1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Canalia, M. Leroy, J.-L. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 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 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking C10 H15 N3 O4 241.244 n 5-METHYL-2'-DEOXYCYTIDINE DNA linking N 1 N O N 2 N P N 3 N O N 4 N O N 5 N O N 6 N C N 7 R C N 8 N O N 9 S C N 10 N O N 11 N C N 12 R C Y 13 N N Y 14 N C Y 15 N N Y 16 N C Y 17 N C N 18 N N Y 19 N N Y 20 N C Y 21 N N Y 22 N C N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N O N 38 N P N 39 N O N 40 N O N 41 N O N 42 N C N 43 R C N 44 N O N 45 S C N 46 N O N 47 N C N 48 R C N 49 N N N 50 N C N 51 N O N 52 N N N 53 N C N 54 N N N 55 N C N 56 N C N 57 N H N 58 N H N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N O N 72 N P N 73 N O N 74 N O N 75 N O N 76 N C N 77 R C N 78 N O N 79 S C N 80 N O N 81 N C N 82 R C N 83 N N N 84 N C N 85 N O N 86 N N N 87 N C N 88 N O N 89 N C N 90 N C N 91 N C N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N H N 107 N N N 108 N C N 109 N N N 110 N C N 111 N C N 112 N C N 113 N O N 114 N N N 115 R C N 116 N C N 117 S C N 118 R C N 119 N O N 120 N O N 121 N C N 122 N O N 123 N C N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H N 131 N H N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 1 N sing N 2 N sing N 3 N doub N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing Y 24 N sing Y 25 N sing Y 26 N doub N 27 N sing Y 28 N sing Y 29 N sing Y 30 N doub N 31 N sing Y 32 N doub N 33 N sing N 34 N sing Y 35 N sing Y 36 N doub N 37 N sing Y 38 N sing N 39 N sing N 40 N sing N 41 N doub N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N doub N 65 N sing N 66 N doub N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N doub N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N doub N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N doub N 100 N sing N 101 N sing N 102 N sing N 103 N doub N 104 N sing N 105 N sing N 106 N doub N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N doub N 116 N doub N 117 N sing N 118 N sing N 119 N doub N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N sing UK Nucleic Acids Res. NARHAD 0389 0305-1048 33 5471 5481 10.1093/nar/gki843 16204453 Structure, internal motions and association-dissociation kinetics of the i-motif dimer of d(5mCCTCACTCC). 2005 10.2210/pdb2awv/pdb pdb_00002awv 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 2545.773 5'-D(*(MCY)P*CP*TP*CP*AP*CP*TP*CP*C)-3' 2 syn polymer no yes (MCY)(DC)(DT)(DC)(DA)(DC)(DT)(DC)(DC) CCTCACTCC A,B polydeoxyribonucleotide n n n n n n n n n 15.171 2 15 A 4 B 4 179.986 A_DC4:DC4_B 1 1.316 2.470 0.004 2.198 4.883 2 15 A 6 B 6 -179.985 A_DC6:DC6_B 2 13.315 -2.328 -0.011 -2.127 -5.963 2 12 A 7 B 7 179.866 A_DT7:DT7_B 3 7.585 2.178 0.053 -2.294 -6.668 2 14 A 2 B 2 179.527 A_DC2:DC2_B 4 -30.320 2.226 -0.085 -0.442 -14.472 2 15 A 8 B 8 179.892 A_DC8:DC8_B 5 -1.014 2.329 -0.029 2.076 -5.567 2 14 A 1 B 1 -179.892 A_MCY1:MCY1_B 6 -15.619 -2.120 -0.004 -0.105 -15.077 2 15 A 9 B 9 179.968 A_DC9:DC9_B 7 5.434 2.488 -0.006 2.111 -0.001 179.934 A A 4 6 71.433 B B 4 6 -0.001 142.853 2.579 1.974 AA_DC4DC6:DC6DC4_BB 1 -109.286 54.648 122.726 0.987 -1.289 3.174 174.738 A A 6 7 -0.037 B B 6 7 3.174 -0.075 0.006 0.008 AA_DC6DT7:DT7DC6_BB 2 0.396 -0.198 174.738 0.004 -0.003 -0.018 -178.971 A A 7 2 78.939 B B 7 2 0.041 -156.976 1.948 -1.087 AA_DT7DC2:DC2DT7_BB 3 -85.960 -43.227 -0.193 0.554 0.969 0.011 179.500 A A 2 8 58.008 B B 2 8 0.011 115.872 2.646 -3.119 AA_DC2DC8:DC8DC2_BB 4 136.866 -68.518 83.923 -1.563 -1.319 0.002 -179.809 A A 8 1 -59.906 B B 8 1 0.003 119.774 -2.316 -2.588 AA_DC8MCY1:MCY1DC8_BB 5 -133.907 -66.975 -112.130 1.293 -1.158 -0.003 179.873 A A 1 9 -74.038 B B 1 9 -0.002 -148.037 -1.937 -1.332 AA_MCY1DC9:DC9MCY1_BB 6 102.057 -51.042 98.008 -0.667 0.968 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_conn chem_comp_atom chem_comp_bond repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations Data collection 1 0 2005-09-20 1 1 2008-05-01 1 2 2011-07-13 1 3 2022-03-09 1 4 2024-05-29 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_conn.pdbx_leaving_atom_flag i-motif structurewithcomparable organisation i-motif structurewithcomparable organisation RCSB Y PDBJ 2005-09-02 REL REL chemicaly synthetized using the phosphoramidite method sample This structure was determined using standard 2D homonuclear and heteronuclear techniques back calculated data agree with experimental NOESY spectrum 10 1 2D NOESY E-COSY 1H-31P COSY 1 Na / phosphate 4.5 1 atm 278 K the structure is based on 565 NOE-derived, distance constraints, 17 dihedral angle restraints, 20 distance restraints from hydrogen bonds. simulated annealing 1 lowest energy strand concentration: 0.1 to 10mM 90% H2O/10% D2O Hare D. processing Felix 97.2 Brunger A structure solution X-PLOR 3.851 Koradi,R.,Billeter, M and W trich, K. data analysis MOLMOL 2.4 refinement X-PLOR 3.851 500 Varian INOVA CYT 1 n 1 MCY 1 A C 2 n 2 DC 2 A T 3 n 3 DT 3 A C 4 n 4 DC 4 A A 5 n 5 DA 5 A C 6 n 6 DC 6 A T 7 n 7 DT 7 A C 8 n 8 DC 8 A C 9 n 9 DC 9 A CYT 1 n 1 MCY 1 B C 2 n 2 DC 2 B T 3 n 3 DT 3 B C 4 n 4 DC 4 B A 5 n 5 DA 5 B C 6 n 6 DC 6 B T 7 n 7 DT 7 B C 8 n 8 DC 8 B C 9 n 9 DC 9 B author_defined_assembly 2 dimeric A MCY 1 5-METHYL-2'-DEOXYCYTIDINE A MCY 1 DC B MCY 1 5-METHYL-2'-DEOXYCYTIDINE B MCY 1 DC 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 B H41 N3 DC DC 2 2 1.43 1 A B O4 H3 DT DT 7 7 1.54 1 A B N3 H41 DC DC 2 2 1.54 1 A B H3 O4 DT DT 7 7 1.58 1 2.61 0.30 108.30 110.91 A A A O4' C1' N1 DT DT DT 3 3 3 N 1 4.03 0.30 108.30 112.33 A A A O4' C1' N1 DC DC DC 4 4 4 N 1 3.11 0.30 108.30 111.41 A A A O4' C1' N9 DA DA DA 5 5 5 N 1 3.57 0.50 113.80 117.37 A A A N7 C8 N9 DA DA DA 5 5 5 N 1 4.49 0.30 108.30 112.79 A A A O4' C1' N1 DC DC DC 6 6 6 N 1 4.67 0.30 108.30 112.97 A A A O4' C1' N1 DT DT DT 7 7 7 N 1 3.70 0.30 108.30 112.00 A A A O4' C1' N1 DC DC DC 8 8 8 N 1 1.99 0.30 108.30 110.29 A A A O4' C1' N1 DC DC DC 9 9 9 N 1 2.60 0.30 108.30 110.90 B B B O4' C1' N1 DT DT DT 3 3 3 N 1 4.05 0.30 108.30 112.35 B B B O4' C1' N1 DC DC DC 4 4 4 N 1 3.12 0.30 108.30 111.42 B B B O4' C1' N9 DA DA DA 5 5 5 N 1 3.64 0.50 113.80 117.44 B B B N7 C8 N9 DA DA DA 5 5 5 N 1 4.64 0.30 108.30 112.94 B B B O4' C1' N1 DC DC DC 6 6 6 N 1 4.72 0.30 108.30 113.02 B B B O4' C1' N1 DT DT DT 7 7 7 N 1 3.68 0.30 108.30 111.98 B B B O4' C1' N1 DC DC DC 8 8 8 N 1 1.94 0.30 108.30 110.24 B B B O4' C1' N1 DC DC DC 9 9 9 N NMR Structural Analysis of the dimer of 5MCCTCATCC 1 N N 1 N N covale 1.615 both A MCY 1 A O3' MCY 1 1_555 A DC 2 A P DC 2 1_555 covale 1.615 both B MCY 1 B O3' MCY 1 1_555 B DC 2 B P DC 2 1_555 hydrog TYPE_14_PAIR A MCY 1 A N3 MCY 1 1_555 B MCY 1 B N4 MCY 1 1_555 hydrog TYPE_14_PAIR A MCY 1 A N4 MCY 1 1_555 B MCY 1 B N3 MCY 1 1_555 hydrog TYPE_14_PAIR A DC 2 A N3 DC 2 1_555 B DC 2 B N4 DC 2 1_555 hydrog TYPE_14_PAIR A DC 2 A N4 DC 2 1_555 B DC 2 B N3 DC 2 1_555 hydrog DC-DT MISPAIR A DC 2 A N4 DC 2 1_555 B DT 7 B O4 DT 7 1_555 hydrog TYPE_15_PAIR A DC 4 A N4 DC 4 1_555 B DC 4 B O2 DC 4 1_555 hydrog TYPE_15_PAIR A DC 4 A O2 DC 4 1_555 B DC 4 B N4 DC 4 1_555 hydrog TYPE_15_PAIR A DC 6 A N4 DC 6 1_555 B DC 6 B O2 DC 6 1_555 hydrog TYPE_15_PAIR A DC 6 A O2 DC 6 1_555 B DC 6 B N4 DC 6 1_555 hydrog DT-DC MISPAIR A DT 7 A O4 DT 7 1_555 B DC 2 B N4 DC 2 1_555 hydrog TYPE_12_PAIR A DT 7 A N3 DT 7 1_555 B DT 7 B O4 DT 7 1_555 hydrog TYPE_12_PAIR A DT 7 A O4 DT 7 1_555 B DT 7 B N3 DT 7 1_555 hydrog TYPE_15_PAIR A DC 8 A N4 DC 8 1_555 B DC 8 B O2 DC 8 1_555 hydrog TYPE_15_PAIR A DC 8 A O2 DC 8 1_555 B DC 8 B N4 DC 8 1_555 hydrog TYPE_15_PAIR A DC 9 A N4 DC 9 1_555 B DC 9 B O2 DC 9 1_555 hydrog TYPE_15_PAIR A DC 9 A O2 DC 9 1_555 B DC 9 B N4 DC 9 1_555 DNA i-motif, hemiprotonated CC+ pairs, dimer, DNA 2AWV PDB 1 2AWV 1 9 2AWV 1 9 2AWV A 1 1 9 1 9 2AWV 1 9 2AWV B 1 1 9