1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Leroy, J.-L. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 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 UK J.Mol.Biol. JMOBAK 0070 0022-2836 333 125 139 10.1016/S0022-2836(03)00945-8 14516748 T.T pair intercalation and duplex inter-conversion within i-motif tetramers 2003 UK J.Mol.Biol. JMOBAK 0070 0022-2836 261 399 414 10.1006/jmbi.1996.0472 Structure and conversion kinetics of a bi-stable DNA i-motif: broken symmetry in the [d(5mCCTCC)]4 tetramer. 1996 10.2210/pdb1q2t/pdb pdb_00001q2t 1943.384 5'-D(*(MCY)P*CP*TP*CP*TP*CP*C)-3' 4 syn polymer no yes (MCY)(DC)(DT)(DC)(DT)(DC)(DC) CCTCTCC A,B,C,D polydeoxyribonucleotide n n n n n n n 24.851 2 15 A 7 C 7 -179.060 A_DC7:DC7_C 1 20.932 -2.145 0.079 -1.916 -15.554 2 14 D 1 B 1 -179.765 D_MCY1:MCY1_B 2 -26.415 -2.031 -0.006 -0.024 2.295 2 15 A 6 C 6 -179.846 A_DC6:DC6_C 3 -19.457 -2.190 -0.083 -2.024 14.049 2 14 D 2 B 2 -179.762 D_DC2:DC2_B 4 -4.505 -2.129 -0.073 -0.217 16.974 2 12 A 5 C 5 179.884 A_DT5:DT5_C 5 23.090 1.456 -0.119 -0.499 26.737 2 14 C 4 A 4 176.334 C_DC4:DC4_A 6 5.745 2.237 0.381 0.001 -9.356 2 14 B 4 D 4 178.912 B_DC4:DC4_D 7 35.472 1.896 -0.101 0.334 -4.202 2 12 C 3 A 3 -178.309 C_DT3:DT3_A 8 -16.685 -1.309 -0.201 0.366 20.912 2 14 A 2 C 2 179.000 A_DC2:DC2_C 9 10.916 2.015 0.094 0.432 -28.293 2 14 D 6 B 6 178.564 D_DC6:DC6_B 10 -40.250 1.748 -0.141 0.889 -3.851 2 14 A 1 C 1 179.626 A_MCY1:MCY1_C 11 1.224 2.095 -0.108 0.062 8.272 2 15 D 7 B 7 -179.912 D_DC7:DC7_B 12 22.326 -1.919 -0.007 -1.628 -0.049 178.937 A D 7 1 60.134 C B 7 1 -0.060 119.870 1.815 -2.039 AD_DC7MCY1:MCY1DC7_BC 1 132.601 -66.521 63.339 -0.999 -0.930 0.008 -179.672 D A 1 6 -62.753 B C 1 6 -0.001 125.439 -3.132 3.180 DA_MCY1DC6:DC6MCY1_CB 2 128.235 64.152 -115.383 -1.591 -1.565 0.005 178.558 A D 6 2 -45.532 C B 6 2 -0.115 -90.531 -1.312 2.145 AD_DC6DC2:DC2DC6_BC 3 -153.820 77.362 35.875 1.052 0.690 -0.002 178.808 D A 2 5 -58.019 B C 2 5 -0.043 -115.595 2.326 2.705 DA_DC2DT5:DT5DC2_CB 4 136.173 -68.347 60.481 1.344 -1.173 -2.709 149.285 A C 5 4 -0.999 C A 5 4 -2.710 -1.926 0.084 -0.077 AC_DT5DC4:DC4DT5_AC 5 2.195 -1.138 149.275 -0.046 -0.051 -0.065 176.747 C B 4 4 -52.148 A D 4 4 0.035 -103.535 -1.022 1.620 CB_DC4DC4:DC4DC4_DA 6 -141.397 71.218 93.530 0.807 0.516 -0.018 -179.918 B C 4 3 55.761 D A 4 3 -0.028 -111.520 2.822 3.714 BC_DC4DT3:DT3DC4_AD 7 140.129 70.066 -169.640 -1.858 1.410 -2.860 -23.668 C A 3 2 -2.013 A C 3 2 -2.865 0.825 0.031 0.030 CA_DT3DC2:DC2DT3_CA 8 1.635 3.990 -23.598 0.168 -0.401 0.686 -178.847 A D 2 6 60.963 C B 2 6 0.622 -121.322 -2.680 3.707 AD_DC2DC6:DC6DC2_BC 9 -131.352 -66.003 -29.254 -1.511 -1.711 0.074 -176.673 D A 6 1 -64.293 B C 6 1 -0.148 127.281 -2.300 1.943 DA_DC6MCY1:MCY1DC6_CB 10 121.598 61.422 -66.112 -0.957 -1.164 0.292 179.507 A D 1 7 -67.682 C B 1 7 0.256 -135.291 -2.589 -2.426 AD_MCY1DC7:DC7MCY1_BC 11 116.721 -58.392 136.071 -1.173 1.330 database_2 pdbx_struct_assembly pdbx_struct_oper_list struct_conn repository Initial release Version format compliance Version format compliance Database references Derived calculations 1 0 2003-09-23 1 1 2008-04-29 1 2 2011-07-13 1 3 2022-03-02 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag i-motif tetramer of 5mCCTCC RCSB Y RCSB 2003-07-26 REL REL back calculated data agree with experimental NOESY spectrum 10 1 2D NOESY 2D TOCSY No added counter-ions 4.4 ambient 273 K the structure is based on a total of 172 restraints. 30 base-pairing restraints from hydrogen bonds, 78 NOE-distance restraints and 36 repulsive restraints reflecting the absence of NOE simulated annealing 10mM DNA strand H2O 90%, D2O 10% Brunger structure solution X-PLOR 3.851 Brunger refinement X-PLOR 3.851 500 Varian INOVA MCY 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 T 5 n 5 DT 5 A C 6 n 6 DC 6 A C 7 n 7 DC 7 A MCY 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 T 5 n 5 DT 5 B C 6 n 6 DC 6 B C 7 n 7 DC 7 B MCY 1 n 1 MCY 1 C C 2 n 2 DC 2 C T 3 n 3 DT 3 C C 4 n 4 DC 4 C T 5 n 5 DT 5 C C 6 n 6 DC 6 C C 7 n 7 DC 7 C MCY 1 n 1 MCY 1 D C 2 n 2 DC 2 D T 3 n 3 DT 3 D C 4 n 4 DC 4 D T 5 n 5 DT 5 D C 6 n 6 DC 6 D C 7 n 7 DC 7 D author_defined_assembly 4 tetrameric A MCY 1 5-METHYL-2'-DEOXYCYTIDINE A MCY 1 DC B MCY 1 5-METHYL-2'-DEOXYCYTIDINE B MCY 1 DC C MCY 1 5-METHYL-2'-DEOXYCYTIDINE C MCY 1 DC D MCY 1 5-METHYL-2'-DEOXYCYTIDINE D 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 B DC 2 0.071 SIDE CHAIN 1 D DC 2 0.063 SIDE CHAIN 1 2.37 0.30 108.30 110.67 A A A O4' C1' N1 DC DC DC 2 2 2 N 1 3.32 0.50 119.90 123.22 A A A C2 N3 C4 DC DC DC 2 2 2 N 1 2.64 0.30 108.30 110.94 A A A O4' C1' N1 DT DT DT 3 3 3 N 1 2.03 0.30 108.30 110.33 A A A O4' C1' N1 DC DC DC 4 4 4 N 1 3.54 0.50 119.90 123.44 A A A C2 N3 C4 DC DC DC 4 4 4 N 1 4.01 0.60 118.90 122.91 A A A N1 C2 O2 DC DC DC 4 4 4 N 1 1.95 0.30 108.30 110.25 A A A O4' C1' N1 DT DT DT 5 5 5 N 1 2.49 0.30 108.30 110.79 A A A O4' C1' N1 DC DC DC 6 6 6 N 1 3.23 0.50 119.90 123.13 A A A C2 N3 C4 DC DC DC 6 6 6 N 1 3.08 0.30 108.30 111.38 A A A O4' C1' N1 DC DC DC 7 7 7 N 1 3.24 0.50 119.90 123.14 A A A C2 N3 C4 DC DC DC 7 7 7 N 1 2.24 0.30 108.30 110.54 B B B O4' C1' N1 DC DC DC 2 2 2 N 1 3.32 0.50 119.90 123.22 B B B C2 N3 C4 DC DC DC 2 2 2 N 1 3.93 0.60 118.90 122.83 B B B N1 C2 O2 DC DC DC 2 2 2 N 1 2.49 0.30 108.30 110.79 B B B O4' C1' N1 DT DT DT 3 3 3 N 1 2.32 0.30 108.30 110.62 B B B O4' C1' N1 DC DC DC 4 4 4 N 1 3.77 0.60 118.90 122.67 B B B N1 C2 O2 DC DC DC 4 4 4 N 1 2.78 0.30 108.30 111.08 B B B O4' C1' N1 DT DT DT 5 5 5 N 1 2.69 0.30 108.30 110.99 B B B O4' C1' N1 DC DC DC 6 6 6 N 1 3.13 0.50 119.90 123.03 B B B C2 N3 C4 DC DC DC 6 6 6 N 1 2.63 0.30 108.30 110.93 B B B O4' C1' N1 DC DC DC 7 7 7 N 1 3.15 0.50 119.90 123.05 B B B C2 N3 C4 DC DC DC 7 7 7 N 1 2.42 0.30 108.30 110.72 C C C O4' C1' N1 DC DC DC 2 2 2 N 1 2.68 0.30 108.30 110.98 C C C O4' C1' N1 DT DT DT 3 3 3 N 1 2.01 0.30 108.30 110.31 C C C O4' C1' N1 DC DC DC 4 4 4 N 1 2.00 0.30 108.30 110.30 C C C O4' C1' N1 DT DT DT 5 5 5 N 1 2.50 0.30 108.30 110.80 C C C O4' C1' N1 DC DC DC 6 6 6 N 1 2.94 0.30 108.30 111.24 C C C O4' C1' N1 DC DC DC 7 7 7 N 1 2.13 0.30 108.30 110.43 D D D O4' C1' N1 DC DC DC 2 2 2 N 1 2.35 0.30 108.30 110.65 D D D O4' C1' N1 DT DT DT 3 3 3 N 1 2.06 0.30 108.30 110.36 D D D O4' C1' N1 DC DC DC 4 4 4 N 1 2.58 0.30 108.30 110.88 D D D O4' C1' N1 DT DT DT 5 5 5 N 1 3.34 0.30 108.30 111.64 D D D O4' C1' N1 DC DC DC 6 6 6 N 1 2.68 0.30 108.30 110.98 D D D O4' C1' N1 DC DC DC 7 7 7 N Solution structure of d(5mCCTCTCC)4 1 N N 1 N N 1 N N 1 N N covale 1.613 both A MCY 1 A O3' MCY 1 1_555 A DC 2 A P DC 2 1_555 covale 1.613 both B MCY 1 B O3' MCY 1 1_555 B DC 2 B P DC 2 1_555 covale 1.614 both C MCY 1 C O3' MCY 1 1_555 C DC 2 C P DC 2 1_555 covale 1.613 both D MCY 1 D O3' MCY 1 1_555 D DC 2 D P DC 2 1_555 hydrog TYPE_14_PAIR A MCY 1 A N3 MCY 1 1_555 C MCY 1 C N4 MCY 1 1_555 hydrog TYPE_14_PAIR A MCY 1 A N4 MCY 1 1_555 C MCY 1 C N3 MCY 1 1_555 hydrog TYPE_14_PAIR A DC 2 A N3 DC 2 1_555 C DC 2 C N4 DC 2 1_555 hydrog TYPE_14_PAIR A DC 2 A N4 DC 2 1_555 C DC 2 C N3 DC 2 1_555 hydrog TYPE_12_PAIR A DT 3 A N3 DT 3 1_555 C DT 3 C O4 DT 3 1_555 hydrog TYPE_12_PAIR A DT 3 A O4 DT 3 1_555 C DT 3 C N3 DT 3 1_555 hydrog TYPE_14_PAIR A DC 4 A N3 DC 4 1_555 B DC 4 B N4 DC 4 1_555 hydrog TYPE_14_PAIR A DC 4 A N4 DC 4 1_555 B DC 4 B N3 DC 4 1_555 hydrog TYPE_14_PAIR A DC 4 A N3 DC 4 1_555 C DC 4 C N4 DC 4 1_555 hydrog TYPE_14_PAIR A DC 4 A N4 DC 4 1_555 C DC 4 C N3 DC 4 1_555 hydrog TYPE_12_PAIR A DT 5 A N3 DT 5 1_555 C DT 5 C O4 DT 5 1_555 hydrog TYPE_12_PAIR A DT 5 A O4 DT 5 1_555 C DT 5 C N3 DT 5 1_555 hydrog TYPE_15_PAIR A DC 6 A N4 DC 6 1_555 C DC 6 C O2 DC 6 1_555 hydrog TYPE_15_PAIR A DC 6 A O2 DC 6 1_555 C DC 6 C N4 DC 6 1_555 hydrog TYPE_15_PAIR A DC 7 A N4 DC 7 1_555 C DC 7 C O2 DC 7 1_555 hydrog TYPE_15_PAIR A DC 7 A O2 DC 7 1_555 C DC 7 C N4 DC 7 1_555 hydrog TYPE_14_PAIR B MCY 1 B N3 MCY 1 1_555 D MCY 1 D N4 MCY 1 1_555 hydrog TYPE_14_PAIR B MCY 1 B N4 MCY 1 1_555 D MCY 1 D N3 MCY 1 1_555 hydrog TYPE_14_PAIR B DC 2 B N3 DC 2 1_555 D DC 2 D N4 DC 2 1_555 hydrog TYPE_14_PAIR B DC 2 B N4 DC 2 1_555 D DC 2 D N3 DC 2 1_555 hydrog DT-DC MISPAIR B DT 3 B O2 DT 3 1_555 B DC 4 B N4 DC 4 1_555 hydrog TYPE_14_PAIR B DC 4 B N3 DC 4 1_555 D DC 4 D N4 DC 4 1_555 hydrog TYPE_14_PAIR B DC 4 B N4 DC 4 1_555 D DC 4 D N3 DC 4 1_555 hydrog TYPE_14_PAIR B DC 6 B N3 DC 6 1_555 D DC 6 D N4 DC 6 1_555 hydrog TYPE_14_PAIR B DC 6 B N4 DC 6 1_555 D DC 6 D N3 DC 6 1_555 hydrog TYPE_15_PAIR B DC 7 B N4 DC 7 1_555 D DC 7 D O2 DC 7 1_555 hydrog TYPE_15_PAIR B DC 7 B O2 DC 7 1_555 D DC 7 D N4 DC 7 1_555 hydrog DC-DC MISPAIR C DC 4 C N3 DC 4 1_555 D DC 4 D N4 DC 4 1_555 DNA DNA solution structure; i-motif; protonated cytidine; hemiprotonated base-pairs, DNA 1Q2T PDB 1 1Q2T 1 7 1Q2T 1 7 1Q2T A 1 1 7 1 7 1Q2T 1 7 1Q2T B 1 1 7 1 7 1Q2T 1 7 1Q2T C 1 1 7 1 7 1Q2T 1 7 1Q2T D 1 1 7