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. Bichenchova, 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 C11 H16 N5 O5 P 329.249 n 2'-DEOXY-ADENOSINE-5'-SP-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/pdb1k1h/pdb pdb_00001k1h 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*(SMP)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)(SMP)(CMR)(RMP) CCAAACA B polydeoxyribonucleotide n n n n n n n n n n n n n n n 5.591 1 20 A 1 B 15 -3.969 A_DT1:RMP15_B 1 3.044 -0.183 0.149 0.016 21.287 1 19 A 2 B 14 1.784 A_DG2:CMR14_B 2 -6.556 -0.349 0.525 0.045 13.941 1 20 A 3 B 13 -4.124 A_DT3:SMP13_B 3 -19.731 -0.439 -0.197 -0.032 6.252 1 20 A 4 B 12 -2.576 A_DT4:RMP12_B 4 -14.813 -0.160 0.080 0.002 -4.979 1 20 A 5 B 11 1.686 A_DT5:RMP11_B 5 -17.556 0.084 0.246 -0.078 2.454 1 19 A 6 B 10 -2.247 A_DG6:CMR10_B 6 -1.748 0.267 0.307 -0.056 14.552 1 19 A 7 B 9 -1.316 A_DG7:DC9_B 7 -3.928 0.257 0.547 -0.032 3.129 36.119 A A 1 2 -1.441 B B 15 14 3.109 -0.893 0.448 -0.493 AA_DT1DG2:CMR14RMP15_BB 1 0.872 -1.406 36.098 -0.675 -0.606 3.503 35.928 A A 2 3 -3.445 B B 14 13 3.502 -2.121 -0.441 -1.035 AA_DG2DT3:SMP13CMR14_BB 2 3.268 -5.308 35.723 -1.352 1.215 3.593 31.842 A A 3 4 -4.892 B B 13 12 3.569 -2.678 0.736 -1.252 AA_DT3DT4:RMP12SMP13_BB 3 -2.481 4.531 31.637 -1.745 -1.840 3.606 35.728 A A 4 5 -1.452 B B 12 11 3.551 -0.890 0.661 -1.230 AA_DT4DT5:RMP11RMP12_BB 4 1.657 -2.702 35.680 -1.864 -0.815 3.024 32.768 A A 5 6 6.585 B B 11 10 3.081 3.705 -0.676 -0.656 AA_DT5DG6:CMR10RMP11_BB 5 -1.960 3.484 32.506 -1.760 0.881 3.096 34.418 A A 6 7 -1.656 B B 10 9 3.100 -0.980 0.368 -0.469 AA_DG6DG7:DC9CMR10_BB 6 -1.275 2.156 34.382 -0.648 -0.810 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 RCSB Y RCSB 2001-09-25 REL 1 2D NOESY DQF-COSY 100 mM 7.0 1 atm 298 K No dihedral restraints were used. molecular dynamics matrix relaxation DNA, 100 mM NaCl, 10 mM Phosphate, 0.1 mM EDTA H2O, D2O Varian processing VNMR 5.1 Post, Meadows, and Gorenstein iterative matrix relaxation MORASS 2.1 UCSF refinement Amber 5.0 750 Varian UNITYPLUS 600 Varian UNITYPLUS 400 Varian UNITYPLUS DT5 1 n 1 DT 1 A DG 2 n 2 DG 2 A DT 3 n 3 DT 3 A DT 4 n 4 DT 4 A DT 5 n 5 DT 5 A DG 6 n 6 DG 6 A DG 7 n 7 DG 7 A DC3 8 n 8 DC 8 A DC5 9 n 1 DC 9 B CMR 10 n 2 CMR 10 B AMR 11 n 3 RMP 11 B AMR 12 n 4 RMP 12 B AMS 13 n 5 SMP 13 B CMR 14 n 6 CMR 14 B AR3 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 SMP 13 B SMP 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 0.057 SIDE CHAIN 1 5.32 0.30 108.30 113.62 A A A O4' C1' N1 DT DT DT 1 1 1 N 1 -3.91 0.60 122.90 118.99 A A A C6 C5 C7 DT DT DT 1 1 1 N 1 3.31 0.30 108.30 111.61 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 2.79 0.30 108.30 111.09 A A A O4' C1' N1 DT DT DT 4 4 4 N 1 -3.85 0.60 122.90 119.05 A A A C6 C5 C7 DT DT DT 4 4 4 N 1 -4.42 0.60 122.90 118.48 A A A C6 C5 C7 DT DT DT 5 5 5 N 1 1.84 0.30 108.30 110.14 A A A O4' C1' N9 DG DG DG 6 6 6 N 1 3.13 0.30 108.30 111.43 A A A O4' C1' N9 DG DG DG 7 7 7 N 1 1.95 0.30 108.30 110.25 A A A O4' C1' N1 DC DC DC 8 8 8 N 1 2.59 0.30 108.30 110.89 B B B O4' C1' N1 DC DC DC 9 9 9 N HETERODUPLEX OF CHIRALLY PURE METHYLPHOSPHONATE/DNA DUPLEX 1 N N 2 N N covale 1.603 both B DC 9 B O3' DC 1 1_555 B CMR 10 B P CMR 2 1_555 covale 1.610 both B CMR 10 B O3' CMR 2 1_555 B RMP 11 B P RMP 3 1_555 covale 1.592 both B RMP 11 B O3' RMP 3 1_555 B RMP 12 B P RMP 4 1_555 covale 1.594 both B RMP 12 B O3' RMP 4 1_555 B SMP 13 B P SMP 5 1_555 covale 1.595 both B SMP 13 B O3' SMP 5 1_555 B CMR 14 B P CMR 6 1_555 covale 1.606 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 SMP 13 B N1 SMP 5 1_555 hydrog WATSON-CRICK A DT 3 A O4 DT 3 1_555 B SMP 13 B N6 SMP 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, anti sense, DNA 1K1H PDB 1 1K1H 1K1H PDB 2 1K1H 1 8 1K1H 1 8 1K1H A 1 1 8 9 15 1K1H 9 15 1K1H B 2 1 7