60 114.95 A A A N1 C6 N6 A A A 3 3 3 N 3 5.56 0.70 108.50 114.06 A A A O4' C1' N9 G G G 4 4 4 N 3 3.77 0.50 117.70 121.47 A A A C5 C6 N1 A A A 5 5 5 N 3 4.77 0.70 108.50 113.27 A A A O4' C1' N9 G G G 6 6 6 N 3 -4.76 0.70 119.90 115.14 A A A N3 C2 N2 G G G 6 6 6 N 3 -3.80 0.60 119.90 116.10 A A A N1 C6 O6 G G G 6 6 6 N 3 3.84 0.50 117.70 121.54 A A A C5 C6 N1 A A A 7 7 7 N 3 -3.79 0.60 118.60 114.81 A A A N1 C6 N6 A A A 7 7 7 N 3 3.89 0.50 117.70 121.59 A A A C5 C6 N1 A A A 8 8 8 N 3 -3.76 0.60 118.60 114.84 A A A N1 C6 N6 A A A 8 8 8 N 3 5.23 0.70 108.50 113.73 A A A O4' C1' N9 G G G 9 9 9 N 3 5.10 0.70 108.50 113.60 A A A O4' C1' N1 C C C 10 10 10 N 3 -4.30 0.70 121.90 117.60 A A A N3 C2 O2 C C C 10 10 10 N 3 -4.48 0.70 119.90 115.42 B B B N3 C2 N2 DG DG DG 1 1 1 N 4 4.21 0.70 108.50 112.71 A A A O4' C1' N9 G G G 1 1 1 N 4 -5.20 0.70 119.90 114.70 A A A N3 C2 N2 G G G 1 1 1 N 4 3.65 0.50 117.70 121.35 A A A C5 C6 N1 A A A 2 2 2 N 4 3.64 0.50 117.70 121.34 A A A C5 C6 N1 A A A 3 3 3 N 4 4.86 0.70 108.50 113.36 A A A O4' C1' N9 G G G 4 4 4 N 4 -4.74 0.70 119.90 115.16 A A A N3 C2 N2 G G G 4 4 4 N 4 3.42 0.50 117.70 121.12 A A A C5 C6 N1 A A A 5 5 5 N 4 -3.66 0.60 118.60 114.94 A A A N1 C6 N6 A A A 5 5 5 N 4 5.58 0.70 108.50 114.08 A A A O4' C1' N9 G G G 6 6 6 N 4 -4.63 0.70 119.90 115.27 A A A N3 C2 N2 G G G 6 6 6 N 4 3.65 0.50 117.70 121.35 A A A C5 C6 N1 A A A 7 7 7 N 4 3.62 0.50 117.70 121.32 A A A C5 C6 N1 A A A 8 8 8 N 4 -3.79 0.60 118.60 114.81 A A A N1 C6 N6 A A A 8 8 8 N 4 5.15 0.70 108.50 113.65 A A A O4' C1' N9 G G G 9 9 9 N 4 -4.56 0.70 119.90 115.34 A A A N3 C2 N2 G G G 9 9 9 N 4 -3.70 0.60 119.90 116.20 A A A N1 C6 O6 G G G 9 9 9 N 4 5.46 0.70 108.50 113.96 A A A O4' C1' N1 C C C 10 10 10 N 4 -4.36 0.70 121.90 117.54 A A A N3 C2 O2 C C C 10 10 10 N 4 2.99 0.30 108.30 111.29 B B B O4' C1' N9 DG DG DG 1 1 1 N 4 -4.49 0.70 119.90 115.41 B B B N3 C2 N2 DG DG DG 1 1 1 N 4 2.15 0.30 108.30 110.45 B B B O4' C1' N1 DC DC DC 10 10 10 N minimized average DNA.RNA HYBRID DUPLEX CONTAINING A 5-PROPYNE DNA STRAND AND PURINE-RICH RNA STRAND, NMR, 4 STRUCTURES 1 N N 2 N N covale 1.609 both B DG 1 B O3' DG 1 1_555 B 5PC 2 B P 5PC 2 1_555 covale 1.602 both B 5PC 2 B O3' 5PC 2 1_555 B PDU 3 B P PDU 3 1_555 covale 1.610 one B PDU 3 B O3' PDU 3 1_555 B PDU 4 B P PDU 4 1_555 covale 1.607 one B PDU 4 B O3' PDU 4 1_555 B 5PC 5 B P 5PC 5 1_555 covale 1.602 both B 5PC 5 B O3' 5PC 5 1_555 B PDU 6 B P PDU 6 1_555 covale 1.609 one B PDU 6 B O3' PDU 6 1_555 B 5PC 7 B P 5PC 7 1_555 covale 1.602 both B 5PC 7 B O3' 5PC 7 1_555 B PDU 8 B P PDU 8 1_555 covale 1.610 one B PDU 8 B O3' PDU 8 1_555 B PDU 9 B P PDU 9 1_555 covale 1.611 one B PDU 9 B O3' PDU 9 1_555 B DC 10 B P DC 10 1_555 hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 B DC 10 B N3 DC 10 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 B DC 10 B O2 DC 10 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 B DC 10 B N4 DC 10 1_555 hydrog WATSON-CRICK A A 2 A N1 A 2 1_555 B PDU 9 B N3 PDU 9 1_555 hydrog WATSON-CRICK A A 2 A N6 A 2 1_555 B PDU 9 B O4 PDU 9 1_555 hydrog WATSON-CRICK A A 3 A N1 A 3 1_555 B PDU 8 B N3 PDU 8 1_555 hydrog WATSON-CRICK A A 3 A N6 A 3 1_555 B PDU 8 B O4 PDU 8 1_555 hydrog WATSON-CRICK A G 4 A N1 G 4 1_555 B 5PC 7 B N3 5PC 7 1_555 hydrog WATSON-CRICK A G 4 A N2 G 4 1_555 B 5PC 7 B O2 5PC 7 1_555 hydrog WATSON-CRICK A G 4 A O6 G 4 1_555 B 5PC 7 B N4 5PC 7 1_555 hydrog WATSON-CRICK A A 5 A N1 A 5 1_555 B PDU 6 B N3 PDU 6 1_555 hydrog WATSON-CRICK A A 5 A N6 A 5 1_555 B PDU 6 B O4 PDU 6 1_555 hydrog WATSON-CRICK A G 6 A N1 G 6 1_555 B 5PC 5 B N3 5PC 5 1_555 hydrog WATSON-CRICK A G 6 A N2 G 6 1_555 B 5PC 5 B O2 5PC 5 1_555 hydrog WATSON-CRICK A G 6 A O6 G 6 1_555 B 5PC 5 B N4 5PC 5 1_555 hydrog WATSON-CRICK A A 7 A N1 A 7 1_555 B PDU 4 B N3 PDU 4 1_555 hydrog WATSON-CRICK A A 7 A N6 A 7 1_555 B PDU 4 B O4 PDU 4 1_555 hydrog WATSON-CRICK A A 8 A N1 A 8 1_555 B PDU 3 B N3 PDU 3 1_555 hydrog WATSON-CRICK A A 8 A N6 A 8 1_555 B PDU 3 B O4 PDU 3 1_555 hydrog WATSON-CRICK A G 9 A N1 G 9 1_555 B 5PC 2 B N3 5PC 2 1_555 hydrog WATSON-CRICK A G 9 A N2 G 9 1_555 B 5PC 2 B O2 5PC 2 1_555 hydrog WATSON-CRICK A G 9 A O6 G 9 1_555 B 5PC 2 B N4 5PC 2 1_555 hydrog WATSON-CRICK A C 10 A N3 C 10 1_555 B DG 1 B N1 DG 1 1_555 hydrog WATSON-CRICK A C 10 A N4 C 10 1_555 B DG 1 B O6 DG 1 1_555 hydrog WATSON-CRICK A C 10 A O2 C 10 1_555 B DG 1 B N2 DG 1 1_555 DNA-RNA HYBRID DNA.RNA HYBRID, PURINE/PYRIMIDINE-RICH STRANDS, ANTISENSE, DNA-RNA COMPLEX, DNA-RNA HYBRID 1OO7 PDB 1 1OO7 1OO7 PDB 2 1OO7 1 10 1OO7 1 10 1OO7 A 1 1 10 1 10 1OO7 1 10 1OO7 B 2 1 10 1 P 1