0.024612 0.014210 0.000000 0.000000 0.028420 0.000000 0.000000 0.000000 0.018093 0.00000 0.00000 0.00000 Paukstelis, P.J. Nowakowski, J. Birktoft, J.J. Seeman, N.C. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.00 90.00 120.00 40.630 40.630 55.270 C9 H12 Br N2 O8 P 387.078 n 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE DNA linking C9 H13 Br N3 O7 P 386.093 n 5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O7 P 347.221 y 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking H2 O 18.015 WATER non-polymer Mg 2 24.305 MAGNESIUM ION non-polymer N 1 N N N 2 N C N 3 N N N 4 N C N 5 N C N 6 N C N 7 N O N 8 N O N 9 N BR N 10 R C N 11 N C N 12 S C N 13 R C N 14 N O N 15 N O N 16 N C N 17 N O N 18 N P N 19 N O N 20 N O N 21 N O N 22 N H 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 BR N 35 N P N 36 N O N 37 N O N 38 N O N 39 N N N 40 N C N 41 N C N 42 N O N 43 N N N 44 N C N 45 N N N 46 N C N 47 N C N 48 N C N 49 R C N 50 N O N 51 R C N 52 S C N 53 N O N 54 N O N 55 N H N 56 N H 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 O N 69 N P N 70 N O N 71 N O N 72 N O N 73 N C N 74 R C N 75 N O N 76 S C N 77 N O N 78 N C N 79 R C Y 80 N N Y 81 N C Y 82 N N Y 83 N C Y 84 N C N 85 N N Y 86 N N Y 87 N C Y 88 N N Y 89 N C N 90 N H N 91 N H N 92 N H N 93 N H 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 O N 105 N P N 106 N O N 107 N O N 108 N O N 109 N C N 110 R C N 111 N O N 112 S C N 113 N O N 114 N C N 115 R C Y 116 N N Y 117 N C Y 118 N N Y 119 N C N 120 N C N 121 N O N 122 N N N 123 N C N 124 N N N 125 N N Y 126 N C N 127 N H N 128 N H N 129 N H N 130 N H N 131 N H N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N O N 142 N H N 143 N H N 144 N MG N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N doub N 6 N sing N 7 N sing N 8 N sing N 9 N doub N 10 N doub 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 N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N doub N 31 N sing N 32 N sing N 33 N sing N 34 N sing N 35 N sing N 36 N doub N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N doub N 46 N sing N 47 N doub N 48 N sing N 49 N doub 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 sing N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N doub N 73 N sing N 74 N sing N 75 N sing N 76 N sing 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 Y 93 N sing Y 94 N sing Y 95 N doub N 96 N sing Y 97 N sing Y 98 N sing Y 99 N doub N 100 N sing Y 101 N doub N 102 N sing N 103 N sing Y 104 N sing Y 105 N doub N 106 N sing Y 107 N sing N 108 N sing N 109 N sing N 110 N doub N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing Y 131 N sing Y 132 N sing Y 133 N doub N 134 N sing Y 135 N sing N 136 N sing Y 137 N doub N 138 N doub N 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N doub N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N sing UK Chem.Biol. CBOLE2 2050 1074-5521 11 1119 1126 10.1016/j.chembiol.2004.05.021 15324813 Crystal structure of a continuous three-dimensional DNA lattice. 2004 10.2210/pdb1p1y/pdb pdb_00001p1y 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 CCD 2002-08-04 ADSC QUANTUM 4 SINGLE WAVELENGTH M x-ray 1 0.92002 1.0 X8C NSLS 0.92002 SYNCHROTRON NSLS BEAMLINE X8C 4249.451 5'-D(*GP*GP*AP*(CBR)P*AP*GP*AP*(BRU)P*GP*GP*GP*AP*G)-3' 1 syn polymer 24.305 MAGNESIUM ION 1 syn non-polymer 18.015 water 23 nat water no yes (DG)(DG)(DA)(CBR)(DA)(DG)(DA)(BRU)(DG)(DG)(DG)(DA)(DG) GGACAGAUGGGAG X polydeoxyribonucleotide n n n n n n n n n n n n n 1 2.97 58.52 VAPOR DIFFUSION, SITTING DROP magnesium formate, mpd, lithium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K 295.5 magnesium formate 1 mpd 1 LiCl 1 mpd 2 LiCl 2 -2.683 4 7 X 1 X 10 -112.497 X_DG1:DG10_X 1 -6.650 -5.716 -0.213 -0.518 -0.455 12 4 X 2 X 11 174.581 X_DG2:DG11_X 2 24.789 3.179 -0.574 8.009 -7.038 7 2 X 3 X 12 -179.699 X_DA3:DA12_X 3 29.923 -5.402 0.167 5.487 -3.306 172.650 X X 1 2 68.114 X X 10 11 1.701 131.801 4.877 -0.870 XX_DG1DG2:DG11DG10_XX 1 -111.194 57.465 26.996 0.048 -2.035 4.480 173.704 X X 2 3 0.875 X X 11 12 4.480 1.746 0.032 0.071 XX_DG2DA3:DA12DG11_XX 2 -0.242 0.121 173.703 0.034 -0.016 chem_comp_atom chem_comp_bond database_2 pdbx_struct_conn_angle struct_conn struct_conn_type struct_site repository Initial release Version format compliance Version format compliance Non-polymer description Data collection Database references Derived calculations 1 0 2004-06-01 1 1 2008-04-29 1 2 2011-07-13 1 3 2011-11-02 1 4 2024-02-14 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.value _struct_conn.conn_type_id _struct_conn.id _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn_type.id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2003-04-14 REL REL MG MAGNESIUM ION HOH water MO4 51 2 MG MG 51 X HOH 1 3 HOH HOH 52 X HOH 2 3 HOH HOH 53 X HOH 3 3 HOH HOH 54 X HOH 4 3 HOH HOH 55 X HOH 5 3 HOH HOH 56 X HOH 6 3 HOH HOH 57 X HOH 7 3 HOH HOH 58 X HOH 8 3 HOH HOH 59 X HOH 9 3 HOH HOH 60 X HOH 11 3 HOH HOH 61 X HOH 13 3 HOH HOH 62 X HOH 14 3 HOH HOH 63 X HOH 15 3 HOH HOH 64 X HOH 20 3 HOH HOH 65 X HOH 22 3 HOH HOH 66 X HOH 23 3 HOH HOH 67 X HOH 25 3 HOH HOH 68 X HOH 26 3 HOH HOH 69 X HOH 27 3 HOH HOH 70 X MO4 51 3 HOH HOH 71 X MO4 51 3 HOH HOH 72 X MO4 51 3 HOH HOH 73 X MO4 51 3 HOH HOH 74 X G 1 n 1 DG 1 X G 2 n 2 DG 2 X A 3 n 3 DA 3 X CBR 4 n 4 CBR 4 X A 5 n 5 DA 5 X G 6 n 6 DG 6 X A 7 n 7 DA 7 X BRU 8 n 8 BRU 8 X G 9 n 9 DG 9 X G 10 n 10 DG 10 X G 11 n 11 DG 11 X A 12 n 12 DA 12 X G 13 n 13 DG 13 X author_defined_assembly 2 dimeric X HOH 71 C O HOH 1_555 X MG 51 B MG MG 1_555 X HOH 72 C O HOH 1_555 178.7 X HOH 71 C O HOH 1_555 X MG 51 B MG MG 1_555 X HOH 73 C O HOH 1_555 93.5 X HOH 72 C O HOH 1_555 X MG 51 B MG MG 1_555 X HOH 73 C O HOH 1_555 87.0 X HOH 71 C O HOH 1_555 X MG 51 B MG MG 1_555 X HOH 74 C O HOH 1_555 83.8 X HOH 72 C O HOH 1_555 X MG 51 B MG MG 1_555 X HOH 74 C O HOH 1_555 95.0 X HOH 73 C O HOH 1_555 X MG 51 B MG MG 1_555 X HOH 74 C O HOH 1_555 93.7 X CBR 4 A CBR 4 DC X BRU 8 A BRU 8 DU 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 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 4_435 -x-1,-y-2,z crystal symmetry operation 0.0000000000 -70.3732243115 0.0000000000 1 X C5' DG 13 A C5' DG 13 1 Y 1 X C4' DG 13 A C4' DG 13 1 Y 1 X O4' DG 13 A O4' DG 13 1 Y 1 X C3' DG 13 A C3' DG 13 1 Y 1 X O3' DG 13 A O3' DG 13 1 Y 1 X C2' DG 13 A C2' DG 13 1 Y 1 X C1' DG 13 A C1' DG 13 1 Y 1 X N9 DG 13 A N9 DG 13 1 Y 1 X C8 DG 13 A C8 DG 13 1 Y 1 X N7 DG 13 A N7 DG 13 1 Y 1 X C5 DG 13 A C5 DG 13 1 Y 1 X C6 DG 13 A C6 DG 13 1 Y 1 X O6 DG 13 A O6 DG 13 1 Y 1 X N1 DG 13 A N1 DG 13 1 Y 1 X C2 DG 13 A C2 DG 13 1 Y 1 X N2 DG 13 A N2 DG 13 1 Y 1 X N3 DG 13 A N3 DG 13 1 Y 1 X C4 DG 13 A C4 DG 13 1 Y 1 1.89 0.30 108.30 110.19 X X X O4' C1' N9 DG DG DG 1 1 1 N 1 -6.15 0.80 105.90 99.75 X X X O4' C1' C2' DG DG DG 2 2 2 N 1 -7.70 0.40 104.50 96.80 X X X O4' C4' C3' DA DA DA 3 3 3 N 1 8.69 0.70 110.30 118.99 X X X C1' O4' C4' DA DA DA 3 3 3 N 1 -7.51 0.80 105.90 98.39 X X X O4' C1' C2' DA DA DA 3 3 3 N 1 -8.35 0.70 108.00 99.65 X X X O4' C1' N9 DA DA DA 3 3 3 N 1 -4.12 0.50 129.30 125.18 X X X N1 C2 N3 DA DA DA 3 3 3 N 1 6.07 0.50 110.60 116.67 X X X C2 N3 C4 DA DA DA 3 3 3 N 1 -3.12 0.50 110.70 107.58 X X X C4 C5 N7 DA DA DA 5 5 5 N 1 -4.41 0.60 118.60 114.19 X X X N1 C6 N6 DA DA DA 5 5 5 N 1 -5.79 0.80 102.40 96.61 X X X C3' C2' C1' DG DG DG 6 6 6 N 1 5.93 0.30 108.30 114.23 X X X O4' C1' N9 DG DG DG 6 6 6 N 1 -3.87 0.60 123.90 120.03 X X X N1 C2 N3 DG DG DG 6 6 6 N 1 2.92 0.30 108.30 111.22 X X X O4' C1' N9 DA DA DA 7 7 7 N 1 -8.92 0.80 102.40 93.48 X X X C3' C2' C1' DG DG DG 9 9 9 N 1 2.49 0.30 108.30 110.79 X X X O4' C1' N9 DG DG DG 9 9 9 N 1 -3.84 0.60 128.60 124.76 X X X C5 C6 O6 DG DG DG 9 9 9 N 1 -2.80 0.40 104.50 101.70 X X X O4' C4' C3' DG DG DG 11 11 11 N 1 4.44 0.70 110.30 114.74 X X X C1' O4' C4' DG DG DG 11 11 11 N 1 -6.42 0.60 119.90 113.48 X X X N1 C6 O6 DG DG DG 11 11 11 N 1 3.61 0.60 128.60 132.21 X X X C5 C6 O6 DG DG DG 11 11 11 N 1 8.02 1.20 110.70 118.72 X X X O5' P OP1 DA DA DA 12 12 12 N 1 -3.41 0.50 110.70 107.29 X X X C4 C5 N7 DA DA DA 12 12 12 N 1 4.54 0.50 103.90 108.44 X X X C5 N7 C8 DA DA DA 12 12 12 N 1 -4.03 0.60 118.60 114.57 X X X N1 C6 N6 DA DA DA 12 12 12 N 1 10.52 1.50 119.60 130.12 X X X OP1 P OP2 DG DG DG 13 13 13 N 1 X X N3 C4 DA DA 3 3 -0.048 0.006 1.344 1.296 N 1 X X O3' C3' DG DG 9 9 -0.041 0.006 1.419 1.378 N 1 X X N3 C4 DA DA 12 12 -0.039 0.006 1.344 1.305 N 39.727 -1.50 -0.75 0.00 -1.50 0.00 2.24 0.956 0.940 0.23256 0.20332 0.20485 0.20485 2.10 35.14 161 2907 2870 5.3 98.70 3.627 0.096 RANDOM 1 THROUGHOUT 2 SAD 0.163 0.156 0.80 0.80 1.40 MAXIMUM LIKELIHOOD WITH PHASES BABINET MODEL WITH MASK 2.10 35.14 23 281 1 257 0 0.020 0.021 292 3.133 3.000 451 0.120 0.200 36 0.013 0.020 142 0.381 0.200 74 0.187 0.200 11 0.113 0.200 20 0.065 0.200 5 0.258 0.228 2.155 16 217 20 1.8 50 1P1Y 5957 3066 0 0.071 0.071 1 20.7 99 0.22 2.10 2.18 13.76 307 1 99.4 refinement REFMAC 5.1.24 data reduction HKL-2000 data scaling SCALEPACK phasing CNS Crystal structure of a continuous three-dimensional DNA lattice from d(GGACAGATGGGAG) 1 N N 2 N N 3 N N covale 1.595 both X DA 3 A O3' DA 3 1_555 X CBR 4 A P CBR 4 1_555 covale 1.593 both X CBR 4 A O3' CBR 4 1_555 X DA 5 A P DA 5 1_555 covale 1.574 both X DA 7 A O3' DA 7 1_555 X BRU 8 A P BRU 8 1_555 covale 1.565 both X BRU 8 A O3' BRU 8 1_555 X DG 9 A P DG 9 1_555 metalc 2.159 X MG 51 B MG MG 1_555 X HOH 71 C O HOH 1_555 metalc 2.168 X MG 51 B MG MG 1_555 X HOH 72 C O HOH 1_555 metalc 2.167 X MG 51 B MG MG 1_555 X HOH 73 C O HOH 1_555 metalc 2.164 X MG 51 B MG MG 1_555 X HOH 74 C O HOH 1_555 hydrog TYPE_7_PAIR X DG 1 A N7 DG 1 1_555 X DG 10 A N1 DG 10 6_454 hydrog TYPE_7_PAIR X DG 1 A O6 DG 1 1_555 X DG 10 A N2 DG 10 6_454 hydrog TYPE_4_PAIR X DG 2 A N2 DG 2 1_555 X DG 11 A N3 DG 11 6_454 hydrog TYPE_4_PAIR X DG 2 A N3 DG 2 1_555 X DG 11 A N2 DG 11 6_454 hydrog TYPE_2_PAIR X DA 3 A N6 DA 3 1_555 X DA 12 A N7 DA 12 6_454 hydrog TYPE_2_PAIR X DA 3 A N7 DA 3 1_555 X DA 12 A N6 DA 12 6_454 DNA continuous three-dimensional dna lattice, parallel-stranded base pairs, DNA 1P1Y PDB 1 1P1Y 1 13 1P1Y 1 13 1P1Y X 1 1 13 BINDING SITE FOR RESIDUE MG X 51 X MG 51 Software 4 X HOH 71 C HOH 4 1_555 X HOH 72 C HOH 4 1_555 X HOH 73 C HOH 4 1_555 X HOH 74 C HOH 4 1_555 172 P 64