1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 0000-0002-1034-2958 Han, Y. 0000-0002-3197-9472 Dickerhoff, J. 0000-0001-7489-7111 Yang, D. 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 H14 N5 O7 P 347.221 y 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE 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 Y 83 N N Y 84 N C Y 85 N N Y 86 N C N 87 N C N 88 N O N 89 N N N 90 N C N 91 N N N 92 N N Y 93 N C 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 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 Y 97 N sing Y 98 N sing Y 99 N doub N 100 N sing Y 101 N sing N 102 N sing Y 103 N doub N 104 N doub N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N doub N 110 N sing N 111 N sing N 112 N sing UK Nucleic Acids Res. NARHAD 0389 1362-4962 54 10.1093/nar/gkag843 42695283 Structures and dynamics of the major G-quadruplex in the human PDGFR-beta gene promoter: insights into vacancy G-quadruplex formation. 2026 0000-0002-3197-9472 0000-0001-7489-7111 10.2210/pdb9p9y/pdb pdb_00009p9y 10.13018/BMR31253 6684.297 DNA (5'-D(*AP*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*GP*CP*AP*GP*G)-3') 1 syn polymer no no (DA)(DA)(DG)(DG)(DG)(DA)(DG)(DG)(DG)(DC)(DG)(DG)(DC)(DG)(DG)(DG)(DG)(DC)(DA)(DG) (DG) AAGGGAGGGCGGCGGGGCAGG X polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n -3.710 3 6 X 3 X 14 90.729 X_DG3:DG14_X 1 -3.482 -1.835 -0.039 -3.267 -5.860 3 6 X 7 X 11 -88.444 X_DG7:DG11_X 2 6.137 1.905 -0.122 3.309 3.149 3 6 X 15 X 12 89.419 X_DG15:DG12_X 3 16.663 -1.638 -0.142 -3.452 15.457 4 7 X 17 X 20 -110.889 X_DG17:DG20_X 4 -39.055 5.611 -1.010 -0.505 2.713 3 6 X 5 X 9 -88.472 X_DG5:DG9_X 5 -6.014 2.170 -0.132 3.089 1.743 3 6 X 16 X 21 92.013 X_DG16:DG21_X 6 10.158 -1.821 -0.442 -3.232 0.474 179.994 X X 3 7 4.330 X X 14 11 0.474 8.661 -1.892 -3.199 XX_DG3DG7:DG11DG14_XX 1 -2.988 1.494 179.994 -1.600 0.946 2.896 114.494 X X 7 15 4.393 X X 11 12 2.985 7.387 -1.712 -3.040 XX_DG7DG15:DG12DG11_XX 2 -4.261 2.534 114.290 -1.880 0.976 -3.024 35.887 X X 17 5 11.742 X X 20 9 -3.411 7.126 0.085 1.113 XX_DG17DG5:DG9DG20_XX 3 8.323 -13.713 34.226 2.836 -1.340 -0.083 178.006 X X 5 16 4.594 X X 9 21 -0.084 9.187 -1.991 -3.260 XX_DG5DG16:DG21DG9_XX 4 -17.060 8.531 177.977 -1.630 0.996 citation citation_author repository Initial release Database references 1 0 2026-08-26 1 1 2026-09-16 _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _citation_author.identifier_ORCID United States National Institutes of Health/National Cancer Institute (NIH/NCI) R01CA177585 United States National Institutes of Health/National Cancer Institute (NIH/NCI) U01 CA240346 United States National Institutes of Health/National Cancer Institute (NIH/NCI) 1R01CA153821 United States National Institutes of Health/National Cancer Institute (NIH/NCI) P30CA023168 yangdz@purdue.edu 0000-0001-7489-7111 Danzhou Yang principal investigator/group leader Solution structure of the major PDGFRB promoter G-quadruplex with a broken-strand G21 fill-in N RCSB Y RCSB 2025-06-25 REL REL 9606 Homo sapiens sample 1 21 N structures with the lowest energy 20 10 isotropic 1 2D 1H-13C HSQC isotropic 1 2D 1H-1H NOESY isotropic 1 2D 1H-1H NOESY 1.06 mM natural abundance 75 mM natural abundance 25 mM natural abundance 100 mM 10C 7.0 pH 1 atm 283 K 100 mM 25C 7.0 pH 1 atm 298 K simulated annealing simulated annealing molecular dynamics 1 lowest energy 1.06 mM DNA (5'-D(*AP*AP*GP*GP*GP*AP*GP*GP*GP*CP*GP*GP*CP*GP*GP*GP*GP*CP*AP*GP*G)-3'), 75 mM potassium chloride, 25 mM potassium phosphate, 90% H2O/10% D2O 21in_Sample 90% H2O/10% D2O solution CCPN chemical shift assignment CcpNmr Analysis 2.4 CCPN peak picking CcpNmr Analysis 2.4 Bruker Biospin processing TopSpin Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman structure calculation Amber Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman refinement Amber Schwieters, Kuszewski, Tjandra and Clore structure calculation X-PLOR NIH 800 Bruker AVANCE III DA 1 n 1 DA 1 X DA 2 n 2 DA 2 X DG 3 n 3 DG 3 X DG 4 n 4 DG 4 X DG 5 n 5 DG 5 X DA 6 n 6 DA 6 X DG 7 n 7 DG 7 X DG 8 n 8 DG 8 X DG 9 n 9 DG 9 X DC 10 n 10 DC 10 X DG 11 n 11 DG 11 X DG 12 n 12 DG 12 X DC 13 n 13 DC 13 X DG 14 n 14 DG 14 X DG 15 n 15 DG 15 X DG 16 n 16 DG 16 X DG 17 n 17 DG 17 X DC 18 n 18 DC 18 X DA 19 n 19 DA 19 X DG 20 n 20 DG 20 X DG 21 n 21 DG 21 X author_and_software_defined_assembly 1 monomeric not applicable NMR Distance Restraints 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0 1_555 x,y,z identity operation 0.0 0.0 0.0 1 X DG 8 0.062 SIDE CHAIN 2 X DG 8 0.060 SIDE CHAIN 3 X DG 8 0.055 SIDE CHAIN 3 X DG 12 0.064 SIDE CHAIN 4 X DG 8 0.052 SIDE CHAIN 7 X DG 8 0.058 SIDE CHAIN 7 X DG 17 0.065 SIDE CHAIN 8 X DG 8 0.054 SIDE CHAIN 9 X DG 8 0.060 SIDE CHAIN 10 X DG 8 0.062 SIDE CHAIN 1 4.26 0.30 108.30 112.56 X X X O4' C1' N9 DA DA DA 1 1 1 N 1 -3.22 0.50 117.00 113.78 X X X C4 C5 C6 DA DA DA 1 1 1 N 1 3.95 0.50 117.70 121.65 X X X C5 C6 N1 DA DA DA 1 1 1 N 1 -5.64 0.60 118.60 112.96 X X X N1 C6 N6 DA DA DA 1 1 1 N 1 -3.58 0.50 117.00 113.42 X X X C4 C5 C6 DA DA DA 2 2 2 N 1 3.70 0.50 117.70 121.40 X X X C5 C6 N1 DA DA DA 2 2 2 N 1 -5.88 0.60 118.60 112.72 X X X N1 C6 N6 DA DA DA 2 2 2 N 1 2.49 0.30 108.30 110.79 X X X O4' C1' N9 DG DG DG 3 3 3 N 1 3.67 0.30 108.30 111.97 X X X O4' C1' N9 DG DG DG 4 4 4 N 1 2.29 0.30 108.30 110.59 X X X O4' C1' N9 DG DG DG 5 5 5 N 1 -3.32 0.50 117.00 113.68 X X X C4 C5 C6 DA DA DA 6 6 6 N 1 3.77 0.50 117.70 121.47 X X X C5 C6 N1 DA DA DA 6 6 6 N 1 -5.62 0.60 118.60 112.98 X X X N1 C6 N6 DA DA DA 6 6 6 N 1 2.52 0.30 108.30 110.82 X X X O4' C1' N9 DG DG DG 7 7 7 N 1 5.02 0.30 108.30 113.32 X X X O4' C1' N9 DG DG DG 8 8 8 N 1 2.55 0.30 108.30 110.85 X X X O4' C1' N9 DG DG DG 9 9 9 N 1 2.06 0.30 108.30 110.36 X X X O4' C1' N1 DC DC DC 10 10 10 N 1 -4.83 0.70 121.90 117.07 X X X N3 C2 O2 DC DC DC 10 10 10 N 1 2.16 0.30 108.30 110.46 X X X O4' C1' N9 DG DG DG 11 11 11 N 1 2.73 0.30 108.30 111.03 X X X O4' C1' N9 DG DG DG 12 12 12 N 1 2.39 0.30 108.30 110.69 X X X O4' C1' N1 DC DC DC 13 13 13 N 1 -4.70 0.70 121.90 117.20 X X X N3 C2 O2 DC DC DC 13 13 13 N 1 3.10 0.30 108.30 111.40 X X X O4' C1' N9 DG DG DG 14 14 14 N 1 3.64 0.30 108.30 111.94 X X X O4' C1' N9 DG DG DG 15 15 15 N 1 2.02 0.30 108.30 110.32 X X X O4' C1' N9 DG DG DG 16 16 16 N 1 2.88 0.30 108.30 111.18 X X X O4' C1' N9 DG DG DG 17 17 17 N 1 2.04 0.30 108.30 110.34 X X X O4' C1' N1 DC DC DC 18 18 18 N 1 -4.68 0.70 121.90 117.22 X X X N3 C2 O2 DC DC DC 18 18 18 N 1 -3.58 0.50 117.00 113.42 X X X C4 C5 C6 DA DA DA 19 19 19 N 1 4.01 0.50 117.70 121.71 X X X C5 C6 N1 DA DA DA 19 19 19 N 1 -6.26 0.60 118.60 112.34 X X X N1 C6 N6 DA DA DA 19 19 19 N 1 3.42 0.30 108.30 111.72 X X X O4' C1' N9 DG DG DG 20 20 20 N 2 4.44 0.30 108.30 112.74 X X X O4' C1' N9 DA DA DA 1 1 1 N 2 -3.10 0.50 117.00 113.90 X X X C4 C5 C6 DA DA DA 1 1 1 N 2 3.88 0.50 117.70 121.58 X X X C5 C6 N1 DA DA DA 1 1 1 N 2 -5.61 0.60 118.60 112.99 X X X N1 C6 N6 DA DA DA 1 1 1 N 2 -3.58 0.50 117.00 113.42 X X X C4 C5 C6 DA DA DA 2 2 2 N 2 3.73 0.50 117.70 121.43 X X X C5 C6 N1 DA DA DA 2 2 2 N 2 -5.83 0.60 118.60 112.77 X X X N1 C6 N6 DA DA DA 2 2 2 N 2 2.33 0.30 108.30 110.63 X X X O4' C1' N9 DG DG DG 3 3 3 N 2 4.57 0.30 108.30 112.87 X X X O4' C1' N9 DG DG DG 4 4 4 N 2 2.71 0.30 108.30 111.01 X X X O4' C1' N9 DG DG DG 5 5 5 N 2 -3.30 0.50 117.00 113.70 X X X C4 C5 C6 DA DA DA 6 6 6 N 2 3.77 0.50 117.70 121.47 X X X C5 C6 N1 DA DA DA 6 6 6 N 2 -5.60 0.60 118.60 113.00 X X X N1 C6 N6 DA DA DA 6 6 6 N 2 2.48 0.30 108.30 110.78 X X X O4' C1' N9 DG DG DG 7 7 7 N 2 5.03 0.30 108.30 113.33 X X X O4' C1' N9 DG DG DG 8 8 8 N 2 2.64 0.30 108.30 110.94 X X X O4' C1' N9 DG DG DG 9 9 9 N 2 -4.79 0.70 121.90 117.11 X X X N3 C2 O2 DC DC DC 10 10 10 N 2 1.88 0.30 108.30 110.18 X X X O4' C1' N9 DG DG DG 11 11 11 N 2 4.50 0.30 108.30 112.80 X X X O4' C1' N9 DG DG DG 12 12 12 N 2 -4.69 0.70 121.90 117.21 X X X N3 C2 O2 DC DC DC 13 13 13 N 2 3.84 0.30 108.30 112.14 X X X O4' C1' N9 DG DG DG 14 14 14 N 2 4.89 0.30 108.30 113.19 X X X O4' C1' N9 DG DG DG 15 15 15 N 2 2.74 0.30 108.30 111.04 X X X O4' C1' N9 DG DG DG 17 17 17 N 2 2.34 0.30 108.30 110.64 X X X O4' C1' N1 DC DC DC 18 18 18 N 2 -4.59 0.70 121.90 117.31 X X X N3 C2 O2 DC DC DC 18 18 18 N 2 -3.58 0.50 117.00 113.42 X X X C4 C5 C6 DA DA DA 19 19 19 N 2 4.11 0.50 117.70 121.81 X X X C5 C6 N1 DA DA DA 19 19 19 N 2 -6.34 0.60 118.60 112.26 X X X N1 C6 N6 DA DA DA 19 19 19 N 2 2.11 0.30 108.30 110.41 X X X O4' C1' N9 DG DG DG 20 20 20 N 2 7.36 1.20 119.70 127.06 X X X C3' O3' P DG DG DG 20 20 21 Y 3 4.41 0.30 108.30 112.71 X X X O4' C1' N9 DA DA DA 1 1 1 N 3 -3.13 0.50 117.00 113.87 X X X C4 C5 C6 DA DA DA 1 1 1 N 3 3.84 0.50 117.70 121.54 X X X C5 C6 N1 DA DA DA 1 1 1 N 3 -5.56 0.60 118.60 113.04 X X X N1 C6 N6 DA DA DA 1 1 1 N 3 -3.60 0.50 117.00 113.40 X X X C4 C5 C6 DA DA DA 2 2 2 N 3 3.67 0.50 117.70 121.37 X X X C5 C6 N1 DA DA DA 2 2 2 N 3 -5.76 0.60 118.60 112.84 X X X N1 C6 N6 DA DA DA 2 2 2 N 3 2.39 0.30 108.30 110.69 X X X O4' C1' N9 DG DG DG 3 3 3 N 3 3.91 0.30 108.30 112.21 X X X O4' C1' N9 DG DG DG 4 4 4 N 3 2.38 0.30 108.30 110.68 X X X O4' C1' N9 DG DG DG 5 5 5 N 3 -3.33 0.50 117.00 113.67 X X X C4 C5 C6 DA DA DA 6 6 6 N 3 3.81 0.50 117.70 121.51 X X X C5 C6 N1 DA DA DA 6 6 6 N 3 -5.60 0.60 118.60 113.00 X X X N1 C6 N6 DA DA DA 6 6 6 N 3 2.75 0.30 108.30 111.05 X X X O4' C1' N9 DG DG DG 7 7 7 N 3 4.98 0.30 108.30 113.28 X X X O4' C1' N9 DG DG DG 8 8 8 N 3 2.54 0.30 108.30 110.84 X X X O4' C1' N9 DG DG DG 9 9 9 N 3 2.06 0.30 108.30 110.36 X X X O4' C1' N1 DC DC DC 10 10 10 N 3 -4.80 0.70 121.90 117.10 X X X N3 C2 O2 DC DC DC 10 10 10 N 3 2.06 0.30 108.30 110.36 X X X O4' C1' N9 DG DG DG 11 11 11 N 3 4.40 0.30 108.30 112.70 X X X O4' C1' N9 DG DG DG 12 12 12 N 3 -4.78 0.70 121.90 117.12 X X X N3 C2 O2 DC DC DC 13 13 13 N 3 4.07 0.30 108.30 112.37 X X X O4' C1' N9 DG DG DG 14 14 14 N 3 4.31 0.30 108.30 112.61 X X X O4' C1' N9 DG DG DG 15 15 15 N 3 3.05 0.30 108.30 111.35 X X X O4' C1' N9 DG DG DG 17 17 17 N 3 2.30 0.30 108.30 110.60 X X X O4' C1' N1 DC DC DC 18 18 18 N 3 -4.77 0.70 121.90 117.13 X X X N3 C2 O2 DC DC DC 18 18 18 N 3 -3.49 0.50 117.00 113.51 X X X C4 C5 C6 DA DA DA 19 19 19 N 3 4.05 0.50 117.70 121.75 X X X C5 C6 N1 DA DA DA 19 19 19 N 3 -6.25 0.60 118.60 112.35 X X X N1 C6 N6 DA DA DA 19 19 19 N 3 2.44 0.30 108.30 110.74 X X X O4' C1' N9 DG DG DG 20 20 20 N 4 4.40 0.30 108.30 112.70 X X X O4' C1' N9 DA DA DA 1 1 1 N 4 -3.05 0.50 117.00 113.95 X X X C4 C5 C6 DA DA DA 1 1 1 N 4 3.77 0.50 117.70 121.47 X X X C5 C6 N1 DA DA DA 1 1 1 N 4 -5.50 0.60 118.60 113.10 X X X N1 C6 N6 DA DA DA 1 1 1 N 4 2.21 0.30 108.30 110.51 X X X O4' C1' N9 DA DA DA 2 2 2 N 4 -3.52 0.50 117.00 113.48 X X X C4 C5 C6 DA DA DA 2 2 2 N 4 3.65 0.50 117.70 121.35 X X X C5 C6 N1 DA DA DA 2 2 2 N 4 -5.78 0.60 118.60 112.82 X X X N1 C6 N6 DA DA DA 2 2 2 N 4 4.24 0.30 108.30 112.54 X X X O4' C1' N9 DG DG DG 4 4 4 N 4 2.42 0.30 108.30 110.72 X X X O4' C1' N9 DG DG DG 5 5 5 N 4 1.84 0.30 108.30 110.14 X X X O4' C1' N9 DA DA DA 6 6 6 N 4 -3.28 0.50 117.00 113.72 X X X C4 C5 C6 DA DA DA 6 6 6 N 4 3.73 0.50 117.70 121.43 X X X C5 C6 N1 DA DA DA 6 6 6 N 4 -5.60 0.60 118.60 113.00 X X X N1 C6 N6 DA DA DA 6 6 6 N 4 2.67 0.30 108.30 110.97 X X X O4' C1' N9 DG DG DG 7 7 7 N 4 5.00 0.30 108.30 113.30 X X X O4' C1' N9 DG DG DG 8 8 8 N 4 2.72 0.30 108.30 111.02 X X X O4' C1' N9 DG DG DG 9 9 9 N 4 2.06 0.30 108.30 110.36 X X X O4' C1' N1 DC DC DC 10 10 10 N 4 -4.80 0.70 121.90 117.10 X X X N3 C2 O2 DC DC DC 10 10 10 N 4 2.13 0.30 108.30 110.43 X X X O4' C1' N9 DG DG DG 11 11 11 N 4 5.03 0.30 108.30 113.33 X X X O4' C1' N9 DG DG DG 12 12 12 N 4 -4.79 0.70 121.90 117.11 X X X N3 C2 O2 DC DC DC 13 13 13 N 4 3.52 0.30 108.30 111.82 X X X O4' C1' N9 DG DG DG 14 14 14 N 4 4.56 0.30 108.30 112.86 X X X O4' C1' N9 DG DG DG 15 15 15 N 4 3.09 0.30 108.30 111.39 X X X O4' C1' N9 DG DG DG 17 17 17 N 4 2.20 0.30 108.30 110.50 X X X O4' C1' N1 DC DC DC 18 18 18 N 4 -4.50 0.70 121.90 117.40 X X X N3 C2 O2 DC DC DC 18 18 18 N 4 -3.47 0.50 117.00 113.53 X X X C4 C5 C6 DA DA DA 19 19 19 N 4 4.08 0.50 117.70 121.78 X X X C5 C6 N1 DA DA DA 19 19 19 N 4 -6.32 0.60 118.60 112.28 X X X N1 C6 N6 DA DA DA 19 19 19 N 4 2.16 0.30 108.30 110.46 X X X O4' C1' N9 DG DG DG 20 20 20 N 5 4.52 0.30 108.30 112.82 X X X O4' C1' N9 DA DA DA 1 1 1 N 5 -3.14 0.50 117.00 113.86 X X X C4 C5 C6 DA DA DA 1 1 1 N 5 3.87 0.50 117.70 121.57 X X X C5 C6 N1 DA DA DA 1 1 1 N 5 -5.60 0.60 118.60 113.00 X X X N1 C6 N6 DA DA DA 1 1 1 N 5 -3.56 0.50 117.00 113.44 X X X C4 C5 C6 DA DA DA 2 2 2 N 5 3.78 0.50 117.70 121.48 X X X C5 C6 N1 DA DA DA 2 2 2 N 5 -5.91 0.60 118.60 112.69 X X X N1 C6 N6 DA DA DA 2 2 2 N 5 2.41 0.30 108.30 110.71 X X X O4' C1' N9 DG DG DG 3 3 3 N 5 2.46 0.30 108.30 110.76 X X X O4' C1' N9 DG DG DG 4 4 4 N 5 -3.27 0.50 117.00 113.73 X X X C4 C5 C6 DA DA DA 6 6 6 N 5 3.73 0.50 117.70 121.43 X X X C5 C6 N1 DA DA DA 6 6 6 N 5 -5.72 0.60 118.60 112.88 X X X N1 C6 N6 DA DA DA 6 6 6 N 5 3.38 0.30 108.30 111.68 X X X O4' C1' N9 DG DG DG 7 7 7 N 5 4.28 0.30 108.30 112.58 X X X O4' C1' N9 DG DG DG 8 8 8 N 5 2.41 0.30 108.30 110.71 X X X O4' C1' N9 DG DG DG 9 9 9 N 5 2.23 0.30 108.30 110.53 X X X O4' C1' N1 DC DC DC 10 10 10 N 5 -4.83 0.70 121.90 117.07 X X X N3 C2 O2 DC DC DC 10 10 10 N 5 2.73 0.30 108.30 111.03 X X X O4' C1' N9 DG DG DG 11 11 11 N 5 3.54 0.30 108.30 111.84 X X X O4' C1' N9 DG DG DG 12 12 12 N 5 -4.58 0.70 121.90 117.32 X X X N3 C2 O2 DC DC DC 13 13 13 N 5 3.03 0.30 108.30 111.33 X X X O4' C1' N9 DG DG DG 14 14 14 N 5 3.26 0.30 108.30 111.56 X X X O4' C1' N9 DG DG DG 15 15 15 N 5 2.14 0.30 108.30 110.44 X X X O4' C1' N9 DG DG DG 16 16 16 N 5 3.10 0.30 108.30 111.40 X X X O4' C1' N9 DG DG DG 17 17 17 N 5 2.21 0.30 108.30 110.51 X X X O4' C1' N1 DC DC DC 18 18 18 N 5 -4.69 0.70 121.90 117.21 X X X N3 C2 O2 DC DC DC 18 18 18 N 5 -3.54 0.50 117.00 113.46 X X X C4 C5 C6 DA DA DA 19 19 19 N 5 4.11 0.50 117.70 121.81 X X X C5 C6 N1 DA DA DA 19 19 19 N 5 -6.37 0.60 118.60 112.23 X X X N1 C6 N6 DA DA DA 19 19 19 N 5 3.44 0.30 108.30 111.74 X X X O4' C1' N9 DG DG DG 20 20 20 N 6 4.23 0.30 108.30 112.53 X X X O4' C1' N9 DA DA DA 1 1 1 N 6 -3.10 0.50 117.00 113.90 X X X C4 C5 C6 DA DA DA 1 1 1 N 6 3.86 0.50 117.70 121.56 X X X C5 C6 N1 DA DA DA 1 1 1 N 6 -5.60 0.60 118.60 113.00 X X X N1 C6 N6 DA DA DA 1 1 1 N 6 -3.63 0.50 117.00 113.37 X X X C4 C5 C6 DA DA DA 2 2 2 N 6 3.80 0.50 117.70 121.50 X X X C5 C6 N1 DA DA DA 2 2 2 N 6 -5.83 0.60 118.60 112.77 X X X N1 C6 N6 DA DA DA 2 2 2 N 6 2.44 0.30 108.30 110.74 X X X O4' C1' N9 DG DG DG 3 3 3 N 6 2.96 0.30 108.30 111.26 X X X O4' C1' N9 DG DG DG 4 4 4 N 6 -3.33 0.50 117.00 113.67 X X X C4 C5 C6 DA DA DA 6 6 6 N 6 3.68 0.50 117.70 121.38 X X X C5 C6 N1 DA DA DA 6 6 6 N 6 -5.57 0.60 118.60 113.03 X X X N1 C6 N6 DA DA DA 6 6 6 N 6 3.49 0.30 108.30 111.79 X X X O4' C1' N9 DG DG DG 7 7 7 N 6 5.01 0.30 108.30 113.31 X X X O4' C1' N9 DG DG DG 8 8 8 N 6 2.78 0.30 108.30 111.08 X X X O4' C1' N9 DG DG DG 9 9 9 N 6 2.37 0.30 108.30 110.67 X X X O4' C1' N1 DC DC DC 10 10 10 N 6 -4.74 0.70 121.90 117.16 X X X N3 C2 O2 DC DC DC 10 10 10 N 6 2.10 0.30 108.30 110.40 X X X O4' C1' N9 DG DG DG 11 11 11 N 6 3.40 0.30 108.30 111.70 X X X O4' C1' N9 DG DG DG 12 12 12 N 6 -4.56 0.70 121.90 117.34 X X X N3 C2 O2 DC DC DC 13 13 13 N 6 3.31 0.30 108.30 111.61 X X X O4' C1' N9 DG DG DG 14 14 14 N 6 4.56 0.30 108.30 112.86 X X X O4' C1' N9 DG DG DG 15 15 15 N 6 2.83 0.30 108.30 111.13 X X X O4' C1' N9 DG DG DG 17 17 17 N 6 2.32 0.30 108.30 110.62 X X X O4' C1' N1 DC DC DC 18 18 18 N 6 -4.61 0.70 121.90 117.29 X X X N3 C2 O2 DC DC DC 18 18 18 N 6 -3.50 0.50 117.00 113.50 X X X C4 C5 C6 DA DA DA 19 19 19 N 6 4.02 0.50 117.70 121.72 X X X C5 C6 N1 DA DA DA 19 19 19 N 6 -6.24 0.60 118.60 112.36 X X X N1 C6 N6 DA DA DA 19 19 19 N 6 2.51 0.30 108.30 110.81 X X X O4' C1' N9 DG DG DG 20 20 20 N 7 4.22 0.30 108.30 112.52 X X X O4' C1' N9 DA DA DA 1 1 1 N 7 -3.12 0.50 117.00 113.88 X X X C4 C5 C6 DA DA DA 1 1 1 N 7 3.79 0.50 117.70 121.49 X X X C5 C6 N1 DA DA DA 1 1 1 N 7 -5.50 0.60 118.60 113.10 X X X N1 C6 N6 DA DA DA 1 1 1 N 7 1.96 0.30 108.30 110.26 X X X O4' C1' N9 DA DA DA 2 2 2 N 7 -3.59 0.50 117.00 113.41 X X X C4 C5 C6 DA DA DA 2 2 2 N 7 3.75 0.50 117.70 121.45 X X X C5 C6 N1 DA DA DA 2 2 2 N 7 -5.86 0.60 118.60 112.74 X X X N1 C6 N6 DA DA DA 2 2 2 N 7 2.50 0.30 108.30 110.80 X X X O4' C1' N9 DG DG DG 3 3 3 N 7 3.09 0.30 108.30 111.39 X X X O4' C1' N9 DG DG DG 4 4 4 N 7 1.82 0.30 108.30 110.12 X X X O4' C1' N9 DG DG DG 5 5 5 N 7 -3.27 0.50 117.00 113.73 X X X C4 C5 C6 DA DA DA 6 6 6 N 7 3.74 0.50 117.70 121.44 X X X C5 C6 N1 DA DA DA 6 6 6 N 7 -5.62 0.60 118.60 112.98 X X X N1 C6 N6 DA DA DA 6 6 6 N 7 2.58 0.30 108.30 110.88 X X X O4' C1' N9 DG DG DG 7 7 7 N 7 4.84 0.30 108.30 113.14 X X X O4' C1' N9 DG DG DG 8 8 8 N 7 2.62 0.30 108.30 110.92 X X X O4' C1' N9 DG DG DG 9 9 9 N 7 1.99 0.30 108.30 110.29 X X X O4' C1' N1 DC DC DC 10 10 10 N 7 -4.85 0.70 121.90 117.05 X X X N3 C2 O2 DC DC DC 10 10 10 N 7 2.19 0.30 108.30 110.49 X X X O4' C1' N9 DG DG DG 11 11 11 N 7 5.15 0.30 108.30 113.45 X X X O4' C1' N9 DG DG DG 12 12 12 N 7 -4.70 0.70 121.90 117.20 X X X N3 C2 O2 DC DC DC 13 13 13 N 7 4.02 0.30 108.30 112.32 X X X O4' C1' N9 DG DG DG 14 14 14 N 7 4.22 0.30 108.30 112.52 X X X O4' C1' N9 DG DG DG 15 15 15 N 7 1.91 0.30 108.30 110.21 X X X O4' C1' N9 DG DG DG 16 16 16 N 7 3.06 0.30 108.30 111.36 X X X O4' C1' N9 DG DG DG 17 17 17 N 7 7.54 1.20 119.70 127.24 X X X C3' O3' P DG DG DC 17 17 18 Y 7 -4.69 0.70 121.90 117.21 X X X N3 C2 O2 DC DC DC 18 18 18 N 7 -3.58 0.50 117.00 113.42 X X X C4 C5 C6 DA DA DA 19 19 19 N 7 3.95 0.50 117.70 121.65 X X X C5 C6 N1 DA DA DA 19 19 19 N 7 -6.42 0.60 118.60 112.18 X X X N1 C6 N6 DA DA DA 19 19 19 N 7 2.66 0.30 108.30 110.96 X X X O4' C1' N9 DG DG DG 20 20 20 N 8 4.32 0.30 108.30 112.62 X X X O4' C1' N9 DA DA DA 1 1 1 N 8 -3.20 0.50 117.00 113.80 X X X C4 C5 C6 DA DA DA 1 1 1 N 8 3.87 0.50 117.70 121.57 X X X C5 C6 N1 DA DA DA 1 1 1 N 8 -5.44 0.60 118.60 113.16 X X X N1 C6 N6 DA DA DA 1 1 1 N 8 -3.56 0.50 117.00 113.44 X X X C4 C5 C6 DA DA DA 2 2 2 N 8 3.66 0.50 117.70 121.36 X X X C5 C6 N1 DA DA DA 2 2 2 N 8 -5.84 0.60 118.60 112.76 X X X N1 C6 N6 DA DA DA 2 2 2 N 8 2.38 0.30 108.30 110.68 X X X O4' C1' N9 DG DG DG 3 3 3 N 8 3.37 0.30 108.30 111.67 X X X O4' C1' N9 DG DG DG 4 4 4 N 8 -3.15 0.50 117.00 113.85 X X X C4 C5 C6 DA DA DA 6 6 6 N 8 3.66 0.50 117.70 121.36 X X X C5 C6 N1 DA DA DA 6 6 6 N 8 -5.55 0.60 118.60 113.05 X X X N1 C6 N6 DA DA DA 6 6 6 N 8 2.51 0.30 108.30 110.81 X X X O4' C1' N9 DG DG DG 7 7 7 N 8 5.11 0.30 108.30 113.41 X X X O4' C1' N9 DG DG DG 8 8 8 N 8 2.63 0.30 108.30 110.93 X X X O4' C1' N9 DG DG DG 9 9 9 N 8 -4.76 0.70 121.90 117.14 X X X N3 C2 O2 DC DC DC 10 10 10 N 8 2.04 0.30 108.30 110.34 X X X O4' C1' N9 DG DG DG 11 11 11 N 8 2.69 0.30 108.30 110.99 X X X O4' C1' N9 DG DG DG 12 12 12 N 8 1.92 0.30 108.30 110.22 X X X O4' C1' N1 DC DC DC 13 13 13 N 8 -4.61 0.70 121.90 117.29 X X X N3 C2 O2 DC DC DC 13 13 13 N 8 3.22 0.30 108.30 111.52 X X X O4' C1' N9 DG DG DG 14 14 14 N 8 4.94 0.30 108.30 113.24 X X X O4' C1' N9 DG DG DG 15 15 15 N 8 2.47 0.30 108.30 110.77 X X X O4' C1' N9 DG DG DG 17 17 17 N 8 2.21 0.30 108.30 110.51 X X X O4' C1' N1 DC DC DC 18 18 18 N 8 -4.69 0.70 121.90 117.21 X X X N3 C2 O2 DC DC DC 18 18 18 N 8 -3.52 0.50 117.00 113.48 X X X C4 C5 C6 DA DA DA 19 19 19 N 8 4.00 0.50 117.70 121.70 X X X C5 C6 N1 DA DA DA 19 19 19 N 8 -6.33 0.60 118.60 112.27 X X X N1 C6 N6 DA DA DA 19 19 19 N 8 2.17 0.30 108.30 110.47 X X X O4' C1' N9 DG DG DG 20 20 20 N 9 4.63 0.30 108.30 112.93 X X X O4' C1' N9 DA DA DA 1 1 1 N 9 -3.12 0.50 117.00 113.88 X X X C4 C5 C6 DA DA DA 1 1 1 N 9 3.86 0.50 117.70 121.56 X X X C5 C6 N1 DA DA DA 1 1 1 N 9 -5.66 0.60 118.60 112.94 X X X N1 C6 N6 DA DA DA 1 1 1 N 9 -3.61 0.50 117.00 113.39 X X X C4 C5 C6 DA DA DA 2 2 2 N 9 3.71 0.50 117.70 121.41 X X X C5 C6 N1 DA DA DA 2 2 2 N 9 -5.80 0.60 118.60 112.80 X X X N1 C6 N6 DA DA DA 2 2 2 N 9 2.35 0.30 108.30 110.65 X X X O4' C1' N9 DG DG DG 3 3 3 N 9 3.58 0.30 108.30 111.88 X X X O4' C1' N9 DG DG DG 4 4 4 N 9 2.16 0.30 108.30 110.46 X X X O4' C1' N9 DG DG DG 5 5 5 N 9 -3.24 0.50 117.00 113.76 X X X C4 C5 C6 DA DA DA 6 6 6 N 9 3.71 0.50 117.70 121.41 X X X C5 C6 N1 DA DA DA 6 6 6 N 9 -5.51 0.60 118.60 113.09 X X X N1 C6 N6 DA DA DA 6 6 6 N 9 2.84 0.30 108.30 111.14 X X X O4' C1' N9 DG DG DG 7 7 7 N 9 4.81 0.30 108.30 113.11 X X X O4' C1' N9 DG DG DG 8 8 8 N 9 2.46 0.30 108.30 110.76 X X X O4' C1' N9 DG DG DG 9 9 9 N 9 2.26 0.30 108.30 110.56 X X X O4' C1' N1 DC DC DC 10 10 10 N 9 -4.79 0.70 121.90 117.11 X X X N3 C2 O2 DC DC DC 10 10 10 N 9 2.36 0.30 108.30 110.66 X X X O4' C1' N9 DG DG DG 11 11 11 N 9 3.79 0.30 108.30 112.09 X X X O4' C1' N9 DG DG DG 12 12 12 N 9 2.06 0.30 108.30 110.36 X X X O4' C1' N1 DC DC DC 13 13 13 N 9 -4.63 0.70 121.90 117.27 X X X N3 C2 O2 DC DC DC 13 13 13 N 9 3.53 0.30 108.30 111.83 X X X O4' C1' N9 DG DG DG 14 14 14 N 9 4.04 0.30 108.30 112.34 X X X O4' C1' N9 DG DG DG 15 15 15 N 9 1.95 0.30 108.30 110.25 X X X O4' C1' N9 DG DG DG 16 16 16 N 9 2.76 0.30 108.30 111.06 X X X O4' C1' N9 DG DG DG 17 17 17 N 9 2.29 0.30 108.30 110.59 X X X O4' C1' N1 DC DC DC 18 18 18 N 9 -4.64 0.70 121.90 117.26 X X X N3 C2 O2 DC DC DC 18 18 18 N 9 -3.59 0.50 117.00 113.41 X X X C4 C5 C6 DA DA DA 19 19 19 N 9 4.10 0.50 117.70 121.80 X X X C5 C6 N1 DA DA DA 19 19 19 N 9 -6.23 0.60 118.60 112.37 X X X N1 C6 N6 DA DA DA 19 19 19 N 9 2.22 0.30 108.30 110.52 X X X O4' C1' N9 DG DG DG 20 20 20 N 10 4.37 0.30 108.30 112.67 X X X O4' C1' N9 DA DA DA 1 1 1 N 10 -3.05 0.50 117.00 113.95 X X X C4 C5 C6 DA DA DA 1 1 1 N 10 3.82 0.50 117.70 121.52 X X X C5 C6 N1 DA DA DA 1 1 1 N 10 -5.60 0.60 118.60 113.00 X X X N1 C6 N6 DA DA DA 1 1 1 N 10 2.13 0.30 108.30 110.43 X X X O4' C1' N9 DA DA DA 2 2 2 N 10 -3.52 0.50 117.00 113.48 X X X C4 C5 C6 DA DA DA 2 2 2 N 10 3.79 0.50 117.70 121.49 X X X C5 C6 N1 DA DA DA 2 2 2 N 10 -5.69 0.60 118.60 112.91 X X X N1 C6 N6 DA DA DA 2 2 2 N 10 2.16 0.30 108.30 110.46 X X X O4' C1' N9 DG DG DG 3 3 3 N 10 3.66 0.30 108.30 111.96 X X X O4' C1' N9 DG DG DG 4 4 4 N 10 2.21 0.30 108.30 110.51 X X X O4' C1' N9 DG DG DG 5 5 5 N 10 -3.28 0.50 117.00 113.72 X X X C4 C5 C6 DA DA DA 6 6 6 N 10 3.77 0.50 117.70 121.47 X X X C5 C6 N1 DA DA DA 6 6 6 N 10 -5.57 0.60 118.60 113.03 X X X N1 C6 N6 DA DA DA 6 6 6 N 10 2.52 0.30 108.30 110.82 X X X O4' C1' N9 DG DG DG 7 7 7 N 10 5.26 0.30 108.30 113.56 X X X O4' C1' N9 DG DG DG 8 8 8 N 10 2.60 0.30 108.30 110.90 X X X O4' C1' N9 DG DG DG 9 9 9 N 10 2.14 0.30 108.30 110.44 X X X O4' C1' N1 DC DC DC 10 10 10 N 10 -4.69 0.70 121.90 117.21 X X X N3 C2 O2 DC DC DC 10 10 10 N 10 1.99 0.30 108.30 110.29 X X X O4' C1' N9 DG DG DG 11 11 11 N 10 3.19 0.30 108.30 111.49 X X X O4' C1' N9 DG DG DG 12 12 12 N 10 2.25 0.30 108.30 110.55 X X X O4' C1' N1 DC DC DC 13 13 13 N 10 -4.67 0.70 121.90 117.23 X X X N3 C2 O2 DC DC DC 13 13 13 N 10 3.36 0.30 108.30 111.66 X X X O4' C1' N9 DG DG DG 14 14 14 N 10 4.24 0.30 108.30 112.54 X X X O4' C1' N9 DG DG DG 15 15 15 N 10 1.81 0.30 108.30 110.11 X X X O4' C1' N9 DG DG DG 16 16 16 N 10 2.83 0.30 108.30 111.13 X X X O4' C1' N9 DG DG DG 17 17 17 N 10 2.15 0.30 108.30 110.45 X X X O4' C1' N1 DC DC DC 18 18 18 N 10 -4.66 0.70 121.90 117.24 X X X N3 C2 O2 DC DC DC 18 18 18 N 10 -3.46 0.50 117.00 113.54 X X X C4 C5 C6 DA DA DA 19 19 19 N 10 3.98 0.50 117.70 121.68 X X X C5 C6 N1 DA DA DA 19 19 19 N 10 -6.29 0.60 118.60 112.31 X X X N1 C6 N6 DA DA DA 19 19 19 N 10 2.50 0.30 108.30 110.80 X X X O4' C1' N9 DG DG DG 20 20 20 N N Solution structure of the major PDGFRB promoter G-quadruplex with a broken-strand G21 fill-in 1 N N hydrog TYPE_6_PAIR X DG 3 A N1 DG 3 1_555 X DG 7 A O6 DG 7 1_555 hydrog TYPE_6_PAIR X DG 3 A N2 DG 3 1_555 X DG 7 A N7 DG 7 1_555 hydrog TYPE_6_PAIR X DG 3 A N7 DG 3 1_555 X DG 14 A N2 DG 14 1_555 hydrog TYPE_6_PAIR X DG 3 A O6 DG 3 1_555 X DG 14 A N1 DG 14 1_555 hydrog TYPE_6_PAIR X DG 4 A N1 DG 4 1_555 X DG 8 A O6 DG 8 1_555 hydrog TYPE_6_PAIR X DG 4 A N2 DG 4 1_555 X DG 8 A N7 DG 8 1_555 hydrog TYPE_6_PAIR X DG 4 A N7 DG 4 1_555 X DG 15 A N2 DG 15 1_555 hydrog TYPE_6_PAIR X DG 4 A O6 DG 4 1_555 X DG 15 A N1 DG 15 1_555 hydrog TYPE_6_PAIR X DG 5 A N1 DG 5 1_555 X DG 9 A O6 DG 9 1_555 hydrog TYPE_6_PAIR X DG 5 A N2 DG 5 1_555 X DG 9 A N7 DG 9 1_555 hydrog TYPE_6_PAIR X DG 5 A N7 DG 5 1_555 X DG 16 A N2 DG 16 1_555 hydrog TYPE_6_PAIR X DG 5 A O6 DG 5 1_555 X DG 16 A N1 DG 16 1_555 hydrog TYPE_6_PAIR X DG 7 A N1 DG 7 1_555 X DG 11 A O6 DG 11 1_555 hydrog TYPE_6_PAIR X DG 7 A N2 DG 7 1_555 X DG 11 A N7 DG 11 1_555 hydrog TYPE_6_PAIR X DG 8 A N1 DG 8 1_555 X DG 12 A O6 DG 12 1_555 hydrog TYPE_6_PAIR X DG 8 A N2 DG 8 1_555 X DG 12 A N7 DG 12 1_555 hydrog TYPE_6_PAIR X DG 9 A N1 DG 9 1_555 X DG 21 A O6 DG 21 1_555 hydrog TYPE_6_PAIR X DG 9 A N2 DG 9 1_555 X DG 21 A N7 DG 21 1_555 hydrog TYPE_6_PAIR X DG 11 A N1 DG 11 1_555 X DG 14 A O6 DG 14 1_555 hydrog TYPE_6_PAIR X DG 11 A N2 DG 11 1_555 X DG 14 A N7 DG 14 1_555 hydrog TYPE_6_PAIR X DG 12 A N1 DG 12 1_555 X DG 15 A O6 DG 15 1_555 hydrog TYPE_6_PAIR X DG 12 A N2 DG 12 1_555 X DG 15 A N7 DG 15 1_555 hydrog TYPE_6_PAIR X DG 16 A N7 DG 16 1_555 X DG 21 A N2 DG 21 1_555 hydrog TYPE_6_PAIR X DG 16 A O6 DG 16 1_555 X DG 21 A N1 DG 21 1_555 hydrog TYPE_7_PAIR X DG 17 A N1 DG 17 1_555 X DG 20 A N7 DG 20 1_555 hydrog TYPE_7_PAIR X DG 17 A N2 DG 17 1_555 X DG 20 A O6 DG 20 1_555 DNA G-quadruplex DNA, PDGFRB, DNA 9P9Y PDB 1 1 9P9Y 1 21 9P9Y 1 21 9P9Y X 1 1 21