0.023568 0.000000 0.000000 0.000000 0.023568 0.000000 0.000000 0.000000 0.040404 0.00000 0.00000 0.00000 Jain, S.C. Zon, G. Sundaralingam, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 42.430 42.430 24.750 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 C10 H26 N4 202.340 SPERMINE non-polymer 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 108 N O N 109 N P N 110 N O N 111 N O N 112 N O N 113 N C N 114 R C N 115 N O N 116 S C N 117 N O N 118 N C N 119 R C N 120 N N N 121 N C N 122 N O N 123 N N N 124 N C N 125 N O N 126 N C N 127 N C N 128 N C 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 H N 142 N H N 143 N H N 144 N N N 145 N C N 146 N C N 147 N C N 148 N N N 149 N C N 150 N C N 151 N C N 152 N C N 153 N N N 154 N C N 155 N C N 156 N C N 157 N N N 158 N H N 159 N H N 160 N H N 161 N H N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N H N 169 N H N 170 N H N 171 N H N 172 N H N 173 N H N 174 N H N 175 N H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N H N 181 N H N 182 N H N 183 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 N 113 N sing N 114 N sing N 115 N doub 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 N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N doub N 139 N sing N 140 N sing N 141 N sing N 142 N doub N 143 N sing N 144 N sing N 145 N doub N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N sing N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N sing US Biochemistry BICHAW 0033 0006-2960 28 2360 2364 10.1021/bi00432a002 2730868 Base only binding of spermine in the deep groove of the A-DNA octamer d(GTGTACAC). 1989 UK J.Mol.Biol. JMOBAK 0070 0022-2836 197 141 145 The Potentially Z-DNA-Forming Sequence d(GTGTACAC) Crystallizes as A-DNA 1987 10.2210/pdb1dns/pdb pdb_00001dns 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 277.00 1 OSCILLATION CAMERA x-ray 1 1.0 ROTATING ANODE ELLIOTT GX-6 2426.617 DNA (5'-D(*GP*TP*GP*TP*AP*CP*AP*C)-3') 1 syn polymer 202.340 SPERMINE 1 syn non-polymer no no (DG)(DT)(DG)(DT)(DA)(DC)(DA)(DC) GTGTACAC A polydeoxyribonucleotide n n n n n n n n 2.30 46.41 VAPOR DIFFUSION VAPOR DIFFUSION WATER 1 MPD 1 MGCL2 1 SPERMINE 1 WATER 2 MPD 2 -11.161 1 19 A 1 A 8 -1.866 A_DG1:DC8_A 1 -11.808 -0.378 -0.048 -0.175 -0.764 1 20 A 2 A 7 1.125 A_DT2:DA7_A 2 -10.255 -0.040 0.173 -0.047 -4.570 1 19 A 3 A 6 -0.799 A_DG3:DC6_A 3 -13.832 -0.334 0.171 -0.201 -5.135 1 20 A 4 A 5 -4.193 A_DT4:DA5_A 4 -7.670 -0.176 0.342 -0.181 5.135 1 20 A 5 A 4 -4.193 A_DA5:DT4_A 5 -7.669 0.176 0.342 -0.181 4.570 1 19 A 6 A 3 -0.799 A_DC6:DG3_A 6 -13.832 0.334 0.171 -0.201 0.764 1 20 A 7 A 2 1.125 A_DA7:DT2_A 7 -10.255 0.040 0.173 -0.047 11.161 1 19 A 8 A 1 -1.866 A_DC8:DG1_A 8 -11.808 0.378 -0.048 -0.175 2.846 33.114 A A 1 2 12.685 A A 8 7 3.190 7.175 0.359 -1.248 AA_DG1DT2:DA7DC8_AA 1 -0.764 1.350 32.340 -3.319 -0.750 2.739 30.453 A A 2 3 18.325 A A 7 6 3.329 9.468 0.376 -1.471 AA_DT2DG3:DC6DA7_AA 2 1.729 -3.347 28.926 -4.601 -0.387 3.007 37.130 A A 3 4 9.175 A A 6 5 3.272 5.820 -0.214 -1.524 AA_DG3DT4:DA5DC6_AA 3 -0.626 0.987 36.681 -3.144 0.255 2.821 30.128 A A 4 5 5.820 A A 5 4 2.974 3.020 0.000 -1.421 AA_DT4DA5:DT4DA5_AA 4 0.000 0.000 29.980 -3.280 0.000 3.007 37.130 A A 5 6 9.175 A A 4 3 3.272 5.820 0.214 -1.524 AA_DA5DC6:DG3DT4_AA 5 0.626 -0.987 36.681 -3.144 -0.255 2.739 30.453 A A 6 7 18.325 A A 3 2 3.329 9.468 -0.376 -1.471 AA_DC6DA7:DT2DG3_AA 6 -1.729 3.347 28.926 -4.601 0.387 2.846 33.114 A A 7 8 12.685 A A 2 1 3.190 7.175 -0.359 -1.248 AA_DA7DC8:DG1DT2_AA 7 0.764 -1.350 32.340 -3.319 0.750 chem_comp_atom chem_comp_bond database_2 struct_site repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 1990-04-15 1 1 2008-05-22 1 2 2011-07-13 1 3 2024-02-07 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id BNL Y BNL 1989-02-22 REL SPM SPERMINE SPM 9 2 SPM SPM 9 A G 1 n 1 DG 1 A T 2 n 2 DT 2 A G 3 n 3 DG 3 A T 4 n 4 DT 4 A A 5 n 5 DA 5 A C 6 n 6 DC 6 A A 7 n 7 DA 7 A C 8 n 8 DC 8 A author_defined_assembly 2 dimeric 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 0.0000000000 1.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 7_555 y,x,-z crystal symmetry operation 0.0000000000 0.0000000000 0.0000000000 1 A C8 SPM 9 B C8 SPM 1 1 N 1 A C9 SPM 9 B C9 SPM 1 1 N 1 A N10 SPM 9 B N10 SPM 1 1 N 1 A C11 SPM 9 B C11 SPM 1 1 N 1 A C12 SPM 9 B C12 SPM 1 1 N 1 A C13 SPM 9 B C13 SPM 1 1 N 1 A N14 SPM 9 B N14 SPM 1 1 N 1 3.28 0.50 111.50 114.78 A A A C5 C6 N1 DG DG DG 1 1 1 N 1 -4.41 0.60 128.60 124.19 A A A C5 C6 O6 DG DG DG 1 1 1 N 1 7.56 1.20 119.70 127.26 A A A C3' O3' P DG DG DT 1 1 2 Y 1 -13.25 1.50 119.60 106.35 A A A OP1 P OP2 DT DT DT 2 2 2 N 1 12.53 1.20 110.70 123.23 A A A O5' P OP1 DT DT DT 2 2 2 N 1 3.14 0.30 108.30 111.44 A A A O4' C1' N1 DT DT DT 2 2 2 N 1 3.64 0.60 114.60 118.24 A A A N1 C2 N3 DT DT DT 2 2 2 N 1 -5.49 0.60 127.20 121.71 A A A C2 N3 C4 DT DT DT 2 2 2 N 1 3.80 0.60 115.20 119.00 A A A N3 C4 C5 DT DT DT 2 2 2 N 1 3.95 0.30 108.30 112.25 A A A O4' C1' N9 DG DG DG 3 3 3 N 1 -6.52 0.70 119.90 113.38 A A A N3 C2 N2 DG DG DG 3 3 3 N 1 9.64 1.20 119.70 129.34 A A A C3' O3' P DG DG DT 3 3 4 Y 1 -7.25 0.90 105.70 98.45 A A A O5' P OP1 DT DT DT 4 4 4 N 1 15.54 1.20 110.70 126.24 A A A O5' P OP2 DT DT DT 4 4 4 N 1 -5.63 0.80 109.40 103.77 A A A O5' C5' C4' DT DT DT 4 4 4 N 1 4.46 0.60 114.60 119.06 A A A N1 C2 N3 DT DT DT 4 4 4 N 1 -6.12 0.60 127.20 121.08 A A A C2 N3 C4 DT DT DT 4 4 4 N 1 4.49 0.60 115.20 119.69 A A A N3 C4 C5 DT DT DT 4 4 4 N 1 -5.16 0.80 123.10 117.94 A A A N1 C2 O2 DT DT DT 4 4 4 N 1 -6.63 0.70 124.90 118.27 A A A C5 C4 O4 DT DT DT 4 4 4 N 1 11.34 1.10 110.50 121.84 A A A O3' P OP2 DT DA DA 4 5 5 Y 1 -3.34 0.50 129.30 125.96 A A A N1 C2 N3 DA DA DA 5 5 5 N 1 7.44 1.10 110.50 117.94 A A A O3' P OP2 DC DA DA 6 7 7 Y 1 -5.92 0.90 105.70 99.78 A A A O5' P OP2 DA DA DA 7 7 7 N 1 -5.94 0.80 109.40 103.46 A A A O5' C5' C4' DA DA DA 7 7 7 N 1 4.08 0.60 118.60 122.68 A A A C6 N1 C2 DA DA DA 7 7 7 N 1 -3.73 0.50 129.30 125.57 A A A N1 C2 N3 DA DA DA 7 7 7 N 1 -3.42 0.50 117.70 114.28 A A A C5 C6 N1 DA DA DA 7 7 7 N 1 10.04 1.20 110.70 120.74 A A A O5' P OP2 DC DC DC 8 8 8 N 1 3.81 0.30 108.30 112.11 A A A O4' C1' N1 DC DC DC 8 8 8 N 1 -3.19 0.40 121.90 118.71 A A A N3 C4 C5 DC DC DC 8 8 8 N 1 A A P OP2 DT DT 4 4 -0.105 0.017 1.485 1.380 N 1 A A P O5' DA DA 7 7 0.112 0.010 1.593 1.705 N 1 A A P O5' DC DC 8 8 -0.071 0.010 1.593 1.522 N 1 A A C7 C7 SPM SPM 9 9 1.55 1_555 7_555 0.1150000 2.000 5.000 1214 1 TR isotropic TR isotropic 2.000 5.000 0 168 7 161 0 0.010 fix fix 2.000 1DNS 1365 3.000 1 refinement NUCLSQ BASE ONLY BINDING OF SPERMINE IN THE DEEP GROOVE OF THE A-DNA OCTAMER D(GTGTACAC) 1 N N 2 N N hydrog WATSON-CRICK A DG 1 A N1 DG 1 1_555 A DC 8 A N3 DC 8 7_555 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 A DC 8 A O2 DC 8 7_555 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 A DC 8 A N4 DC 8 7_555 hydrog WATSON-CRICK A DT 2 A N3 DT 2 1_555 A DA 7 A N1 DA 7 7_555 hydrog WATSON-CRICK A DT 2 A O4 DT 2 1_555 A DA 7 A N6 DA 7 7_555 hydrog WATSON-CRICK A DG 3 A N1 DG 3 1_555 A DC 6 A N3 DC 6 7_555 hydrog WATSON-CRICK A DG 3 A N2 DG 3 1_555 A DC 6 A O2 DC 6 7_555 hydrog WATSON-CRICK A DG 3 A O6 DG 3 1_555 A DC 6 A N4 DC 6 7_555 hydrog WATSON-CRICK A DT 4 A N3 DT 4 1_555 A DA 5 A N1 DA 5 7_555 hydrog WATSON-CRICK A DT 4 A O4 DT 4 1_555 A DA 5 A N6 DA 5 7_555 hydrog WATSON-CRICK A DA 5 A N1 DA 5 1_555 A DT 4 A N3 DT 4 7_555 hydrog WATSON-CRICK A DA 5 A N6 DA 5 1_555 A DT 4 A O4 DT 4 7_555 hydrog WATSON-CRICK A DC 6 A N3 DC 6 1_555 A DG 3 A N1 DG 3 7_555 hydrog WATSON-CRICK A DC 6 A N4 DC 6 1_555 A DG 3 A O6 DG 3 7_555 hydrog WATSON-CRICK A DC 6 A O2 DC 6 1_555 A DG 3 A N2 DG 3 7_555 hydrog WATSON-CRICK A DA 7 A N1 DA 7 1_555 A DT 2 A N3 DT 2 7_555 hydrog WATSON-CRICK A DA 7 A N6 DA 7 1_555 A DT 2 A O4 DT 2 7_555 hydrog WATSON-CRICK A DC 8 A N3 DC 8 1_555 A DG 1 A N1 DG 1 7_555 hydrog WATSON-CRICK A DC 8 A N4 DC 8 1_555 A DG 1 A O6 DG 1 7_555 hydrog WATSON-CRICK A DC 8 A O2 DC 8 1_555 A DG 1 A N2 DG 1 7_555 DNA A-DNA, DOUBLE HELIX, DNA 1DNS PDB 1 1DNS 1 8 1DNS 1 8 1DNS A 1 1 8 BINDING SITE FOR RESIDUE SPM A 9 A SPM 9 Software 4 A DT 2 A DT 2 4 1_555 A DG 3 A DG 3 4 1_555 A DT 4 A DT 4 4 1_555 A DC 6 A DC 6 4 7_555 96 P 43 21 2