1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Germann, M.W. Aramini, J.M. 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 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA linking C9 H14 N3 O8 P 323.197 y CYTIDINE-5'-MONOPHOSPHATE RNA 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 C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking C10 H15 N2 O8 P 322.208 n THYMIDINE-3'-PHOSPHATE ALPHA-ANOMERIC THYMIDINE-3'-PHOSPHATE DNA linking C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking US Biochemistry BICHAW 0033 0006-2960 38 15448 15458 10.1021/bi9915418 10569927 Solution structure of a DNA.RNA hybrid containing an alpha-anomeric thymidine and polarity reversals: d(ATGG-3'-3'-alphaT-5'-5'-GCTC). r(gagcaccau). 1999 UK Nucleic Acids Res. NARHAD 0389 0305-1048 26 5644 5654 10.1093/nar/26.24.5644 NMR solution structures of [d(GCGAAT-3'-3'-(alpha-T)-5'-5'-CGC)2] and its unmodified control 1998 10.2210/pdb1c2q/pdb pdb_00001c2q 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 T5 IS ALPHAT ANOMERIC 2746.809 5'-D(ATGG-3'-3'-(T3P)-5'-5'-GCTC)-3' 1 syn polymer 2854.782 5'-R(GAGCACCAU)-3' 1 syn polymer no yes (DA)(DT)(DG)(DG)(T3P)(DG)(DC)(DT)(DC) ATGGTGCTC A polydeoxyribonucleotide no no GAGCACCAU GAGCACCAU B polyribonucleotide n n n n n n n n n n n n n n n n n n -14.855 1 20 A 1 B 18 -3.483 A_DA1:U18_B 1 -12.112 0.056 -0.338 -0.063 12.981 1 20 A 2 B 17 1.104 A_DT2:A17_B 2 -16.507 0.084 -0.340 -0.102 -0.196 1 19 A 3 B 16 0.620 A_DG3:C16_B 3 -15.757 -0.426 -0.030 -0.223 -3.473 1 19 A 4 B 15 0.089 A_DG4:C15_B 4 -11.723 -0.463 0.154 -0.224 9.001 1 20 A 5 B 14 -2.179 A_T3P5:A14_B 5 -10.114 0.055 -0.043 -0.116 4.801 1 19 A 6 B 13 0.826 A_DG6:C13_B 6 -13.429 -0.151 0.243 -0.146 4.033 1 19 A 7 B 12 0.535 A_DC7:G12_B 7 -16.100 0.405 0.054 -0.237 15.181 1 20 A 8 B 11 -1.579 A_DT8:A11_B 8 -9.147 -0.026 -0.258 0.018 19.727 1 19 A 9 B 10 0.677 A_DC9:G10_B 9 -22.747 0.289 -0.450 -0.173 2.691 29.187 A A 1 2 1.292 B B 18 17 2.710 0.650 0.021 -0.578 AA_DA1DT2:A17U18_BB 1 2.162 -4.295 29.102 -1.263 0.348 2.598 36.012 A A 2 3 25.911 B B 17 16 3.444 15.463 -0.038 -1.181 AA_DT2DG3:C16A17_BB 2 -5.524 9.256 32.161 -4.065 -0.708 3.005 32.039 A A 3 4 9.919 B B 16 15 3.218 5.416 -0.536 -1.285 AA_DG3DG4:C15C16_BB 3 -6.256 11.458 30.979 -3.272 -0.121 2.987 34.812 A A 4 5 -0.343 B B 15 14 2.987 -0.205 -0.566 -0.586 AA_DG4T3P5:A14C15_BB 4 0.187 -0.313 34.811 -0.951 0.972 2.975 34.970 A A 5 6 9.268 B B 14 13 3.233 5.508 0.063 -0.913 AA_T3P5DG6:C13A14_BB 5 -7.287 12.260 33.791 -2.322 -1.166 2.883 32.625 A A 6 7 10.050 B B 13 12 3.204 5.616 -0.356 -1.733 AA_DG6DC7:G12C13_BB 6 -1.817 3.251 32.100 -4.000 0.337 2.739 27.805 A A 7 8 10.351 B B 12 11 3.109 4.922 -0.402 -1.170 AA_DC7DT8:A11G12_BB 7 4.982 -10.476 26.925 -3.509 1.924 2.945 31.179 A A 8 9 8.611 B B 11 10 3.150 4.611 0.288 -1.107 AA_DT8DC9:G10A11_BB 8 -1.172 2.188 30.823 -2.883 -0.744 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 1999-11-29 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 SOLUTION STRUCTURE OF A SELF-COMPLEMENTARY DNA DUPLEX CONTAINING THE SAME MODIFICATIONS (1 ALPHA-ANOMERIC THYMIDINE AND FLANKING 3'-3' AND 5'-5' PHOSPHODIESTER LINKAGES PER STRAND) RCSB Y RCSB 1999-07-26 REL REL SYNTHETIC sample SYNTHETIC sample THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR NMR TECHNIQUES 1 2D NOESY DQF-COSY 31P-1H CORRELATION SPECTROSCOPY 2D NOESY 6.6 AMBIENT 298 K 6.7 AMBIENT 298 K THE STRUCTURE IS BASED ON A TOTAL OF 405 RESTRAINTS: 268 RANDMARDI DERIVED INTERPROTON DISTANCE RESTRAINTS (NON-EXCHANGEABLE: 246; EXCHANGEABLE: 22); 45 DEOXYRIBOSE ENDOCYCLIC TORSION ANGLE RESTRAINTS DERIVED FROM PSEUDOROTATION ANALYSIS; 45 RIBOSE ENDOCYCLIC TORSION ANGLE RESTRAINTS (BROAD, N-TYPE); 46 WATSON-CRICK DISTANCE AND ANGLE RESTRAINTS. THE FINAL AVERAGE STRUCTURE WAS OBTAINED BY COORDINATE AVERAGING OF THE FINAL ENSEMBLE OF RMD/REM STRUCTURES, FOLLOWED BY RESTRAINED ENERGY MINIMIZATION. ALL STRUCTURE CALCULATIONS WERE PERFORMED USING THE SANDER PROGRAM WITHIN AMBER 4.1, AND THE 1994 ALL ATOM NUCLEIC ACID PARAMETERIZATION. ALL CALCULATIONS WERE CONDUCTED IN VACUO, USING A DISTANCE DEPENDENT DIELECTRIC CONSTANT AND 30 A CUT-OFF FOR NON-BONDED INTERACTIONS. SIMULATED ANNEALING/MOLECULAR DYNAMICS 1 minimized average structure 0.89 MM HYBRID, 50 MM NACL, 10 MM PHOSPHATE BUFFER, 0.5 MM EDTA, PH* 6.6, D2O 0.89 MM HYBRID, 50 MM NACL, 10 MM PHOSPHATE BUFFER, 0.5 MM EDTA, PH 6.7, 90% H2O/10% D2O BRUKER collection UXNMR 2.1 BORGIAS & JAMES, 1989 iterative matrix relaxation MARDIGRAS 3.2 BORGIAS & JAMES, 1988 data analysis CORMA 5.2 UCSF data analysis Sparky 3.33 PEARLMAN ET AL., 1995 refinement Amber 4.1 WIDMER & WUTHRICH, 1987 data analysis SPHINX/LINSHA LAVERY & SKLENAR, 1996 data analysis Curves 5.1 PEARLMAN ET AL., 1995 structure solution Amber 4.1 600 Bruker AMX A 1 n 1 DA 1 A T 2 n 2 DT 2 A G 3 n 3 DG 3 A G 4 n 4 DG 4 A X 5 n 5 T3P 5 A G 6 n 6 DG 6 A C 7 n 7 DC 7 A T 8 n 8 DT 8 A C 9 n 9 DC 9 A G 10 n 1 G 10 B A 11 n 2 A 11 B G 12 n 3 G 12 B C 13 n 4 C 13 B A 14 n 5 A 14 B C 15 n 6 C 15 B C 16 n 7 C 16 B A 17 n 8 A 17 B U 18 n 9 U 18 B author_defined_assembly 2 dimeric A T3P 5 THYMIDINE-3'-PHOSPHATE A T3P 5 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 C1' T3P 5 WRONG HAND 1 A DG 6 0.070 SIDE CHAIN 1 B A 11 0.057 SIDE CHAIN 1 B A 14 0.097 SIDE CHAIN 1 B A 17 0.079 SIDE CHAIN 1 3.70 0.60 106.00 109.70 A A A O4' C4' C3' DA DA DA 1 1 1 N 1 2.46 0.30 108.30 110.76 A A A O4' C1' N9 DA DA DA 1 1 1 N 1 2.63 0.30 108.30 110.93 A A A O4' C1' N1 DT DT DT 2 2 2 N 1 3.19 0.30 108.30 111.49 A A A O4' C1' N9 DG DG DG 3 3 3 N 1 3.66 0.60 106.00 109.66 A A A O4' C4' C3' DG DG DG 4 4 4 N 1 4.18 0.30 108.30 112.48 A A A O4' C1' N9 DG DG DG 4 4 4 N 1 53.17 1.90 104.00 157.17 A A A O3' P O5' DG T3P T3P 4 5 5 Y 1 5.30 0.60 106.00 111.30 A A A O4' C4' C3' DG DG DG 6 6 6 N 1 8.25 1.20 102.50 110.75 A A A C3' C2' C1' DG DG DG 6 6 6 N 1 3.65 0.30 108.30 111.95 A A A O4' C1' N9 DG DG DG 6 6 6 N 1 4.21 0.60 106.00 110.21 A A A O4' C4' C3' DC DC DC 7 7 7 N 1 7.14 1.10 109.80 116.94 A A A C5' C4' O4' DC DC DC 7 7 7 N 1 3.05 0.30 108.30 111.35 A A A O4' C1' N1 DT DT DT 8 8 8 N 1 -3.82 0.60 122.90 119.08 A A A C6 C5 C7 DT DT DT 8 8 8 N 1 4.40 0.30 108.30 112.70 A A A O4' C1' N1 DC DC DC 9 9 9 N 1 5.90 0.70 108.50 114.40 B B B O4' C1' N9 G G G 10 10 10 N 1 4.30 0.70 108.50 112.80 B B B O4' C1' N9 A A A 11 11 11 N 1 -3.80 0.60 118.60 114.80 B B B N1 C6 N6 A A A 11 11 11 N 1 6.64 0.70 108.50 115.14 B B B O4' C1' N9 G G G 12 12 12 N 1 6.25 0.70 108.50 114.75 B B B O4' C1' N1 C C C 13 13 13 N 1 6.41 0.70 108.50 114.91 B B B O4' C1' N1 C C C 15 15 15 N 1 6.89 0.70 108.50 115.39 B B B O4' C1' N1 C C C 16 16 16 N 1 4.79 0.70 108.50 113.29 B B B O4' C1' N1 U U U 18 18 18 N minimized average SOLUTION STRUCTURE OF A DNA.RNA HYBRID CONTAINING AN ALPHAT-ANOMERIC THYMIDINE AND POLARITY REVERSALS 1 N N 2 N N covale 1.614 both A DG 4 A O3' DG 4 1_555 A T3P 5 A P T3P 5 1_555 covale 1.608 one A T3P 5 A O5' T3P 5 1_555 A DG 6 A P DG 6 1_555 hydrog WATSON-CRICK A DA 1 A N1 DA 1 1_555 B U 18 B N3 U 9 1_555 hydrog WATSON-CRICK A DA 1 A N6 DA 1 1_555 B U 18 B O4 U 9 1_555 hydrog WATSON-CRICK A DT 2 A N3 DT 2 1_555 B A 17 B N1 A 8 1_555 hydrog WATSON-CRICK A DT 2 A O4 DT 2 1_555 B A 17 B N6 A 8 1_555 hydrog WATSON-CRICK A DG 3 A N1 DG 3 1_555 B C 16 B N3 C 7 1_555 hydrog WATSON-CRICK A DG 3 A N2 DG 3 1_555 B C 16 B O2 C 7 1_555 hydrog WATSON-CRICK A DG 3 A O6 DG 3 1_555 B C 16 B N4 C 7 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B C 15 B N3 C 6 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B C 15 B O2 C 6 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B C 15 B N4 C 6 1_555 hydrog WATSON-CRICK A T3P 5 A N3 T3P 5 1_555 B A 14 B N1 A 5 1_555 hydrog WATSON-CRICK A T3P 5 A O4 T3P 5 1_555 B A 14 B N6 A 5 1_555 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 B C 13 B N3 C 4 1_555 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 B C 13 B O2 C 4 1_555 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 B C 13 B N4 C 4 1_555 hydrog WATSON-CRICK A DC 7 A N3 DC 7 1_555 B G 12 B N1 G 3 1_555 hydrog WATSON-CRICK A DC 7 A N4 DC 7 1_555 B G 12 B O6 G 3 1_555 hydrog WATSON-CRICK A DC 7 A O2 DC 7 1_555 B G 12 B N2 G 3 1_555 hydrog WATSON-CRICK A DT 8 A N3 DT 8 1_555 B A 11 B N1 A 2 1_555 hydrog WATSON-CRICK A DT 8 A O4 DT 8 1_555 B A 11 B N6 A 2 1_555 hydrog WATSON-CRICK A DC 9 A N3 DC 9 1_555 B G 10 B N1 G 1 1_555 hydrog WATSON-CRICK A DC 9 A N4 DC 9 1_555 B G 10 B O6 G 1 1_555 hydrog WATSON-CRICK A DC 9 A O2 DC 9 1_555 B G 10 B N2 G 1 1_555 DNA-RNA HYBRID DNA/RNA HYBRID, ALPHAT-ANOMERIC THYMIDINE, 3'-3'/5'-5' PHOSPHODIESTER LINKAGES, DNA-RNA HYBRID 1C2Q PDB 1 1C2Q 1C2Q PDB 2 1C2Q 1 9 1C2Q 1 9 1C2Q A 1 1 9 10 18 1C2Q 10 18 1C2Q B 2 1 9 1 P 1