1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Hosur, R.V. Patel, P.K. 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 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 UK Nucleic Acids Res. NARHAD 0389 0305-1048 27 2457 2464 10.1093/nar/27.12.2457 10352174 NMR observation of T-tetrads in a parallel stranded DNA quadruplex formed by Saccharomyces cerevisiae telomere repeats. 1999 10.2210/pdb1emq/pdb pdb_00001emq 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 ONLY TWO REPEATS AND ONE C AT 3' END 2169.433 DNA (5'-D(*TP*GP*GP*TP*GP*GP*C)-3') YEAST TELOMERE REPEATS 4 syn polymer no no (DT)(DG)(DG)(DT)(DG)(DG)(DC) TGGTGGC A,B,C,D polydeoxyribonucleotide n n n n n n n database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2000-04-04 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-16 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name RCSB Y RCSB 2000-03-17 REL This sequence is two repeats of Saccharomyces cerevisiae telomere sequence sample 0-70 C Temperature dependent one dimensional spectra. pH dependent spectra. structures with the lowest energy 8 1 2D NOESY E-COSY 2D-TOCSY 7.0 1 atm 293 K A total of 234 NOEs constarint. 20 hydrogen bonds constraints. 8 convergant structure after IRMA refinement. R1 factor = 0.31-0.33. r.m.s.d.s from average structure 0.2-0.4. Nil violation exceeding 0.2 A. An initial model of quadruplex was generated on a IRIS workastation.Energy minimization by steepest descent followed by conjugate gradients methods was done using AMBER force field. Conformational search for the cquadruplex was performed by simulated annealing-reastarined molecular dynamics using AMBER forcefield. Relaxation matrix refinement was performed. 1 minimized average structure 1-2 mM DNA in 0.6 ml(90%H20/10%D2O) having 10 mM potassium phosphate, 0.2 mM EDTA, pH 7.0 and 100 mM KCl 90% H2O/10% D2O 1-2 mM DNA in 0.6 ml(D2O) having 10 mM potassium phosphate, 0.2 mM EDTA, pH 7.0 and 100 mM KCl D2O MSI processing Felix 230 Varian collection VNMR 6.1 MSI structure solution Discover 3.1 MSI refinement IRMA 2.3 600 Varian UNITYPLUS 500 Bruker AMX T 101 n 1 DT 101 A G 102 n 2 DG 102 A G 103 n 3 DG 103 A T 104 n 4 DT 104 A G 105 n 5 DG 105 A G 106 n 6 DG 106 A C 107 n 7 DC 107 A T 201 n 1 DT 201 B G 202 n 2 DG 202 B G 203 n 3 DG 203 B T 204 n 4 DT 204 B G 205 n 5 DG 205 B G 206 n 6 DG 206 B C 207 n 7 DC 207 B T 401 n 1 DT 401 C G 402 n 2 DG 402 C G 403 n 3 DG 403 C T 404 n 4 DT 404 C G 405 n 5 DG 405 C G 406 n 6 DG 406 C C 407 n 7 DC 407 C T 301 n 1 DT 301 D G 302 n 2 DG 302 D G 303 n 3 DG 303 D T 304 n 4 DT 304 D G 305 n 5 DG 305 D G 306 n 6 DG 306 D C 307 n 7 DC 307 D author_defined_assembly 4 tetrameric 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 102 0.089 SIDE CHAIN 1 A DT 104 0.060 SIDE CHAIN 1 A DC 107 0.076 SIDE CHAIN 1 B DG 202 0.090 SIDE CHAIN 1 B DT 204 0.078 SIDE CHAIN 1 B DC 207 0.091 SIDE CHAIN 1 C DG 402 0.132 SIDE CHAIN 1 C DG 406 0.052 SIDE CHAIN 1 C DC 407 0.138 SIDE CHAIN 1 D DG 302 0.087 SIDE CHAIN 1 D DT 304 0.069 SIDE CHAIN 1 3.46 0.30 108.30 111.76 A A A O4' C1' N1 DT DT DT 101 101 101 N 1 -4.67 0.60 122.90 118.23 A A A C6 C5 C7 DT DT DT 101 101 101 N 1 -5.43 0.80 105.90 100.47 A A A O4' C1' C2' DT DT DT 104 104 104 N 1 -4.94 0.60 122.90 117.96 A A A C6 C5 C7 DT DT DT 104 104 104 N 1 2.29 0.30 108.30 110.59 A A A O4' C1' N9 DG DG DG 106 106 106 N 1 -4.92 0.70 119.90 114.98 A A A N3 C2 N2 DG DG DG 106 106 106 N 1 -5.38 0.70 118.00 112.62 A A A N3 C4 N4 DC DC DC 107 107 107 N 1 3.78 0.30 108.30 112.08 B B B O4' C1' N1 DT DT DT 201 201 201 N 1 -4.62 0.60 122.90 118.28 B B B C6 C5 C7 DT DT DT 201 201 201 N 1 -5.29 0.80 105.90 100.61 B B B O4' C1' C2' DT DT DT 204 204 204 N 1 -4.63 0.60 122.90 118.27 B B B C6 C5 C7 DT DT DT 204 204 204 N 1 1.87 0.30 108.30 110.17 B B B O4' C1' N9 DG DG DG 206 206 206 N 1 -4.95 0.70 118.00 113.05 B B B N3 C4 N4 DC DC DC 207 207 207 N 1 2.95 0.30 108.30 111.25 C C C O4' C1' N1 DT DT DT 401 401 401 N 1 -3.64 0.60 122.30 118.66 C C C N3 C2 O2 DT DT DT 401 401 401 N 1 -4.64 0.60 122.90 118.26 C C C C6 C5 C7 DT DT DT 401 401 401 N 1 -5.62 0.80 105.90 100.28 C C C O4' C1' C2' DT DT DT 404 404 404 N 1 1.91 0.30 108.30 110.21 C C C O4' C1' N1 DT DT DT 404 404 404 N 1 3.61 0.60 114.60 118.21 C C C N1 C2 N3 DT DT DT 404 404 404 N 1 -5.18 0.60 122.90 117.72 C C C C6 C5 C7 DT DT DT 404 404 404 N 1 2.76 0.30 108.30 111.06 C C C O4' C1' N9 DG DG DG 406 406 406 N 1 -4.49 0.70 118.00 113.51 C C C N3 C4 N4 DC DC DC 407 407 407 N 1 3.16 0.30 108.30 111.46 D D D O4' C1' N1 DT DT DT 301 301 301 N 1 -4.94 0.60 122.90 117.96 D D D C6 C5 C7 DT DT DT 301 301 301 N 1 -5.66 0.80 105.90 100.24 D D D O4' C1' C2' DT DT DT 304 304 304 N 1 -4.97 0.60 122.90 117.93 D D D C6 C5 C7 DT DT DT 304 304 304 N 1 2.59 0.30 108.30 110.89 D D D O4' C1' N9 DG DG DG 306 306 306 N minimized average NMR OBSERVATION OF T-TETRADS IN A PARALLEL STRANDED DNA QUADRUPLEX FORMED BY SACCHAROMYCES CEREVISIAE TELOMERE REPEATS 1 N N 1 N N 1 N N 1 N N hydrog DT-DT MISPAIR A DT 101 A O4 DT 1 1_555 B DT 201 B N3 DT 1 1_555 hydrog DT-DT MISPAIR A DT 101 A N3 DT 1 1_555 C DT 401 C O4 DT 1 1_555 hydrog TYPE_6_PAIR A DG 102 A N7 DG 2 1_555 B DG 202 B N2 DG 2 1_555 hydrog TYPE_6_PAIR A DG 102 A O6 DG 2 1_555 B DG 202 B N1 DG 2 1_555 hydrog TYPE_6_PAIR A DG 102 A N1 DG 2 1_555 C DG 402 C O6 DG 2 1_555 hydrog TYPE_6_PAIR A DG 102 A N2 DG 2 1_555 C DG 402 C N7 DG 2 1_555 hydrog TYPE_6_PAIR A DG 103 A N7 DG 3 1_555 B DG 203 B N2 DG 3 1_555 hydrog TYPE_6_PAIR A DG 103 A O6 DG 3 1_555 B DG 203 B N1 DG 3 1_555 hydrog TYPE_6_PAIR A DG 103 A N1 DG 3 1_555 C DG 403 C O6 DG 3 1_555 hydrog TYPE_6_PAIR A DG 103 A N2 DG 3 1_555 C DG 403 C N7 DG 3 1_555 hydrog DT-DT MISPAIR A DT 104 A O4 DT 4 1_555 B DT 204 B N3 DT 4 1_555 hydrog DT-DT MISPAIR A DT 104 A N3 DT 4 1_555 C DT 404 C O4 DT 4 1_555 hydrog TYPE_6_PAIR A DG 105 A N7 DG 5 1_555 B DG 205 B N2 DG 5 1_555 hydrog TYPE_6_PAIR A DG 105 A O6 DG 5 1_555 B DG 205 B N1 DG 5 1_555 hydrog TYPE_6_PAIR A DG 105 A N1 DG 5 1_555 C DG 405 C O6 DG 5 1_555 hydrog TYPE_6_PAIR A DG 105 A N2 DG 5 1_555 C DG 405 C N7 DG 5 1_555 hydrog TYPE_6_PAIR A DG 106 A N7 DG 6 1_555 B DG 206 B N2 DG 6 1_555 hydrog TYPE_6_PAIR A DG 106 A O6 DG 6 1_555 B DG 206 B N1 DG 6 1_555 hydrog TYPE_6_PAIR A DG 106 A N1 DG 6 1_555 C DG 406 C O6 DG 6 1_555 hydrog TYPE_6_PAIR A DG 106 A N2 DG 6 1_555 C DG 406 C N7 DG 6 1_555 hydrog DC-DC MISPAIR A DC 107 A N4 DC 7 1_555 B DC 207 B N3 DC 7 1_555 hydrog DC-DC MISPAIR A DC 107 A N3 DC 7 1_555 C DC 407 C N4 DC 7 1_555 hydrog DT-DT MISPAIR B DT 201 B O4 DT 1 1_555 D DT 301 D N3 DT 1 1_555 hydrog TYPE_6_PAIR B DG 202 B N7 DG 2 1_555 D DG 302 D N2 DG 2 1_555 hydrog TYPE_6_PAIR B DG 202 B O6 DG 2 1_555 D DG 302 D N1 DG 2 1_555 hydrog TYPE_6_PAIR B DG 203 B N7 DG 3 1_555 D DG 303 D N2 DG 3 1_555 hydrog TYPE_6_PAIR B DG 203 B O6 DG 3 1_555 D DG 303 D N1 DG 3 1_555 hydrog DT-DT MISPAIR B DT 204 B O4 DT 4 1_555 D DT 304 D N3 DT 4 1_555 hydrog TYPE_6_PAIR B DG 205 B N7 DG 5 1_555 D DG 305 D N2 DG 5 1_555 hydrog TYPE_6_PAIR B DG 205 B O6 DG 5 1_555 D DG 305 D N1 DG 5 1_555 hydrog TYPE_6_PAIR B DG 206 B N7 DG 6 1_555 D DG 306 D N2 DG 6 1_555 hydrog TYPE_6_PAIR B DG 206 B O6 DG 6 1_555 D DG 306 D N1 DG 6 1_555 hydrog DC-DC MISPAIR B DC 207 B N4 DC 7 1_555 D DC 307 D N3 DC 7 1_555 hydrog DT-DT MISPAIR C DT 401 C N3 DT 1 1_555 D DT 301 D O4 DT 1 1_555 hydrog TYPE_6_PAIR C DG 402 C N1 DG 2 1_555 D DG 302 D O6 DG 2 1_555 hydrog TYPE_6_PAIR C DG 402 C N2 DG 2 1_555 D DG 302 D N7 DG 2 1_555 hydrog TYPE_6_PAIR C DG 403 C N1 DG 3 1_555 D DG 303 D O6 DG 3 1_555 hydrog TYPE_6_PAIR C DG 403 C N2 DG 3 1_555 D DG 303 D N7 DG 3 1_555 hydrog DT-DT MISPAIR C DT 404 C N3 DT 4 1_555 D DT 304 D O4 DT 4 1_555 hydrog TYPE_6_PAIR C DG 405 C N1 DG 5 1_555 D DG 305 D O6 DG 5 1_555 hydrog TYPE_6_PAIR C DG 405 C N2 DG 5 1_555 D DG 305 D N7 DG 5 1_555 hydrog TYPE_6_PAIR C DG 406 C N1 DG 6 1_555 D DG 306 D O6 DG 6 1_555 hydrog TYPE_6_PAIR C DG 406 C N2 DG 6 1_555 D DG 306 D N7 DG 6 1_555 hydrog DC-DG PAIR C DC 407 C N4 DC 7 1_555 D DG 306 D O6 DG 6 1_555 hydrog DC-DC MISPAIR C DC 407 C N3 DC 7 1_555 D DC 307 D N4 DC 7 1_555 DNA T-tetrad, G-quadruplex, Telomere, Yeast, Saccharomyces cerevisiae, DNA 1EMQ PDB 1 1EMQ 101 107 1EMQ 101 107 1EMQ A 1 1 7 201 207 1EMQ 201 207 1EMQ B 1 1 7 401 407 1EMQ 401 407 1EMQ C 1 1 7 301 307 1EMQ 301 307 1EMQ D 1 1 7 1 P 1