1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 SOME OF THE CYTIDINES ARE PROTONATED AT THE N3 POSITION. THESE RESIDUES HAVE BEEN ASSIGNED THE RESIDUE NAME C IN THE ENTRY AND ATOM H3 HAS BEEN FOOTNOTED. Leroy, J.-L. Gueron, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 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 Structure STRUE6 2005 0969-2126 3 101 120 10.1016/S0969-2126(01)00138-1 7743125 Solution structures of the i-motif tetramers of d(TCC), d(5methylCCT) and d(T5methylCC): novel NOE connections between amino protons and sugar protons. 1995 10.2210/pdb106d/pdb pdb_0000106d 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 771.646 DNA (5'-D(*MCYP*CP*T)-3') 4 syn polymer no yes (MCY)(DC)(DT) CCT A,B,C,D polydeoxyribonucleotide n n n -21.458 2 14 A 1 C 7 179.007 A_MCY1:MCY7_C 1 12.891 2.094 -0.173 0.183 11.400 2 15 D 11 B 5 178.287 D_DC11:DC5_B 2 31.811 2.486 0.743 2.477 -6.151 2 15 A 2 C 8 -179.371 A_DC2:DC8_C 3 -26.612 -2.238 -0.070 -2.274 -8.183 2 15 D 10 B 4 179.363 D_MCY10:MCY4_B 4 13.564 2.423 -0.074 2.151 -0.021 -170.870 A D 1 11 -58.376 C B 7 5 -0.211 112.622 -2.981 3.287 AD_MCY1DC11:DC5MCY7_BC 1 127.617 66.149 -42.438 -1.596 -1.555 0.757 -174.244 D A 11 2 73.763 B C 5 8 0.932 -144.398 -1.812 -0.708 DA_DC11DC2:DC8DC5_CB 2 96.575 49.333 -47.266 0.814 -0.600 -0.019 -179.577 A D 2 10 72.330 C B 8 4 -0.022 -144.428 3.440 2.525 AD_DC2MCY10:MCY4DC8_BC 3 106.663 53.417 -43.065 -1.274 1.712 database_2 pdbx_database_status pdbx_struct_assembly pdbx_struct_oper_list struct_conn repository Initial release Version format compliance Version format compliance Database references Derived calculations Other 1 0 1995-02-07 1 1 2008-03-24 1 2 2011-07-13 1 3 2022-02-16 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site _struct_conn.pdbx_leaving_atom_flag Y BNL 1994-12-22 REL 8 5MC STANDS FOR 5-METHYLCYTIDINE. THE STRUCTURE IS FORMED OF FOUR EQUIVALENT 5MCCT STRANDS DESIGNATED A, B, C, D. STRANDS A AND C, CONNECTED BY TWO HEMI-PROTONATED BASE PAIRS (5MC1.5MC1+ AND C2.C2+), FORM A PARALLEL-STRANDED DUPLEX. THE RELATION BETWEEN STRANDS B AND D IS THE SAME AS THAT BETWEEN STRANDS A AND C. THE STRANDS OF EACH DUPLEX ARE RELATED BY A LONGITUDINAL TWO-FOLD SYMMETRY AXIS. THE DUPLEXES HAVE THE SAME LONGITUDINAL AXIS, AND THEY ARE ANTI-PARALLEL. THEIR HEMI-PROTONATED C.C+ BASE PAIRS ARE INTERCALATED FACE-TO-FACE. THE DUPLEXES CAN BE TRANSFORMED INTO ONE ANOTHER BY A 180 DEGREE ROTATION AROUND A TWO-FOLD AXIS PERPENDICULAR TO THE LONGITUDINAL AXIS, AND CONSEQUENTLY AROUND A THIRD AXIS PERPENDICULAR TO THE FIRST TWO. THE H3 IMINO PROTONS OF THE HEMI-PROTONATED 5MC1.5MC1+ PAIRS WERE NOT INCORPORATED IN THE COMPUTATIONS. THOSE OF THE C2.C2+ PAIRS WERE ARBITRARILY LOCATED ON THE C2 RESIDUES OF STRANDS A AND B, RESPECTIVELY. MCY 1 n 1 MCY 1 A DC 2 n 2 DC 2 A DT 3 n 3 DT 3 A MCY 4 n 1 MCY 4 B DC 5 n 2 DC 5 B DT 6 n 3 DT 6 B MCY 7 n 1 MCY 7 C DC 8 n 2 DC 8 C DT 9 n 3 DT 9 C MCY 10 n 1 MCY 10 D DC 11 n 2 DC 11 D DT 12 n 3 DT 12 D author_defined_assembly 4 tetrameric A MCY 1 5-METHYL-2'-DEOXYCYTIDINE A MCY 1 DC B MCY 4 5-METHYL-2'-DEOXYCYTIDINE B MCY 1 DC C MCY 7 5-METHYL-2'-DEOXYCYTIDINE C MCY 1 DC D MCY 10 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 2 B C HO3' HO5' DT MCY 6 7 1.26 8 B C HO5' HO3' MCY DT 4 9 1.24 8 B C HO3' HO5' DT MCY 6 7 1.34 1 2.91 0.30 108.30 111.21 A A A O4' C1' N1 DC DC DC 2 2 2 N 1 3.25 0.50 119.90 123.15 A A A C2 N3 C4 DC DC DC 2 2 2 N 1 2.49 0.30 108.30 110.79 A A A O4' C1' N1 DT DT DT 3 3 3 N 1 2.01 0.30 108.30 110.31 B B B O4' C1' N1 DC DC DC 5 5 5 N 1 3.24 0.50 119.90 123.14 B B B C2 N3 C4 DC DC DC 5 5 5 N 1 2.68 0.30 108.30 110.98 B B B O4' C1' N1 DT DT DT 6 6 6 N 1 2.17 0.30 108.30 110.47 C C C O4' C1' N1 DC DC DC 8 8 8 N 1 2.73 0.30 108.30 111.03 C C C O4' C1' N1 DT DT DT 9 9 9 N 1 2.74 0.30 108.30 111.04 D D D O4' C1' N1 DC DC DC 11 11 11 N 1 2.87 0.30 108.30 111.17 D D D O4' C1' N1 DT DT DT 12 12 12 N 2 2.28 0.30 108.30 110.58 A A A O4' C1' N1 DC DC DC 2 2 2 N 2 3.18 0.50 119.90 123.08 A A A C2 N3 C4 DC DC DC 2 2 2 N 2 2.44 0.30 108.30 110.74 A A A O4' C1' N1 DT DT DT 3 3 3 N 2 1.82 0.30 108.30 110.12 B B B O4' C1' N1 DC DC DC 5 5 5 N 2 3.37 0.50 119.90 123.27 B B B C2 N3 C4 DC DC DC 5 5 5 N 2 3.83 0.60 118.90 122.73 B B B N1 C2 O2 DC DC DC 5 5 5 N 2 2.73 0.30 108.30 111.03 B B B O4' C1' N1 DT DT DT 6 6 6 N 2 2.28 0.30 108.30 110.58 C C C O4' C1' N1 DC DC DC 8 8 8 N 2 2.51 0.30 108.30 110.81 C C C O4' C1' N1 DT DT DT 9 9 9 N 2 2.63 0.30 108.30 110.93 D D D O4' C1' N1 DC DC DC 11 11 11 N 2 2.53 0.30 108.30 110.83 D D D O4' C1' N1 DT DT DT 12 12 12 N 3 2.27 0.30 108.30 110.57 A A A O4' C1' N1 DC DC DC 2 2 2 N 3 3.22 0.50 119.90 123.12 A A A C2 N3 C4 DC DC DC 2 2 2 N 3 2.51 0.30 108.30 110.81 A A A O4' C1' N1 DT DT DT 3 3 3 N 3 2.23 0.30 108.30 110.53 B B B O4' C1' N1 DC DC DC 5 5 5 N 3 3.29 0.50 119.90 123.19 B B B C2 N3 C4 DC DC DC 5 5 5 N 3 2.61 0.30 108.30 110.91 B B B O4' C1' N1 DT DT DT 6 6 6 N 3 2.36 0.30 108.30 110.66 C C C O4' C1' N1 DC DC DC 8 8 8 N 3 2.39 0.30 108.30 110.69 C C C O4' C1' N1 DT DT DT 9 9 9 N 3 2.99 0.30 108.30 111.29 D D D O4' C1' N1 DC DC DC 11 11 11 N 3 2.55 0.30 108.30 110.85 D D D O4' C1' N1 DT DT DT 12 12 12 N 4 3.00 0.30 108.30 111.30 A A A O4' C1' N1 DC DC DC 2 2 2 N 4 3.18 0.50 119.90 123.08 A A A C2 N3 C4 DC DC DC 2 2 2 N 4 2.76 0.30 108.30 111.06 A A A O4' C1' N1 DT DT DT 3 3 3 N 4 3.19 0.50 119.90 123.09 B B B C2 N3 C4 DC DC DC 5 5 5 N 4 3.72 0.60 118.90 122.62 B B B N1 C2 O2 DC DC DC 5 5 5 N 4 2.81 0.30 108.30 111.11 B B B O4' C1' N1 DT DT DT 6 6 6 N 4 3.06 0.30 108.30 111.36 C C C O4' C1' N1 DC DC DC 8 8 8 N 4 2.73 0.30 108.30 111.03 C C C O4' C1' N1 DT DT DT 9 9 9 N 4 2.53 0.30 108.30 110.83 D D D O4' C1' N1 DC DC DC 11 11 11 N 4 2.73 0.30 108.30 111.03 D D D O4' C1' N1 DT DT DT 12 12 12 N 5 2.46 0.30 108.30 110.76 A A A O4' C1' N1 DC DC DC 2 2 2 N 5 3.31 0.50 119.90 123.21 A A A C2 N3 C4 DC DC DC 2 2 2 N 5 2.72 0.30 108.30 111.02 A A A O4' C1' N1 DT DT DT 3 3 3 N 5 2.51 0.30 108.30 110.81 B B B O4' C1' N1 DC DC DC 5 5 5 N 5 3.34 0.50 119.90 123.24 B B B C2 N3 C4 DC DC DC 5 5 5 N 5 2.88 0.30 108.30 111.18 B B B O4' C1' N1 DT DT DT 6 6 6 N 5 2.26 0.30 108.30 110.56 C C C O4' C1' N1 DC DC DC 8 8 8 N 5 2.40 0.30 108.30 110.70 C C C O4' C1' N1 DT DT DT 9 9 9 N 5 2.46 0.30 108.30 110.76 D D D O4' C1' N1 DC DC DC 11 11 11 N 5 2.55 0.30 108.30 110.85 D D D O4' C1' N1 DT DT DT 12 12 12 N 6 2.16 0.30 108.30 110.46 A A A O4' C1' N1 DC DC DC 2 2 2 N 6 3.27 0.50 119.90 123.17 A A A C2 N3 C4 DC DC DC 2 2 2 N 6 2.67 0.30 108.30 110.97 A A A O4' C1' N1 DT DT DT 3 3 3 N 6 2.05 0.30 108.30 110.35 B B B O4' C1' N1 DC DC DC 5 5 5 N 6 3.31 0.50 119.90 123.21 B B B C2 N3 C4 DC DC DC 5 5 5 N 6 2.70 0.30 108.30 111.00 B B B O4' C1' N1 DT DT DT 6 6 6 N 6 2.42 0.30 108.30 110.72 C C C O4' C1' N1 DC DC DC 8 8 8 N 6 2.51 0.30 108.30 110.81 C C C O4' C1' N1 DT DT DT 9 9 9 N 6 2.33 0.30 108.30 110.63 D D D O4' C1' N1 DC DC DC 11 11 11 N 6 2.60 0.30 108.30 110.90 D D D O4' C1' N1 DT DT DT 12 12 12 N 7 2.40 0.30 108.30 110.70 A A A O4' C1' N1 DC DC DC 2 2 2 N 7 3.29 0.50 119.90 123.19 A A A C2 N3 C4 DC DC DC 2 2 2 N 7 2.51 0.30 108.30 110.81 A A A O4' C1' N1 DT DT DT 3 3 3 N 7 2.39 0.30 108.30 110.69 B B B O4' C1' N1 DC DC DC 5 5 5 N 7 3.24 0.50 119.90 123.14 B B B C2 N3 C4 DC DC DC 5 5 5 N 7 2.58 0.30 108.30 110.88 B B B O4' C1' N1 DT DT DT 6 6 6 N 7 2.58 0.30 108.30 110.88 C C C O4' C1' N1 DC DC DC 8 8 8 N 7 2.44 0.30 108.30 110.74 C C C O4' C1' N1 DT DT DT 9 9 9 N 7 2.09 0.30 108.30 110.39 D D D O4' C1' N1 DC DC DC 11 11 11 N 7 2.67 0.30 108.30 110.97 D D D O4' C1' N1 DT DT DT 12 12 12 N 8 2.15 0.30 108.30 110.45 A A A O4' C1' N1 DC DC DC 2 2 2 N 8 3.33 0.50 119.90 123.23 A A A C2 N3 C4 DC DC DC 2 2 2 N 8 2.61 0.30 108.30 110.91 A A A O4' C1' N1 DT DT DT 3 3 3 N 8 2.18 0.30 108.30 110.48 B B B O4' C1' N1 DC DC DC 5 5 5 N 8 3.32 0.50 119.90 123.22 B B B C2 N3 C4 DC DC DC 5 5 5 N 8 2.48 0.30 108.30 110.78 B B B O4' C1' N1 DT DT DT 6 6 6 N 8 2.40 0.30 108.30 110.70 C C C O4' C1' N1 DC DC DC 8 8 8 N 8 3.08 0.30 108.30 111.38 C C C O4' C1' N1 DT DT DT 9 9 9 N 8 2.28 0.30 108.30 110.58 D D D O4' C1' N1 DC DC DC 11 11 11 N 8 2.58 0.30 108.30 110.88 D D D O4' C1' N1 DT DT DT 12 12 12 N model building X-PLOR refinement X-PLOR phasing X-PLOR Solution structures of the i-motif tetramers of D(TCC), D(5MCCT) and D(T5MCC). Novel NOE connections between amino protons and sugar protons 1 N N 1 N N 1 N N 1 N N covale 1.614 both A MCY 1 A O3' MCY 1 1_555 A DC 2 A P DC 2 1_555 covale 1.611 both B MCY 4 B O3' MCY 1 1_555 B DC 5 B P DC 2 1_555 covale 1.612 both C MCY 7 C O3' MCY 1 1_555 C DC 8 C P DC 2 1_555 covale 1.613 both D MCY 10 D O3' MCY 1 1_555 D DC 11 D P DC 2 1_555 hydrog TYPE_14_PAIR A MCY 1 A N3 MCY 1 1_555 C MCY 7 C N4 MCY 1 1_555 hydrog TYPE_14_PAIR A MCY 1 A N4 MCY 1 1_555 C MCY 7 C N3 MCY 1 1_555 hydrog DC-DC MISPAIR A DC 2 A N4 DC 2 1_555 B DC 5 B N3 DC 2 1_555 hydrog TYPE_15_PAIR A DC 2 A N4 DC 2 1_555 C DC 8 C O2 DC 2 1_555 hydrog TYPE_15_PAIR A DC 2 A O2 DC 2 1_555 C DC 8 C N4 DC 2 1_555 hydrog TYPE_15_PAIR B MCY 4 B N4 MCY 1 1_555 D MCY 10 D O2 MCY 1 1_555 hydrog TYPE_15_PAIR B MCY 4 B O2 MCY 1 1_555 D MCY 10 D N4 MCY 1 1_555 hydrog TYPE_15_PAIR B DC 5 B N4 DC 2 1_555 D DC 11 D O2 DC 2 1_555 hydrog TYPE_15_PAIR B DC 5 B O2 DC 2 1_555 D DC 11 D N4 DC 2 1_555 DNA DNA 106D PDB 1 106D 1 3 106D 1 3 106D A 1 1 3 4 6 106D 4 6 106D B 1 1 3 7 9 106D 7 9 106D C 1 1 3 10 12 106D 10 12 106D D 1 1 3 1 P 1