0.055772 0.000000 0.000000 0.000000 0.031888 0.000000 0.000000 0.000000 0.022411 0.00000 0.00000 0.00000 Ohishi, H. Tomita, K.-i. Nakanishi, I. Ohtsuchi, M. Hakoshima, T. Rich, A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.0 90.0 90.0 17.93 31.36 44.62 C6 H18 N4 146.234 N,N'-BIS(2-AMINOETHYL)-1,2-ETHANEDIAMINE TRIENTINE non-polymer 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 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 C N 4 N N N 5 N C N 6 N C N 7 N N N 8 N C N 9 N C N 10 N N N 11 N H N 12 N H N 13 N H N 14 N H N 15 N H N 16 N H N 17 N H N 18 N H N 19 N H N 20 N H N 21 N H 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 O N 30 N P N 31 N O N 32 N O N 33 N O N 34 N C N 35 R C N 36 N O N 37 S C N 38 N O N 39 N C N 40 R C N 41 N N N 42 N C N 43 N O N 44 N N N 45 N C N 46 N N N 47 N C N 48 N C N 49 N H N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H 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 O N 64 N P N 65 N O N 66 N O N 67 N O N 68 N C N 69 R C N 70 N O N 71 S C N 72 N O N 73 N C N 74 R C Y 75 N N Y 76 N C Y 77 N N Y 78 N C N 79 N C N 80 N O N 81 N N N 82 N C N 83 N N N 84 N N Y 85 N C N 86 N H N 87 N H N 88 N H N 89 N H 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 O N 101 N H N 102 N H N 103 N MG N 1 N sing N 2 N sing N 3 N sing 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 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 sing 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 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 doub N 54 N sing N 55 N doub N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N doub N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N doub 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 sing 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 Y 86 N sing Y 87 N sing Y 88 N doub N 89 N sing Y 90 N sing N 91 N sing Y 92 N doub N 93 N doub N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N doub N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing NE FEBS Lett. FEBLAL 0165 0014-5793 523 29 34 10.1016/S0014-5793(02)02922-8 12123799 The crystal structure of N1-[2-(2-amino-ethylamino)-ethyl]-ethane-1,2-diamine (polyamines) binding to the minor groove of d(CGCGCG)2, hexamer at room temperature 2002 10.2210/pdb1dj6/pdb pdb_00001dj6 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 283.0 1 DIFFRACTOMETER NICOLET P3 SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 SEALED TUBE OTHER 1810.205 5'-D(*CP*GP*CP*GP*CP*G)-3' 2 syn polymer 24.305 MAGNESIUM ION 1 syn non-polymer 146.234 N,N'-BIS(2-AMINOETHYL)-1,2-ETHANEDIAMINE 2 syn non-polymer 18.015 water 88 nat water no no (DC)(DG)(DC)(DG)(DC)(DG) CGCGCG A,B polydeoxyribonucleotide n n n n n n 6 1.73 29.00 VAPOR DIFFUSION, HANGING DROP 7.0 2MM AMMONIUM SALT OF D(CG)3, 10MM POLYAMINE PA(222) TETRACHLORIDE, 15MM MGCL2, 30MM SODIUM CACODYLATE BUFFER, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K 283 MGCL2 1 SODIUM CACODYLATE BUFFER 1 POLYAMINE PA(222) TETRACHLORIDE 1 1.946 1 19 A 1 B 12 0.374 A_DC1:DG12_B 1 0.580 -0.435 0.107 -0.152 -5.725 1 19 A 2 B 11 0.091 A_DG2:DC11_B 2 -0.213 0.371 -0.138 -0.169 2.482 1 19 A 3 B 10 0.876 A_DC3:DG10_B 3 -5.211 -0.342 0.026 -0.143 -6.892 1 19 A 4 B 9 2.162 A_DG4:DC9_B 4 -1.949 0.182 0.252 -0.128 -1.281 1 19 A 5 B 8 1.251 A_DC5:DG8_B 5 -0.069 -0.194 -0.017 -0.088 3.253 1 19 A 6 B 7 4.079 A_DG6:DC7_B 6 3.063 0.218 0.145 -0.227 6.404 -7.253 A A 1 2 46.827 B B 12 11 3.643 -5.280 0.077 5.398 AA_DC1DG2:DC11DG12_BB 1 0.578 5.122 -4.940 -8.301 4.368 3.280 -51.737 A A 2 3 4.821 B B 11 10 3.365 -4.202 -0.039 -0.976 AA_DG2DC3:DG10DC11_BB 2 -1.481 -1.699 -51.558 1.407 -0.146 5.749 -7.916 A A 3 4 29.732 B B 10 9 3.792 -3.865 -0.005 5.363 AA_DC3DG4:DC9DG10_BB 3 -2.221 -17.082 -6.544 -20.397 -10.637 3.386 -53.371 A A 4 5 2.557 B B 9 8 3.431 -2.295 0.014 -0.958 AA_DG4DC5:DG8DC9_BB 4 2.598 2.894 -53.266 1.218 0.186 4.136 -9.234 A A 5 6 8.634 B B 8 7 3.401 -1.385 0.113 5.196 AA_DC5DG6:DC7DG8_BB 5 0.243 1.518 -9.126 -28.753 1.320 software diffrn_source chem_comp_atom chem_comp_bond database_2 pdbx_struct_conn_angle struct_conn struct_site pdbx_initial_refinement_model repository Initial release Version format compliance Version format compliance Refinement description Data collection Data collection Database references Derived calculations Refinement description 1 0 1999-12-18 1 1 2008-04-27 1 2 2011-07-13 1 3 2017-10-04 1 4 2018-04-04 1 5 2024-02-07 1 6 2024-04-03 _software.name _diffrn_source.type _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _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.ptnr1_symmetry _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.ptnr2_symmetry _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id CRYSTAL STRUCTURE OF D(CG)3+PA(24) COMPLEX CRYSTAL STRUCTURE OF D(CG)3+SPERMIDINE COMPLEX CRYSTAL STRUCTURE OF D(CG)3+THERMOSPERMINE COMPLEX RCSB Y RCSB 1999-12-01 REL REL MG MAGNESIUM ION 104 N,N'-BIS(2-AMINOETHYL)-1,2-ETHANEDIAMINE HOH water Z-DNA Other experimental model MG 80 2 MG MG 104 A 104 13 3 104 104 13 A 104 14 3 104 104 14 B WAT 17 4 HOH HOH 17 A WAT 21 4 HOH HOH 21 A WAT 26 4 HOH HOH 26 A WAT 27 4 HOH HOH 27 A WAT 31 4 HOH HOH 31 A WAT 33 4 HOH HOH 33 A WAT 34 4 HOH HOH 34 A WAT 35 4 HOH HOH 35 A WAT 36 4 HOH HOH 36 A WAT 37 4 HOH HOH 37 A WAT 39 4 HOH HOH 39 A WAT 40 4 HOH HOH 40 A WAT 41 4 HOH HOH 41 A WAT 42 4 HOH HOH 42 A WAT 43 4 HOH HOH 43 A WAT 44 4 HOH HOH 44 A WAT 45 4 HOH HOH 45 A WAT 46 4 HOH HOH 46 A WAT 47 4 HOH HOH 47 A WAT 49 4 HOH HOH 49 A WAT 50 4 HOH HOH 50 A WAT 51 4 HOH HOH 51 A WAT 53 4 HOH HOH 53 A WAT 54 4 HOH HOH 54 A WAT 55 4 HOH HOH 55 A WAT 56 4 HOH HOH 56 A WAT 57 4 HOH HOH 57 A WAT 58 4 HOH HOH 58 A WAT 59 4 HOH HOH 59 A WAT 61 4 HOH HOH 61 A WAT 64 4 HOH HOH 64 A WAT 65 4 HOH HOH 65 A WAT 68 4 HOH HOH 68 A WAT 72 4 HOH HOH 72 A WAT 73 4 HOH HOH 73 A WAT 74 4 HOH HOH 74 A WAT 75 4 HOH HOH 75 A WAT 79 4 HOH HOH 79 A WAT 81 4 HOH HOH 81 A WAT 82 4 HOH HOH 82 A WAT 83 4 HOH HOH 83 A WAT 84 4 HOH HOH 84 A WAT 85 4 HOH HOH 85 A WAT 86 4 HOH HOH 86 A WAT 87 4 HOH HOH 87 A WAT 88 4 HOH HOH 88 A WAT 89 4 HOH HOH 89 A WAT 90 4 HOH HOH 90 A WAT 91 4 HOH HOH 91 A WAT 92 4 HOH HOH 92 A WAT 93 4 HOH HOH 93 A WAT 97 4 HOH HOH 97 A WAT 99 4 HOH HOH 99 A WAT 101 4 HOH HOH 101 A WAT 102 4 HOH HOH 102 A WAT 103 4 HOH HOH 103 A WAT 15 4 HOH HOH 15 B WAT 16 4 HOH HOH 16 B WAT 18 4 HOH HOH 18 B WAT 19 4 HOH HOH 19 B WAT 20 4 HOH HOH 20 B WAT 22 4 HOH HOH 22 B WAT 23 4 HOH HOH 23 B WAT 24 4 HOH HOH 24 B WAT 25 4 HOH HOH 25 B WAT 28 4 HOH HOH 28 B WAT 29 4 HOH HOH 29 B WAT 30 4 HOH HOH 30 B WAT 32 4 HOH HOH 32 B WAT 38 4 HOH HOH 38 B WAT 48 4 HOH HOH 48 B WAT 52 4 HOH HOH 52 B WAT 60 4 HOH HOH 60 B WAT 62 4 HOH HOH 62 B WAT 63 4 HOH HOH 63 B WAT 66 4 HOH HOH 66 B WAT 67 4 HOH HOH 67 B WAT 69 4 HOH HOH 69 B WAT 70 4 HOH HOH 70 B WAT 71 4 HOH HOH 71 B WAT 76 4 HOH HOH 76 B WAT 77 4 HOH HOH 77 B WAT 78 4 HOH HOH 78 B WAT 94 4 HOH HOH 94 B WAT 95 4 HOH HOH 95 B WAT 96 4 HOH HOH 96 B WAT 98 4 HOH HOH 98 B WAT 100 4 HOH HOH 100 B C 1 n 1 DC 1 A G 2 n 2 DG 2 A C 3 n 3 DC 3 A G 4 n 4 DG 4 A C 5 n 5 DC 5 A G 6 n 6 DG 6 A C 7 n 1 DC 7 B G 8 n 2 DG 8 B C 9 n 3 DC 9 B G 10 n 4 DG 10 B C 11 n 5 DC 11 B G 12 n 6 DG 12 B author_defined_assembly 2 dimeric A DC 3 A OP2 DC 3 4_465 A MG 104 C MG MG 1_555 A HOH 51 F O HOH 4_465 91.5 A DC 3 A OP2 DC 3 4_465 A MG 104 C MG MG 1_555 A HOH 82 F O HOH 1_555 121.3 A HOH 51 F O HOH 4_465 A MG 104 C MG MG 1_555 A HOH 82 F O HOH 1_555 131.9 A DC 3 A OP2 DC 3 4_465 A MG 104 C MG MG 1_555 A HOH 84 F O HOH 4_465 139.4 A HOH 51 F O HOH 4_465 A MG 104 C MG MG 1_555 A HOH 84 F O HOH 4_465 69.0 A HOH 82 F O HOH 1_555 A MG 104 C MG MG 1_555 A HOH 84 F O HOH 4_465 97.0 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 A O O HOH HOH 65 83 1.31 1 A B O O HOH HOH 55 62 1.49 1 A A O O HOH HOH 61 73 1.54 1 A A O O HOH HOH 26 44 1.81 1 A B C5 O 104 HOH 13 15 1.84 1 A A C2' O DG HOH 2 87 1.94 1 A A O O HOH HOH 35 36 1.96 1 B B O O HOH HOH 29 95 2.05 1 A A N1 O 104 HOH 13 81 2.07 1 A A O O HOH HOH 41 92 2.14 1 B B N1 O 104 HOH 14 20 2.16 1 B B N1 O 104 HOH 14 70 2.17 1 A A O O HOH HOH 102 103 2.18 1 A A O O HOH HOH 79 93 2.19 1 B DG 10 0.044 SIDE CHAIN 1 -5.04 0.80 109.40 104.36 A A A O5' C5' C4' DC DC DC 1 1 1 N 1 -5.85 0.80 102.40 96.55 A A A C3' C2' C1' DC DC DC 1 1 1 N 1 -4.85 0.70 108.00 103.15 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 5.35 0.40 120.30 125.65 A A A C6 N1 C2 DC DC DC 1 1 1 N 1 -6.38 0.70 119.20 112.82 A A A N1 C2 N3 DC DC DC 1 1 1 N 1 5.50 0.50 119.90 125.40 A A A C2 N3 C4 DC DC DC 1 1 1 N 1 -10.45 0.40 121.90 111.45 A A A N3 C4 C5 DC DC DC 1 1 1 N 1 8.40 0.50 117.40 125.80 A A A C4 C5 C6 DC DC DC 1 1 1 N 1 -3.52 0.50 121.00 117.48 A A A C5 C6 N1 DC DC DC 1 1 1 N 1 4.54 0.60 118.90 123.44 A A A N1 C2 O2 DC DC DC 1 1 1 N 1 7.72 0.70 120.20 127.92 A A A C5 C4 N4 DC DC DC 1 1 1 N 1 -7.24 1.10 118.80 111.56 A A A C2 N1 C1' DC DC DC 1 1 1 N 1 -3.27 0.40 104.50 101.23 A A A O4' C4' C3' DG DG DG 2 2 2 N 1 -6.90 0.70 102.20 95.30 A A A C4' C3' C2' DG DG DG 2 2 2 N 1 14.00 1.20 102.50 116.50 A A A C3' C2' C1' DG DG DG 2 2 2 N 1 -9.44 0.80 105.90 96.46 A A A O4' C1' C2' DG DG DG 2 2 2 N 1 -8.69 0.70 108.00 99.31 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 -5.94 0.50 111.90 105.96 A A A C2 N3 C4 DG DG DG 2 2 2 N 1 10.22 0.50 128.60 138.82 A A A N3 C4 C5 DG DG DG 2 2 2 N 1 -12.34 0.60 118.80 106.46 A A A C4 C5 C6 DG DG DG 2 2 2 N 1 10.79 0.50 111.50 122.29 A A A C5 C6 N1 DG DG DG 2 2 2 N 1 7.51 0.40 110.80 118.31 A A A C4 C5 N7 DG DG DG 2 2 2 N 1 -8.88 0.40 105.40 96.52 A A A N9 C4 C5 DG DG DG 2 2 2 N 1 4.82 0.60 130.40 135.22 A A A C6 C5 N7 DG DG DG 2 2 2 N 1 7.11 0.90 116.20 123.31 A A A N1 C2 N2 DG DG DG 2 2 2 N 1 -5.46 0.70 119.90 114.44 A A A N3 C2 N2 DG DG DG 2 2 2 N 1 -7.54 0.60 128.60 121.06 A A A C5 C6 O6 DG DG DG 2 2 2 N 1 -8.73 1.30 127.00 118.27 A A A C8 N9 C1' DG DG DG 2 2 2 N 1 -5.56 0.80 102.40 96.84 A A A C3' C2' C1' DC DC DC 3 3 3 N 1 -10.97 0.70 108.00 97.03 A A A O4' C1' N1 DC DC DC 3 3 3 N 1 5.10 0.70 119.20 124.30 A A A N1 C2 N3 DC DC DC 3 3 3 N 1 -5.04 0.50 119.90 114.86 A A A C2 N3 C4 DC DC DC 3 3 3 N 1 5.69 0.40 121.90 127.59 A A A N3 C4 C5 DC DC DC 3 3 3 N 1 -5.56 0.50 117.40 111.84 A A A C4 C5 C6 DC DC DC 3 3 3 N 1 -6.10 0.60 118.90 112.80 A A A N1 C2 O2 DC DC DC 3 3 3 N 1 -5.57 0.80 109.40 103.83 A A A O5' C5' C4' DG DG DG 4 4 4 N 1 -4.36 0.40 104.50 100.14 A A A O4' C4' C3' DG DG DG 4 4 4 N 1 5.51 0.90 103.10 108.61 A A A C4' C3' C2' DG DG DG 4 4 4 N 1 -6.86 0.70 108.00 101.14 A A A O4' C1' N9 DG DG DG 4 4 4 N 1 -13.60 0.60 125.10 111.50 A A A C6 N1 C2 DG DG DG 4 4 4 N 1 6.81 0.60 123.90 130.71 A A A N1 C2 N3 DG DG DG 4 4 4 N 1 -5.49 0.50 111.90 106.41 A A A C2 N3 C4 DG DG DG 4 4 4 N 1 5.78 0.50 128.60 134.38 A A A N3 C4 C5 DG DG DG 4 4 4 N 1 8.67 0.50 111.50 120.17 A A A C5 C6 N1 DG DG DG 4 4 4 N 1 3.68 0.40 110.80 114.48 A A A C4 C5 N7 DG DG DG 4 4 4 N 1 -4.19 0.60 126.00 121.81 A A A N3 C4 N9 DG DG DG 4 4 4 N 1 -9.63 0.90 116.20 106.57 A A A N1 C2 N2 DG DG DG 4 4 4 N 1 -17.14 0.60 119.90 102.76 A A A N1 C6 O6 DG DG DG 4 4 4 N 1 8.45 0.60 128.60 137.05 A A A C5 C6 O6 DG DG DG 4 4 4 N 1 -8.84 1.30 127.00 118.16 A A A C8 N9 C1' DG DG DG 4 4 4 N 1 9.84 1.30 126.50 136.34 A A A C4 N9 C1' DG DG DG 4 4 4 N 1 8.97 1.20 115.70 124.67 A A A C5' C4' C3' DC DC DC 5 5 5 N 1 -7.28 0.70 108.00 100.72 A A A O4' C1' N1 DC DC DC 5 5 5 N 1 3.09 0.40 120.30 123.39 A A A C6 N1 C2 DC DC DC 5 5 5 N 1 5.60 0.40 121.90 127.50 A A A N3 C4 C5 DC DC DC 5 5 5 N 1 -3.33 0.50 117.40 114.07 A A A C4 C5 C6 DC DC DC 5 5 5 N 1 -5.95 0.50 121.00 115.05 A A A C5 C6 N1 DC DC DC 5 5 5 N 1 -6.28 0.70 120.20 113.92 A A A C5 C4 N4 DC DC DC 5 5 5 N 1 3.26 0.30 108.30 111.56 A A A O4' C1' N9 DG DG DG 6 6 6 N 1 -6.88 0.60 123.90 117.02 A A A N1 C2 N3 DG DG DG 6 6 6 N 1 8.23 0.50 111.90 120.13 A A A C2 N3 C4 DG DG DG 6 6 6 N 1 -6.68 0.50 128.60 121.92 A A A N3 C4 C5 DG DG DG 6 6 6 N 1 -2.44 0.40 110.80 108.36 A A A C4 C5 N7 DG DG DG 6 6 6 N 1 -3.06 0.50 104.30 101.24 A A A C5 N7 C8 DG DG DG 6 6 6 N 1 3.44 0.40 105.40 108.84 A A A N9 C4 C5 DG DG DG 6 6 6 N 1 4.50 0.70 119.90 124.40 A A A N3 C2 N2 DG DG DG 6 6 6 N 1 -3.63 0.60 128.60 124.97 A A A C5 C6 O6 DG DG DG 6 6 6 N 1 3.66 0.60 106.00 109.66 B B B O4' C4' C3' DC DC DC 7 7 7 N 1 -6.30 0.80 102.40 96.10 B B B C3' C2' C1' DC DC DC 7 7 7 N 1 -4.98 0.70 108.00 103.02 B B B O4' C1' N1 DC DC DC 7 7 7 N 1 -6.29 0.40 120.30 114.01 B B B C6 N1 C2 DC DC DC 7 7 7 N 1 6.43 0.50 119.90 126.33 B B B C2 N3 C4 DC DC DC 7 7 7 N 1 -6.02 0.40 121.90 115.88 B B B N3 C4 C5 DC DC DC 7 7 7 N 1 5.30 0.50 117.40 122.70 B B B C4 C5 C6 DC DC DC 7 7 7 N 1 6.01 0.70 120.20 126.21 B B B C5 C4 N4 DC DC DC 7 7 7 N 1 4.26 0.50 106.80 111.06 B B B O4' C1' C2' DG DG DG 8 8 8 N 1 2.34 0.30 108.30 110.64 B B B O4' C1' N9 DG DG DG 8 8 8 N 1 7.37 0.60 125.10 132.47 B B B C6 N1 C2 DG DG DG 8 8 8 N 1 -8.02 0.50 111.50 103.48 B B B C5 C6 N1 DG DG DG 8 8 8 N 1 -4.38 0.50 113.10 108.72 B B B N7 C8 N9 DG DG DG 8 8 8 N 1 2.62 0.40 105.40 108.02 B B B N9 C4 C5 DG DG DG 8 8 8 N 1 8.32 0.60 119.90 128.22 B B B N1 C6 O6 DG DG DG 8 8 8 N 1 -8.06 1.30 127.00 118.94 B B B C8 N9 C1' DG DG DG 8 8 8 N 1 4.23 0.60 106.00 110.23 B B B O4' C4' C3' DC DC DC 9 9 9 N 1 -9.03 0.80 102.40 93.37 B B B C3' C2' C1' DC DC DC 9 9 9 N 1 -5.06 0.70 108.00 102.94 B B B O4' C1' N1 DC DC DC 9 9 9 N 1 4.38 0.50 119.90 124.28 B B B C2 N3 C4 DC DC DC 9 9 9 N 1 9.65 0.90 103.10 112.75 B B B C4' C3' C2' DG DG DG 10 10 10 N 1 -9.08 0.80 102.40 93.32 B B B C3' C2' C1' DG DG DG 10 10 10 N 1 6.75 0.50 106.80 113.55 B B B O4' C1' C2' DG DG DG 10 10 10 N 1 -6.03 0.70 108.00 101.97 B B B O4' C1' N9 DG DG DG 10 10 10 N 1 3.60 0.50 111.90 115.50 B B B C2 N3 C4 DG DG DG 10 10 10 N 1 -3.52 0.50 128.60 125.08 B B B N3 C4 C5 DG DG DG 10 10 10 N 1 -7.75 0.40 110.80 103.05 B B B C4 C5 N7 DG DG DG 10 10 10 N 1 5.83 0.50 104.30 110.13 B B B C5 N7 C8 DG DG DG 10 10 10 N 1 -4.57 0.50 113.10 108.53 B B B N7 C8 N9 DG DG DG 10 10 10 N 1 4.06 0.40 106.40 110.46 B B B C8 N9 C4 DG DG DG 10 10 10 N 1 7.12 0.60 130.40 137.52 B B B C6 C5 N7 DG DG DG 10 10 10 N 1 4.37 0.70 119.90 124.27 B B B N3 C2 N2 DG DG DG 10 10 10 N 1 5.13 0.60 119.90 125.03 B B B N1 C6 O6 DG DG DG 10 10 10 N 1 -3.93 0.60 128.60 124.67 B B B C5 C6 O6 DG DG DG 10 10 10 N 1 -10.61 1.30 127.00 116.39 B B B C8 N9 C1' DG DG DG 10 10 10 N 1 6.46 0.70 110.30 116.76 B B B C1' O4' C4' DC DC DC 11 11 11 N 1 -7.07 0.70 102.20 95.13 B B B C4' C3' C2' DC DC DC 11 11 11 N 1 3.15 0.30 108.30 111.45 B B B O4' C1' N1 DC DC DC 11 11 11 N 1 2.47 0.40 120.30 122.77 B B B C6 N1 C2 DC DC DC 11 11 11 N 1 -9.43 0.70 119.20 109.77 B B B N1 C2 N3 DC DC DC 11 11 11 N 1 10.66 0.50 119.90 130.56 B B B C2 N3 C4 DC DC DC 11 11 11 N 1 -10.18 0.40 121.90 111.72 B B B N3 C4 C5 DC DC DC 11 11 11 N 1 -5.23 0.50 117.40 112.17 B B B C4 C5 C6 DC DC DC 11 11 11 N 1 11.80 0.50 121.00 132.80 B B B C5 C6 N1 DC DC DC 11 11 11 N 1 5.95 0.60 118.90 124.85 B B B N1 C2 O2 DC DC DC 11 11 11 N 1 4.33 0.70 118.00 122.33 B B B N3 C4 N4 DC DC DC 11 11 11 N 1 5.70 0.70 120.20 125.90 B B B C5 C4 N4 DC DC DC 11 11 11 N 1 -3.69 0.50 111.90 108.21 B B B C2 N3 C4 DG DG DG 12 12 12 N 1 6.20 0.50 128.60 134.80 B B B N3 C4 C5 DG DG DG 12 12 12 N 1 6.91 0.40 110.80 117.71 B B B C4 C5 N7 DG DG DG 12 12 12 N 1 -3.91 0.50 104.30 100.39 B B B C5 N7 C8 DG DG DG 12 12 12 N 1 3.43 0.50 113.10 116.53 B B B N7 C8 N9 DG DG DG 12 12 12 N 1 -6.92 0.40 105.40 98.48 B B B N9 C4 C5 DG DG DG 12 12 12 N 1 -5.51 0.60 130.40 124.89 B B B C6 C5 N7 DG DG DG 12 12 12 N 1 A A O5' C5' DC DC 1 1 0.148 0.016 1.440 1.588 N 1 A A C3' C2' DC DC 1 1 0.083 0.012 1.518 1.601 N 1 A A C2' C1' DC DC 1 1 0.072 0.010 1.519 1.591 N 1 A A O3' C3' DC DC 1 1 0.081 0.013 1.435 1.516 N 1 A A C1' N1 DC DC 1 1 0.119 0.013 1.488 1.607 N 1 A A C4 N4 DC DC 1 1 -0.056 0.009 1.335 1.279 N 1 A A C4 C5 DC DC 1 1 0.088 0.008 1.425 1.513 N 1 A A C5 C6 DC DC 1 1 -0.134 0.008 1.339 1.205 N 1 A A O5' C5' DG DG 2 2 0.124 0.016 1.440 1.564 N 1 A A C5' C4' DG DG 2 2 -0.080 0.011 1.509 1.429 N 1 A A C4' C3' DG DG 2 2 0.076 0.010 1.529 1.605 N 1 A A C3' C2' DG DG 2 2 0.163 0.012 1.518 1.681 N 1 A A C2' C1' DG DG 2 2 -0.087 0.010 1.518 1.431 N 1 A A O4' C1' DG DG 2 2 0.225 0.011 1.420 1.645 N 1 A A C2 N3 DG DG 2 2 0.173 0.008 1.323 1.496 N 1 A A N3 C4 DG DG 2 2 -0.075 0.007 1.350 1.275 N 1 A A C4 C5 DG DG 2 2 0.094 0.007 1.379 1.473 N 1 A A C6 N1 DG DG 2 2 -0.073 0.007 1.391 1.318 N 1 A A C5 N7 DG DG 2 2 -0.059 0.006 1.388 1.329 N 1 A A N9 C4 DG DG 2 2 0.145 0.008 1.375 1.520 N 1 A A C2' C1' DC DC 3 3 0.102 0.010 1.519 1.621 N 1 A A O4' C4' DC DC 3 3 0.089 0.009 1.449 1.538 N 1 A A C1' N1 DC DC 3 3 0.130 0.013 1.488 1.618 N 1 A A C2 O2 DC DC 3 3 0.110 0.009 1.240 1.350 N 1 A A C4 N4 DC DC 3 3 0.097 0.009 1.335 1.432 N 1 A A N1 C6 DC DC 3 3 -0.068 0.006 1.367 1.299 N 1 A A C2 N3 DC DC 3 3 -0.065 0.008 1.353 1.288 N 1 A A N3 C4 DC DC 3 3 -0.046 0.007 1.335 1.289 N 1 A A C5' C4' DG DG 4 4 0.093 0.007 1.512 1.605 N 1 A A C4' C3' DG DG 4 4 0.113 0.010 1.529 1.642 N 1 A A C3' C2' DG DG 4 4 -0.088 0.008 1.516 1.428 N 1 A A C2' C1' DG DG 4 4 0.105 0.010 1.519 1.624 N 1 A A O4' C1' DG DG 4 4 0.072 0.011 1.420 1.492 N 1 A A C2 N3 DG DG 4 4 -0.058 0.008 1.323 1.265 N 1 A A C5 C6 DG DG 4 4 -0.261 0.010 1.419 1.158 N 1 A A C6 N1 DG DG 4 4 0.196 0.007 1.391 1.587 N 1 A A N7 C8 DG DG 4 4 -0.048 0.006 1.305 1.257 N 1 A A C6 O6 DG DG 4 4 0.150 0.009 1.237 1.387 N 1 A A C2 O2 DC DC 5 5 -0.063 0.009 1.240 1.177 N 1 A A C4 N4 DC DC 5 5 0.065 0.009 1.335 1.400 N 1 A A N1 C2 DC DC 5 5 0.080 0.010 1.397 1.477 N 1 A A N1 C6 DC DC 5 5 0.052 0.006 1.367 1.419 N 1 A A C2 N3 DC DC 5 5 -0.052 0.008 1.353 1.301 N 1 A A C5 C6 DC DC 5 5 0.148 0.008 1.339 1.487 N 1 A A C2' C1' DG DG 6 6 0.098 0.010 1.519 1.617 N 1 A A C1' N9 DG DG 6 6 -0.137 0.014 1.468 1.331 N 1 A A N1 C2 DG DG 6 6 0.111 0.008 1.373 1.484 N 1 A A C4 C5 DG DG 6 6 0.100 0.007 1.379 1.479 N 1 A A C5 C6 DG DG 6 6 -0.061 0.010 1.419 1.358 N 1 A A C5 N7 DG DG 6 6 0.068 0.006 1.388 1.456 N 1 A A N7 C8 DG DG 6 6 0.134 0.006 1.305 1.439 N 1 B B O5' C5' DC DC 7 7 0.164 0.016 1.440 1.604 N 1 B B C5' C4' DC DC 7 7 -0.074 0.011 1.509 1.435 N 1 B B O4' C4' DC DC 7 7 -0.142 0.010 1.446 1.304 N 1 B B C4 N4 DC DC 7 7 -0.158 0.009 1.335 1.177 N 1 B B N1 C6 DC DC 7 7 0.135 0.006 1.367 1.502 N 1 B B N3 C4 DC DC 7 7 0.080 0.007 1.335 1.415 N 1 B B C4 C5 DC DC 7 7 -0.077 0.008 1.425 1.348 N 1 B B C3' C2' DG DG 8 8 0.186 0.012 1.518 1.704 N 1 B B N3 C4 DG DG 8 8 0.042 0.007 1.350 1.392 N 1 B B C5 C6 DG DG 8 8 0.135 0.010 1.419 1.554 N 1 B B C6 N1 DG DG 8 8 0.068 0.007 1.391 1.459 N 1 B B C5 N7 DG DG 8 8 -0.071 0.006 1.388 1.317 N 1 B B N7 C8 DG DG 8 8 0.116 0.006 1.305 1.421 N 1 B B C6 O6 DG DG 8 8 -0.108 0.009 1.237 1.129 N 1 B B C4' C3' DC DC 9 9 -0.061 0.010 1.521 1.460 N 1 B B C3' C2' DC DC 9 9 0.105 0.012 1.518 1.623 N 1 B B O4' C4' DC DC 9 9 -0.078 0.010 1.446 1.368 N 1 B B C1' N1 DC DC 9 9 0.109 0.013 1.488 1.597 N 1 B B N1 C6 DC DC 9 9 0.080 0.006 1.367 1.447 N 1 B B C4 C5 DC DC 9 9 0.069 0.008 1.425 1.494 N 1 B B O5' C5' DG DG 10 10 0.112 0.016 1.440 1.552 N 1 B B C4' C3' DG DG 10 10 0.063 0.010 1.529 1.592 N 1 B B C3' C2' DG DG 10 10 -0.133 0.008 1.516 1.383 N 1 B B C2' C1' DG DG 10 10 0.156 0.010 1.519 1.675 N 1 B B O4' C4' DG DG 10 10 -0.109 0.010 1.446 1.337 N 1 B B O3' C3' DG DG 10 10 0.107 0.013 1.435 1.542 N 1 B B C1' N9 DG DG 10 10 0.132 0.013 1.488 1.620 N 1 B B C2 N3 DG DG 10 10 -0.048 0.008 1.323 1.275 N 1 B B N3 C4 DG DG 10 10 -0.043 0.007 1.350 1.307 N 1 B B C5 N7 DG DG 10 10 -0.050 0.006 1.388 1.338 N 1 B B N7 C8 DG DG 10 10 -0.041 0.006 1.305 1.264 N 1 B B C8 N9 DG DG 10 10 -0.091 0.007 1.374 1.283 N 1 B B N9 C4 DG DG 10 10 -0.108 0.008 1.375 1.267 N 1 B B C5' C4' DC DC 11 11 -0.168 0.011 1.509 1.341 N 1 B B C4' C3' DC DC 11 11 0.292 0.010 1.529 1.821 N 1 B B C3' C2' DC DC 11 11 0.147 0.012 1.518 1.665 N 1 B B C2' C1' DC DC 11 11 0.063 0.010 1.519 1.582 N 1 B B O4' C4' DC DC 11 11 -0.105 0.010 1.446 1.341 N 1 B B C4 N4 DC DC 11 11 -0.139 0.009 1.335 1.196 N 1 B B N1 C6 DC DC 11 11 -0.079 0.006 1.367 1.288 N 1 B B C2 N3 DC DC 11 11 0.106 0.008 1.353 1.459 N 1 B B N3 C4 DC DC 11 11 0.114 0.007 1.335 1.449 N 1 B B C4 C5 DC DC 11 11 0.093 0.008 1.425 1.518 N 1 B B P O5' DG DG 12 12 -0.061 0.010 1.593 1.532 N 1 B B C4' C3' DG DG 12 12 0.118 0.010 1.529 1.647 N 1 B B C2' C1' DG DG 12 12 0.076 0.010 1.519 1.595 N 1 B B N3 C4 DG DG 12 12 -0.102 0.007 1.350 1.248 N 1 B B N7 C8 DG DG 12 12 -0.043 0.006 1.305 1.262 N 1 B B N9 C4 DG DG 12 12 0.067 0.008 1.375 1.442 N 1 A B O O HOH HOH 99 94 1.46 1_555 3_655 1 A B O O HOH HOH 99 100 1.53 1_555 3_655 1 A A O O HOH HOH 35 75 1.75 1_555 4_465 1 A B O O HOH HOH 33 32 1.86 1_555 2_564 1 A A O O HOH HOH 59 64 1.88 1_555 4_565 1 A B N7 N1 DG 104 6 14 2.13 1_555 3_655 0.169 0.14 0.169 0.165 1.0 10.0 11627 11212 96.4 RANDOM 1 THROUGHOUT 3 Z-DNA 1.0 10.0 89 349 20 240 0 0.001 0.01 5.7 1.0 10.0 1DJ6 11627 11212 3.0 1 40000 0.07 96.4 data reduction DIFDAT model building X-PLOR refinement SHELXL phasing X-PLOR COMPLEX OF A Z-DNA HEXAMER, D(CG)3, WITH SYNTHETIC POLYAMINE AT ROOM TEMPERATURE 1 N N 1 N N 2 N N 3 N N 3 N N 4 N N 4 N N metalc 2.703 A DC 3 A OP2 DC 3 4_465 A MG 104 C MG MG 1_555 metalc 2.960 A HOH 51 F O HOH 4_465 A MG 104 C MG MG 1_555 metalc 2.576 A HOH 82 F O HOH 1_555 A MG 104 C MG MG 1_555 metalc 2.636 A HOH 84 F O HOH 4_465 A MG 104 C MG MG 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 B DG 12 B N1 DG 6 1_555 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 B DG 12 B O6 DG 6 1_555 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 B DG 12 B N2 DG 6 1_555 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 B DC 11 B N3 DC 5 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B DC 11 B O2 DC 5 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B DC 11 B N4 DC 5 1_555 hydrog WATSON-CRICK A DC 3 A N3 DC 3 1_555 B DG 10 B N1 DG 4 1_555 hydrog WATSON-CRICK A DC 3 A N4 DC 3 1_555 B DG 10 B O6 DG 4 1_555 hydrog WATSON-CRICK A DC 3 A O2 DC 3 1_555 B DG 10 B N2 DG 4 1_555 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 B DC 9 B N3 DC 3 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B DC 9 B O2 DC 3 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B DC 9 B N4 DC 3 1_555 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 B DG 8 B N1 DG 2 1_555 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 B DG 8 B O6 DG 2 1_555 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 B DG 8 B N2 DG 2 1_555 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 B DC 7 B N3 DC 1 1_555 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 B DC 7 B O2 DC 1 1_555 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 B DC 7 B N4 DC 1 1_555 DNA Z-DNA:POLYAMINE COMPLEX, X-RAY CRYSTAL STRUCTURE, POLYAMINE BINDING IN MINOR GROOVE OF Z-DNA, DNA 1DJ6 PDB 1 1DJ6 1 6 1DJ6 1 6 1DJ6 A 1 1 6 7 12 1DJ6 7 12 1DJ6 B 1 1 6 BINDING SITE FOR RESIDUE MG A 104 A MG 104 Software 4 BINDING SITE FOR RESIDUE 104 A 13 A 104 13 Software 12 BINDING SITE FOR RESIDUE 104 B 14 B 104 14 Software 15 A DC 3 A DC 3 4 4_465 A HOH 51 F HOH 4 4_465 A HOH 82 F HOH 4 1_555 A HOH 84 F HOH 4 4_465 A DC 3 A DC 3 12 1_555 A DG 4 A DG 4 12 1_555 A DC 5 A DC 5 12 1_555 A DG 6 A DG 6 12 1_555 A HOH 72 F HOH 12 1_555 A HOH 79 F HOH 12 1_655 A HOH 81 F HOH 12 1_555 A HOH 90 F HOH 12 1_655 A HOH 101 F HOH 12 3_645 B DC 9 B DC 3 12 1_555 B HOH 15 G HOH 12 1_555 B HOH 22 G HOH 12 1_655 A DC 5 A DC 5 15 3_645 A DG 6 A DG 6 15 3_645 B DC 7 B DC 1 15 3_645 B DG 8 B DG 2 15 1_555 B DG 12 B DG 6 15 4_455 B HOH 19 G HOH 15 3_645 B HOH 20 G HOH 15 1_555 B HOH 24 G HOH 15 1_555 B HOH 25 G HOH 15 1_555 B HOH 30 G HOH 15 1_555 B HOH 69 G HOH 15 1_555 B HOH 70 G HOH 15 1_555 B HOH 77 G HOH 15 1_555 B HOH 78 G HOH 15 1_555 B HOH 95 G HOH 15 1_555 19 orthorhombic P 21 21 21