1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Webba da Silva, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 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 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 US Biochemistry BICHAW 0033 0006-2960 42 14356 14365 10.1021/bi0355185 14661946 Association of DNA quadruplexes through G:C:G:C tetrads. Solution structure of d(GCGGTGGAT). 2003 10.2210/pdb1nyd/pdb pdb_00001nyd 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 2811.846 5'-D(*GP*CP*GP*GP*TP*GP*GP*AP*T)-3' 4 syn polymer no no (DG)(DC)(DG)(DG)(DT)(DG)(DG)(DA)(DT) GCGGTGGAT A,B,C,D polydeoxyribonucleotide n n 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 2004-02-24 1 1 2008-04-29 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name RCSB Y RCSB 2003-02-12 REL REL Structure determined using homo- and heteronuclear techniques with explicit correlations between exchangeable and non-exchangeable signals. 1 2D NOESY 2D TOCSY DQF-COSY (1H,13C)HSQC (1H,15N)HSQC JR-HMBC 100 mM NaCl 6.6 1 atm 293 K 100 mM NaCl 6.6 1 atm 273 K distance geometry, simulated annealing, molecular dynamics 4 mM sample in 100 mM NaCl, 2 mM phosphate 99.9% D2O 4 mM sample in 100 mM NaCl, 2 mM phosphate 90% H2O/10% D2O MSI processing Felix 1998 Brunger refinement X-PLOR 3.1 Accelrys data analysis Insight II 2000 400 Varian UNITY 500 Varian INOVA 600 Varian INOVA G 1 n 1 DG 1 A C 2 n 2 DC 2 A G 3 n 3 DG 3 A G 4 n 4 DG 4 A T 5 n 5 DT 5 A G 6 n 6 DG 6 A G 7 n 7 DG 7 A A 8 n 8 DA 8 A T 9 n 9 DT 9 A G 1 n 1 DG 1 B C 2 n 2 DC 2 B G 3 n 3 DG 3 B G 4 n 4 DG 4 B T 5 n 5 DT 5 B G 6 n 6 DG 6 B G 7 n 7 DG 7 B A 8 n 8 DA 8 B T 9 n 9 DT 9 B G 1 n 1 DG 1 C C 2 n 2 DC 2 C G 3 n 3 DG 3 C G 4 n 4 DG 4 C T 5 n 5 DT 5 C G 6 n 6 DG 6 C G 7 n 7 DG 7 C A 8 n 8 DA 8 C T 9 n 9 DT 9 C G 1 n 1 DG 1 D C 2 n 2 DC 2 D G 3 n 3 DG 3 D G 4 n 4 DG 4 D T 5 n 5 DT 5 D G 6 n 6 DG 6 D G 7 n 7 DG 7 D A 8 n 8 DA 8 D T 9 n 9 DT 9 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 8.65 1.40 114.30 122.95 A A A N9 C1' C2' DG DG DG 1 1 1 N 1 6.46 0.30 108.30 114.76 A A A O4' C1' N9 DG DG DG 1 1 1 N 1 -4.64 0.70 102.20 97.56 A A A C4' C3' C2' DC DC DC 2 2 2 N 1 11.41 1.40 114.30 125.71 A A A N1 C1' C2' DC DC DC 2 2 2 N 1 4.22 0.60 118.90 123.12 A A A N1 C2 O2 DC DC DC 2 2 2 N 1 11.63 1.20 119.70 131.33 A A A C3' O3' P DC DC DG 2 2 3 Y 1 -5.12 0.70 102.20 97.08 A A A C4' C3' C2' DG DG DG 3 3 3 N 1 9.17 0.30 108.30 117.47 A A A O4' C1' N9 DG DG DG 3 3 3 N 1 -5.63 0.80 102.40 96.77 A A A C3' C2' C1' DG DG DG 4 4 4 N 1 2.19 0.30 108.30 110.49 A A A O4' C1' N9 DG DG DG 4 4 4 N 1 -8.66 0.80 105.90 97.24 A A A O4' C1' C2' DT DT DT 5 5 5 N 1 5.20 0.30 108.30 113.50 A A A O4' C1' N1 DT DT DT 5 5 5 N 1 -5.86 0.70 102.20 96.34 A A A C4' C3' C2' DG DG DG 6 6 6 N 1 -8.61 0.80 105.90 97.29 A A A O4' C1' C2' DG DG DG 6 6 6 N 1 4.28 0.30 108.30 112.58 A A A O4' C1' N9 DG DG DG 6 6 6 N 1 -5.34 0.80 105.90 100.56 A A A O4' C1' C2' DG DG DG 7 7 7 N 1 9.33 1.20 119.70 129.03 A A A C3' O3' P DG DG DA 7 7 8 Y 1 -4.45 0.70 102.20 97.75 A A A C4' C3' C2' DA DA DA 8 8 8 N 1 -4.90 0.80 102.40 97.50 A A A C3' C2' C1' DA DA DA 8 8 8 N 1 3.36 0.30 108.30 111.66 A A A O4' C1' N9 DA DA DA 8 8 8 N 1 -2.43 0.40 104.50 102.07 A A A O4' C4' C3' DT DT DT 9 9 9 N 1 -4.52 0.70 102.20 97.68 A A A C4' C3' C2' DT DT DT 9 9 9 N 1 2.09 0.30 108.30 110.39 A A A O4' C1' N1 DT DT DT 9 9 9 N 1 -5.49 0.60 122.90 117.41 A A A C6 C5 C7 DT DT DT 9 9 9 N 1 8.60 1.40 114.30 122.90 B B B N9 C1' C2' DG DG DG 1 1 1 N 1 6.47 0.30 108.30 114.77 B B B O4' C1' N9 DG DG DG 1 1 1 N 1 -4.72 0.70 102.20 97.48 B B B C4' C3' C2' DC DC DC 2 2 2 N 1 11.44 1.40 114.30 125.74 B B B N1 C1' C2' DC DC DC 2 2 2 N 1 4.19 0.60 118.90 123.09 B B B N1 C2 O2 DC DC DC 2 2 2 N 1 11.64 1.20 119.70 131.34 B B B C3' O3' P DC DC DG 2 2 3 Y 1 -4.95 0.70 102.20 97.25 B B B C4' C3' C2' DG DG DG 3 3 3 N 1 9.20 0.30 108.30 117.50 B B B O4' C1' N9 DG DG DG 3 3 3 N 1 -5.76 0.80 102.40 96.64 B B B C3' C2' C1' DG DG DG 4 4 4 N 1 2.10 0.30 108.30 110.40 B B B O4' C1' N9 DG DG DG 4 4 4 N 1 -8.64 0.80 105.90 97.26 B B B O4' C1' C2' DT DT DT 5 5 5 N 1 5.27 0.30 108.30 113.57 B B B O4' C1' N1 DT DT DT 5 5 5 N 1 -5.66 0.70 102.20 96.54 B B B C4' C3' C2' DG DG DG 6 6 6 N 1 -8.56 0.80 105.90 97.34 B B B O4' C1' C2' DG DG DG 6 6 6 N 1 4.32 0.30 108.30 112.62 B B B O4' C1' N9 DG DG DG 6 6 6 N 1 -5.62 0.80 105.90 100.28 B B B O4' C1' C2' DG DG DG 7 7 7 N 1 9.34 1.20 119.70 129.04 B B B C3' O3' P DG DG DA 7 7 8 Y 1 -4.43 0.70 102.20 97.77 B B B C4' C3' C2' DA DA DA 8 8 8 N 1 -4.93 0.80 102.40 97.47 B B B C3' C2' C1' DA DA DA 8 8 8 N 1 3.15 0.30 108.30 111.45 B B B O4' C1' N9 DA DA DA 8 8 8 N 1 -2.44 0.40 104.50 102.06 B B B O4' C4' C3' DT DT DT 9 9 9 N 1 -4.24 0.70 102.20 97.96 B B B C4' C3' C2' DT DT DT 9 9 9 N 1 1.88 0.30 108.30 110.18 B B B O4' C1' N1 DT DT DT 9 9 9 N 1 -5.50 0.60 122.90 117.40 B B B C6 C5 C7 DT DT DT 9 9 9 N 1 8.63 1.40 114.30 122.93 C C C N9 C1' C2' DG DG DG 1 1 1 N 1 6.50 0.30 108.30 114.80 C C C O4' C1' N9 DG DG DG 1 1 1 N 1 -4.69 0.70 102.20 97.51 C C C C4' C3' C2' DC DC DC 2 2 2 N 1 11.45 1.40 114.30 125.75 C C C N1 C1' C2' DC DC DC 2 2 2 N 1 4.18 0.60 118.90 123.08 C C C N1 C2 O2 DC DC DC 2 2 2 N 1 11.59 1.20 119.70 131.29 C C C C3' O3' P DC DC DG 2 2 3 Y 1 -4.96 0.70 102.20 97.24 C C C C4' C3' C2' DG DG DG 3 3 3 N 1 9.16 0.30 108.30 117.46 C C C O4' C1' N9 DG DG DG 3 3 3 N 1 -5.72 0.80 102.40 96.68 C C C C3' C2' C1' DG DG DG 4 4 4 N 1 2.11 0.30 108.30 110.41 C C C O4' C1' N9 DG DG DG 4 4 4 N 1 -8.68 0.80 105.90 97.22 C C C O4' C1' C2' DT DT DT 5 5 5 N 1 5.23 0.30 108.30 113.53 C C C O4' C1' N1 DT DT DT 5 5 5 N 1 -5.67 0.70 102.20 96.53 C C C C4' C3' C2' DG DG DG 6 6 6 N 1 -8.51 0.80 105.90 97.39 C C C O4' C1' C2' DG DG DG 6 6 6 N 1 4.29 0.30 108.30 112.59 C C C O4' C1' N9 DG DG DG 6 6 6 N 1 -5.59 0.80 105.90 100.31 C C C O4' C1' C2' DG DG DG 7 7 7 N 1 9.37 1.20 119.70 129.07 C C C C3' O3' P DG DG DA 7 7 8 Y 1 -4.47 0.70 102.20 97.73 C C C C4' C3' C2' DA DA DA 8 8 8 N 1 -4.90 0.80 102.40 97.50 C C C C3' C2' C1' DA DA DA 8 8 8 N 1 3.13 0.30 108.30 111.43 C C C O4' C1' N9 DA DA DA 8 8 8 N 1 -2.45 0.40 104.50 102.05 C C C O4' C4' C3' DT DT DT 9 9 9 N 1 -4.28 0.70 102.20 97.92 C C C C4' C3' C2' DT DT DT 9 9 9 N 1 1.87 0.30 108.30 110.17 C C C O4' C1' N1 DT DT DT 9 9 9 N 1 -5.46 0.60 122.90 117.44 C C C C6 C5 C7 DT DT DT 9 9 9 N 1 8.54 1.40 114.30 122.84 D D D N9 C1' C2' DG DG DG 1 1 1 N 1 6.50 0.30 108.30 114.80 D D D O4' C1' N9 DG DG DG 1 1 1 N 1 -4.70 0.70 102.20 97.50 D D D C4' C3' C2' DC DC DC 2 2 2 N 1 11.50 1.40 114.30 125.80 D D D N1 C1' C2' DC DC DC 2 2 2 N 1 4.26 0.60 118.90 123.16 D D D N1 C2 O2 DC DC DC 2 2 2 N 1 11.65 1.20 119.70 131.35 D D D C3' O3' P DC DC DG 2 2 3 Y 1 -4.99 0.70 102.20 97.21 D D D C4' C3' C2' DG DG DG 3 3 3 N 1 9.16 0.30 108.30 117.46 D D D O4' C1' N9 DG DG DG 3 3 3 N 1 -5.73 0.80 102.40 96.67 D D D C3' C2' C1' DG DG DG 4 4 4 N 1 2.14 0.30 108.30 110.44 D D D O4' C1' N9 DG DG DG 4 4 4 N 1 -8.68 0.80 105.90 97.22 D D D O4' C1' C2' DT DT DT 5 5 5 N 1 5.23 0.30 108.30 113.53 D D D O4' C1' N1 DT DT DT 5 5 5 N 1 -5.68 0.70 102.20 96.52 D D D C4' C3' C2' DG DG DG 6 6 6 N 1 -8.56 0.80 105.90 97.34 D D D O4' C1' C2' DG DG DG 6 6 6 N 1 4.33 0.30 108.30 112.63 D D D O4' C1' N9 DG DG DG 6 6 6 N 1 -5.65 0.80 105.90 100.25 D D D O4' C1' C2' DG DG DG 7 7 7 N 1 9.36 1.20 119.70 129.06 D D D C3' O3' P DG DG DA 7 7 8 Y 1 -4.48 0.70 102.20 97.72 D D D C4' C3' C2' DA DA DA 8 8 8 N 1 -4.90 0.80 102.40 97.50 D D D C3' C2' C1' DA DA DA 8 8 8 N 1 3.12 0.30 108.30 111.42 D D D O4' C1' N9 DA DA DA 8 8 8 N 1 -2.41 0.40 104.50 102.09 D D D O4' C4' C3' DT DT DT 9 9 9 N 1 -4.28 0.70 102.20 97.92 D D D C4' C3' C2' DT DT DT 9 9 9 N 1 1.94 0.30 108.30 110.24 D D D O4' C1' N1 DT DT DT 9 9 9 N 1 -5.52 0.60 122.90 117.38 D D D C6 C5 C7 DT DT DT 9 9 9 N 1 B B C5 C7 DT DT 5 5 0.036 0.006 1.496 1.532 N 1 D D C6 N1 DG DG 4 4 -0.042 0.007 1.391 1.349 N Solution structure of DNA quadruplex GCGGTGGAT 1 N N 1 N N 1 N N 1 N N hydrog WATSON-CRICK A DG 1 A N1 DG 1 1_555 C DC 2 C N3 DC 2 1_555 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 C DC 2 C O2 DC 2 1_555 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 C DC 2 C N4 DC 2 1_555 hydrog DG-DC PAIR A DG 1 A O6 DG 1 1_555 D DC 2 D N4 DC 2 1_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 C DG 1 C N1 DG 1 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 C DG 1 C O6 DG 1 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 C DG 1 C N2 DG 1 1_555 hydrog DC-DG PAIR A DC 2 A N4 DC 2 1_555 D DG 1 D O6 DG 1 1_555 hydrog TYPE_6_PAIR A DG 3 A N1 DG 3 1_555 A DG 6 A O6 DG 6 1_555 hydrog TYPE_6_PAIR A DG 3 A N2 DG 3 1_555 A DG 6 A N7 DG 6 1_555 hydrog TYPE_6_PAIR A DG 3 A N7 DG 3 1_555 B DG 6 B N2 DG 6 1_555 hydrog TYPE_6_PAIR A DG 3 A O6 DG 3 1_555 B DG 6 B N1 DG 6 1_555 hydrog TYPE_6_PAIR A DG 4 A N1 DG 4 1_555 A DG 7 A O6 DG 7 1_555 hydrog TYPE_6_PAIR A DG 4 A N2 DG 4 1_555 A DG 7 A N7 DG 7 1_555 hydrog TYPE_6_PAIR A DG 4 A N7 DG 4 1_555 B DG 7 B N2 DG 7 1_555 hydrog TYPE_6_PAIR A DG 4 A O6 DG 4 1_555 B DG 7 B N1 DG 7 1_555 hydrog TYPE_6_PAIR A DG 6 A N1 DG 6 1_555 B DG 3 B O6 DG 3 1_555 hydrog TYPE_6_PAIR A DG 6 A N2 DG 6 1_555 B DG 3 B N7 DG 3 1_555 hydrog TYPE_6_PAIR A DG 7 A N1 DG 7 1_555 B DG 4 B O6 DG 4 1_555 hydrog TYPE_6_PAIR A DG 7 A N2 DG 7 1_555 B DG 4 B N7 DG 4 1_555 hydrog TYPE_1_PAIR A DA 8 A N1 DA 8 1_555 B DA 8 B N6 DA 8 1_555 hydrog TYPE_1_PAIR A DA 8 A N6 DA 8 1_555 B DA 8 B N1 DA 8 1_555 hydrog DG-DC PAIR B DG 1 B O6 DG 1 1_555 C DC 2 C N4 DC 2 1_555 hydrog WATSON-CRICK B DG 1 B N1 DG 1 1_555 D DC 2 D N3 DC 2 1_555 hydrog WATSON-CRICK B DG 1 B N2 DG 1 1_555 D DC 2 D O2 DC 2 1_555 hydrog WATSON-CRICK B DG 1 B O6 DG 1 1_555 D DC 2 D N4 DC 2 1_555 hydrog DC-DG PAIR B DC 2 B N4 DC 2 1_555 C DG 1 C O6 DG 1 1_555 hydrog WATSON-CRICK B DC 2 B N3 DC 2 1_555 D DG 1 D N1 DG 1 1_555 hydrog WATSON-CRICK B DC 2 B N4 DC 2 1_555 D DG 1 D O6 DG 1 1_555 hydrog WATSON-CRICK B DC 2 B O2 DC 2 1_555 D DG 1 D N2 DG 1 1_555 hydrog TYPE_6_PAIR B DG 3 B N1 DG 3 1_555 B DG 6 B O6 DG 6 1_555 hydrog TYPE_6_PAIR B DG 3 B N2 DG 3 1_555 B DG 6 B N7 DG 6 1_555 hydrog TYPE_6_PAIR B DG 4 B N1 DG 4 1_555 B DG 7 B O6 DG 7 1_555 hydrog TYPE_6_PAIR B DG 4 B N2 DG 4 1_555 B DG 7 B N7 DG 7 1_555 hydrog TYPE_6_PAIR C DG 3 C N1 DG 3 1_555 C DG 6 C O6 DG 6 1_555 hydrog TYPE_6_PAIR C DG 3 C N2 DG 3 1_555 C DG 6 C N7 DG 6 1_555 hydrog TYPE_6_PAIR C DG 3 C N7 DG 3 1_555 D DG 6 D N2 DG 6 1_555 hydrog TYPE_6_PAIR C DG 3 C O6 DG 3 1_555 D DG 6 D N1 DG 6 1_555 hydrog TYPE_6_PAIR C DG 4 C N1 DG 4 1_555 C DG 7 C O6 DG 7 1_555 hydrog TYPE_6_PAIR C DG 4 C N2 DG 4 1_555 C DG 7 C N7 DG 7 1_555 hydrog TYPE_6_PAIR C DG 4 C N7 DG 4 1_555 D DG 7 D N2 DG 7 1_555 hydrog TYPE_6_PAIR C DG 4 C O6 DG 4 1_555 D DG 7 D N1 DG 7 1_555 hydrog TYPE_6_PAIR C DG 6 C N1 DG 6 1_555 D DG 3 D O6 DG 3 1_555 hydrog TYPE_6_PAIR C DG 6 C N2 DG 6 1_555 D DG 3 D N7 DG 3 1_555 hydrog TYPE_6_PAIR C DG 7 C N1 DG 7 1_555 D DG 4 D O6 DG 4 1_555 hydrog TYPE_6_PAIR C DG 7 C N2 DG 7 1_555 D DG 4 D N7 DG 4 1_555 hydrog TYPE_1_PAIR C DA 8 C N1 DA 8 1_555 D DA 8 D N6 DA 8 1_555 hydrog TYPE_1_PAIR C DA 8 C N6 DA 8 1_555 D DA 8 D N1 DA 8 1_555 hydrog TYPE_6_PAIR D DG 3 D N1 DG 3 1_555 D DG 6 D O6 DG 6 1_555 hydrog TYPE_6_PAIR D DG 3 D N2 DG 3 1_555 D DG 6 D N7 DG 6 1_555 hydrog TYPE_6_PAIR D DG 4 D N1 DG 4 1_555 D DG 7 D O6 DG 7 1_555 hydrog TYPE_6_PAIR D DG 4 D N2 DG 4 1_555 D DG 7 D N7 DG 7 1_555 DNA quadruplex, parallel quadruplex, molecular propeller topology, double chain reversal, DNA 1NYD PDB 1 1NYD 1 9 1NYD 1 9 1NYD A 1 1 9 1 9 1NYD 1 9 1NYD B 1 1 9 1 9 1NYD 1 9 1NYD C 1 1 9 1 9 1NYD 1 9 1NYD D 1 1 9 1 P 1