1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Thiviyanathan, V. Vyazovkina, K.V. Gozansky, E.K. Bichenkova, E. Abramova, T.V. Luxon, B.A. Lebedev, A.V. Gorenstein, D.G. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic C10 H16 N3 O6 P 305.224 n 2'-DEOXY-CYTIDINE-5'-RP-MONOMETHYLPHOSPHONATE 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 C11 H16 N5 O5 P 329.249 n 2'-DEOXY-ADENOSINE-5'-RP-MONOMETHYLPHOSPHONATE DNA linking US Biochemistry BICHAW 0033 0006-2960 41 827 838 10.1021/bi011551k 11790104 Structure of hybrid backbone methylphosphonate DNA heteroduplexes: effect of R and S stereochemistry. 2002 10.2210/pdb1k1r/pdb pdb_00001k1r 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 2448.613 5'-D(*TP*GP*TP*TP*TP*GP*GP*C)-3' 1 syn polymer 2063.577 5'-D(*CP*(CMR)P*(RMP)P*(RMP)P*(RMP)P*(CMR)P*(RMP))-3' 1 syn polymer no no (DT)(DG)(DT)(DT)(DT)(DG)(DG)(DC) TGTTTGGC A polydeoxyribonucleotide no yes (DC)(CMR)(RMP)(RMP)(RMP)(CMR)(RMP) CCAAACA B polydeoxyribonucleotide n n n n n n n n n n n n n n n 15.133 1 20 A 1 B 15 -0.202 A_DT1:RMP15_B 1 -26.104 -0.100 -0.504 -0.073 -8.314 1 19 A 2 B 14 -1.850 A_DG2:CMR14_B 2 -21.540 -0.208 -0.063 -0.243 -20.532 1 20 A 3 B 13 1.382 A_DT3:RMP13_B 3 -18.306 0.110 -0.309 -0.215 -28.320 1 20 A 4 B 12 2.673 A_DT4:RMP12_B 4 -21.719 0.083 -0.168 -0.157 -20.246 1 20 A 5 B 11 0.738 A_DT5:RMP11_B 5 -10.334 -0.108 0.025 -0.088 -19.590 1 19 A 6 B 10 -5.610 A_DG6:CMR10_B 6 0.604 0.107 -0.377 -0.066 -2.709 1 19 A 7 B 9 -5.570 A_DG7:DC9_B 7 11.041 0.436 -0.111 -0.139 3.860 42.049 A A 1 2 15.043 B B 15 14 4.176 10.597 -0.686 -0.983 AA_DT1DG2:CMR14RMP15_BB 1 -9.580 13.598 39.652 -2.762 -0.302 3.534 35.181 A A 2 3 -0.619 B B 14 13 3.557 -0.374 -0.470 -0.190 AA_DG2DT3:RMP13CMR14_BB 2 1.600 -2.648 35.144 -0.255 1.035 3.546 44.002 A A 3 4 20.125 B B 13 12 3.606 14.809 0.283 0.445 AA_DT3DT4:RMP12RMP13_BB 3 -1.475 2.004 41.527 -0.984 -0.535 3.118 32.107 A A 4 5 6.139 B B 12 11 3.207 3.373 0.510 0.582 AA_DT4DT5:RMP11RMP12_BB 4 -5.558 10.116 31.459 0.462 -1.896 2.986 29.126 A A 5 6 13.142 B B 11 10 3.338 6.522 -0.124 -0.908 AA_DT5DG6:CMR10RMP11_BB 5 5.067 -10.211 27.955 -3.213 1.341 3.175 30.601 A A 6 7 -5.086 B B 10 9 3.063 -2.681 0.760 -1.394 AA_DG6DG7:DC9CMR10_BB 6 0.157 -0.297 30.485 -2.134 -1.411 database_2 pdbx_nmr_exptl_sample_conditions 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 Experimental preparation 1 0 2002-06-19 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_exptl_sample_conditions.pressure_units _pdbx_nmr_software.name _struct_conn.pdbx_leaving_atom_flag HETERODUPLEX OF CHIRALLY PURE R-METHYLPHOSPHONATE / DNA DUPLEX Chiral center at the fifth position of chain B is changed to S. RCSB Y RCSB 2001-09-25 REL 1 2D NOESY DQF-COSY 100 mM 7.0 1 atm 298 K molecular dynamics matrix relaxation 100 mM NaCl, 10 mM Phosphate, 0.1 mM EDTA H2O, D2O varian data analysis VNMR 5.1 UCSF refinement Amber 5.0 Post, Meadows, Gorenstein iterative matrix relaxation MORASS 2.0 750 Varian UNITYPLUS 600 Varian UNITYPLUS 400 Varian UNITYPLUS T 1 n 1 DT 1 A G 2 n 2 DG 2 A T 3 n 3 DT 3 A T 4 n 4 DT 4 A T 5 n 5 DT 5 A G 6 n 6 DG 6 A G 7 n 7 DG 7 A C 8 n 8 DC 8 A C 9 n 1 DC 9 B CMR 10 n 2 CMR 10 B RMP 11 n 3 RMP 11 B RMP 12 n 4 RMP 12 B RMP 13 n 5 RMP 13 B CMR 14 n 6 CMR 14 B RMP 15 n 7 RMP 15 B author_defined_assembly 2 dimeric B CMR 10 B CMR 2 DC B RMP 11 B RMP 3 DA B RMP 12 B RMP 4 DA B RMP 13 B RMP 5 DA B CMR 14 B CMR 6 DC B RMP 15 B RMP 7 DA 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 DG 7 0.092 SIDE CHAIN 1 3.65 0.30 108.30 111.95 A A A O4' C1' N1 DT DT DT 1 1 1 N 1 1.98 0.30 108.30 110.28 A A A O4' C1' N1 DT DT DT 3 3 3 N 1 2.92 0.30 108.30 111.22 A A A O4' C1' N1 DT DT DT 5 5 5 N 1 -4.27 0.60 122.90 118.63 A A A C6 C5 C7 DT DT DT 5 5 5 N 1 4.21 0.30 108.30 112.51 A A A O4' C1' N9 DG DG DG 6 6 6 N 1 2.06 0.30 108.30 110.36 A A A O4' C1' N9 DG DG DG 7 7 7 N 1 -4.38 0.70 121.90 117.52 A A A N3 C2 O2 DC DC DC 8 8 8 N HETERODUPLEX OF CHIRALLY PURE R-METHYLPHOSPHONATE/DNA DUPLEX 1 N N 2 N N covale 1.616 both B DC 9 B O3' DC 1 1_555 B CMR 10 B P CMR 2 1_555 covale 1.623 both B CMR 10 B O3' CMR 2 1_555 B RMP 11 B P RMP 3 1_555 covale 1.611 both B RMP 11 B O3' RMP 3 1_555 B RMP 12 B P RMP 4 1_555 covale 1.617 both B RMP 12 B O3' RMP 4 1_555 B RMP 13 B P RMP 5 1_555 covale 1.622 both B RMP 13 B O3' RMP 5 1_555 B CMR 14 B P CMR 6 1_555 covale 1.626 both B CMR 14 B O3' CMR 6 1_555 B RMP 15 B P RMP 7 1_555 hydrog WATSON-CRICK A DT 1 A N3 DT 1 1_555 B RMP 15 B N1 RMP 7 1_555 hydrog WATSON-CRICK A DT 1 A O4 DT 1 1_555 B RMP 15 B N6 RMP 7 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B CMR 14 B N3 CMR 6 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B CMR 14 B O2 CMR 6 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B CMR 14 B N4 CMR 6 1_555 hydrog WATSON-CRICK A DT 3 A N3 DT 3 1_555 B RMP 13 B N1 RMP 5 1_555 hydrog WATSON-CRICK A DT 3 A O4 DT 3 1_555 B RMP 13 B N6 RMP 5 1_555 hydrog WATSON-CRICK A DT 4 A N3 DT 4 1_555 B RMP 12 B N1 RMP 4 1_555 hydrog WATSON-CRICK A DT 4 A O4 DT 4 1_555 B RMP 12 B N6 RMP 4 1_555 hydrog WATSON-CRICK A DT 5 A N3 DT 5 1_555 B RMP 11 B N1 RMP 3 1_555 hydrog WATSON-CRICK A DT 5 A O4 DT 5 1_555 B RMP 11 B N6 RMP 3 1_555 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 B CMR 10 B N3 CMR 2 1_555 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 B CMR 10 B O2 CMR 2 1_555 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 B CMR 10 B N4 CMR 2 1_555 hydrog WATSON-CRICK A DG 7 A N1 DG 7 1_555 B DC 9 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 7 A N2 DG 7 1_555 B DC 9 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 7 A O6 DG 7 1_555 B DC 9 B N4 DC 1 1_555 DNA methyl phosphonate, modified DNA, anti sense, aptamers, DNA 1K1R PDB 1 1K1R 1K1R PDB 2 1K1R 1 8 1K1R 1 8 1K1R A 1 1 8 9 15 1K1R 9 15 1K1R B 2 1 7