0.014495 0.000000 0.000000 0.000000 0.014495 0.000000 0.000000 0.000000 0.017800 0.00000 0.00000 0.00000 Labiuk, S.L. Delbaere, L.T. Lee, J.S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 40 90 90 90 68.99 68.99 56.18 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 Ni 2 58.693 NICKEL (II) ION 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 N 13 N N N 14 N C N 15 N O N 16 N N N 17 N C N 18 N N N 19 N C N 20 N C 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 H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N O N 36 N P N 37 N O N 38 N O N 39 N O N 40 N C N 41 R C N 42 N O N 43 S C N 44 N O N 45 N C N 46 R C Y 47 N N Y 48 N C Y 49 N N Y 50 N C N 51 N C N 52 N O N 53 N N N 54 N C N 55 N N N 56 N N Y 57 N C 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 H N 72 N O N 73 N H N 74 N H N 75 N NI 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 N 24 N sing N 25 N sing N 26 N doub N 27 N sing N 28 N doub N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N doub 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 sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing Y 59 N sing Y 60 N sing Y 61 N doub N 62 N sing Y 63 N sing N 64 N sing Y 65 N doub 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 sing GW J.Biol.Inorg.Chem. JJBCFA 2154 0949-8257 8 715 720 10.1007/s00775-003-0473-4 14505075 Cobalt(II), nickel(II) and zinc(II) do not bind to intra-helical N(7) guanine positions in the B-form crystal structure of d(GGCGCC) 2003 10.2210/pdb1p25/pdb pdb_00001p25 110 1 CCD 2002-08-06 ADSC QUANTUM 4 SINGLE WAVELENGTH M x-ray 1 0.9000 1.0 14-BM-D APS 0.9000 SYNCHROTRON APS BEAMLINE 14-BM-D 1810.205 5'-D(*GP*GP*CP*GP*CP*C)-3' 5 syn polymer 58.693 NICKEL (II) ION 5 syn non-polymer 18.015 water 25 nat water no no (DG)(DG)(DC)(DG)(DC)(DC) GGCGCC A,B,C,D,E polydeoxyribonucleotide n n n n n n 1 3.79 67.3 VAPOR DIFFUSION, HANGING DROP 8.0 DNA, TAPS-HCl, NiCl2, MPD, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K 277 Taps-HCl 1 NiCl2 1 MPD 1 MPD 2 1.912 1 19 B 7 C 18 0.445 B_DG7:DC18_C 1 -12.189 0.392 0.194 -0.281 -1.919 1 19 B 8 C 17 -11.187 B_DG8:DC17_C 2 -5.287 -0.565 0.074 -0.520 -3.540 1 19 B 9 C 16 -4.298 B_DC9:DG16_C 3 -1.898 0.029 0.284 -0.272 6.123 1 19 B 10 C 15 -7.021 B_DG10:DC15_C 4 -0.583 -0.068 0.167 -0.429 0.278 1 19 B 11 C 14 -1.082 B_DC11:DG14_C 5 -3.756 0.196 0.201 -0.327 -10.213 1 19 B 12 C 13 -0.407 B_DC12:DG13_C 6 -6.119 0.354 0.529 -0.126 0.665 1 19 D 19 E 30 -2.284 D_DG19:DC30_E 7 -9.894 0.092 0.356 -0.204 1.397 1 19 D 20 E 29 -3.094 D_DG20:DC29_E 8 -0.360 -0.068 0.259 -0.349 2.820 1 19 D 21 E 28 -8.526 D_DC21:DG28_E 9 -4.805 0.047 0.222 -0.397 0.830 1 19 D 22 E 27 -6.363 D_DG22:DC27_E 10 -2.484 0.006 0.045 -0.464 0.933 1 19 D 23 E 26 -3.557 D_DC23:DG26_E 11 5.414 -0.102 0.091 -0.448 -1.762 1 19 D 24 E 25 -1.117 D_DC24:DG25_E 12 -3.356 0.431 0.307 -0.394 -2.841 1 19 A 1 A 6 -4.654 A_DG1:DC6_A 13 -5.508 -0.414 0.071 -0.358 4.706 1 19 A 2 A 5 -1.959 A_DG2:DC5_A 14 -3.446 0.111 0.214 -0.292 -1.599 1 19 A 3 A 4 -2.035 A_DC3:DG4_A 15 -0.955 0.399 0.022 -0.657 1.599 1 19 A 4 A 3 -2.035 A_DG4:DC3_A 16 -0.955 -0.399 0.022 -0.657 -4.706 1 19 A 5 A 2 -1.959 A_DC5:DG2_A 17 -3.446 -0.111 0.214 -0.292 2.841 1 19 A 6 A 1 -4.654 A_DC6:DG1_A 18 -5.508 0.414 0.071 -0.358 3.162 30.640 B B 7 8 4.307 C C 18 17 3.161 2.272 -0.793 -0.606 BB_DG7DG8:DC17DC18_CC 1 -2.532 4.800 30.455 -1.580 1.016 3.336 37.888 B B 8 9 4.885 C C 17 16 3.404 3.168 0.805 -0.937 BB_DG8DC9:DG16DC17_CC 2 0.955 -1.473 37.749 -1.862 -1.113 2.977 36.259 B B 9 10 6.060 C C 16 15 2.944 3.762 0.258 0.368 BB_DC9DG10:DC15DG16_CC 3 2.424 -3.904 35.991 0.112 -0.105 3.502 36.051 B B 10 11 1.339 C C 15 14 3.504 0.828 -0.302 -0.279 BB_DG10DC11:DG14DC15_CC 4 -0.665 1.074 36.036 -0.576 0.386 3.288 36.227 B B 11 12 10.218 C C 14 13 3.427 6.323 0.316 -0.564 BB_DC11DC12:DG13DG14_CC 5 0.733 -1.185 35.682 -1.825 -0.402 3.254 -25.303 B D 12 19 7.920 C E 13 30 3.233 -3.453 -0.057 0.450 BD_DC12DG19:DC30DG13_EC 6 2.474 5.674 -24.949 -0.026 0.588 3.054 30.416 D D 19 20 10.791 E E 30 29 3.115 5.630 -0.504 -0.084 DD_DG19DG20:DC29DC30_EE 7 -0.349 0.669 29.901 -1.233 0.894 3.071 36.580 D D 20 21 6.926 E E 29 28 3.152 4.337 0.380 -0.576 DD_DG20DC21:DG28DC29_EE 8 0.663 -1.059 36.325 -1.488 -0.518 3.387 32.962 D D 21 22 6.034 E E 28 27 3.432 3.416 0.337 -0.410 DD_DC21DG22:DC27DG28_EE 9 2.029 -3.584 32.728 -1.330 -0.233 3.214 33.217 D D 22 23 6.958 E E 27 26 3.238 3.966 -0.270 -0.104 DD_DG22DC23:DG26DC27_EE 10 -1.873 3.286 32.934 -0.840 0.161 3.411 35.835 D D 23 24 -1.067 E E 26 25 3.412 -0.657 0.290 -0.256 DD_DC23DC24:DG25DG26_EE 11 -0.494 0.803 35.826 -0.318 -0.545 3.099 34.029 A A 1 2 4.468 A A 6 5 3.144 2.611 0.115 -0.331 AA_DG1DG2:DC5DC6_AA 12 -2.003 3.428 33.874 -0.963 -0.502 3.333 35.207 A A 2 3 5.622 A A 5 4 3.398 3.396 -0.395 -0.486 AA_DG2DC3:DG4DC5_AA 13 0.417 -0.691 35.045 -1.324 0.717 3.256 29.266 A A 3 4 11.935 A A 4 3 3.307 5.990 0.000 0.080 AA_DC3DG4:DC3DG4_AA 14 0.000 0.000 28.659 -1.155 0.000 3.333 35.207 A A 4 5 5.622 A A 3 2 3.398 3.396 0.395 -0.486 AA_DG4DC5:DG2DC3_AA 15 -0.417 0.691 35.045 -1.324 -0.717 3.099 34.029 A A 5 6 4.468 A A 2 1 3.144 2.611 -0.115 -0.331 AA_DC5DC6:DG1DG2_AA 16 2.003 -3.428 33.874 -0.963 0.502 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 Data collection Database references Derived calculations Refinement description 1 0 2003-12-09 1 1 2008-04-29 1 2 2011-07-13 1 3 2024-02-14 1 4 2024-04-03 _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.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.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.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_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 NI NICKEL (II) ION HOH water Synthesized by AlphaDNA (Quebec, PQ, Canada) sample 1F6C NDB ENTRY BD0040 PDB experimental model NI 101 2 NI NI 101 A NI 102 2 NI NI 102 B NI 103 2 NI NI 103 C NI 104 2 NI NI 104 D NI 105 2 NI NI 105 E HOH 201 3 HOH HOH 201 A HOH 202 3 HOH HOH 202 A HOH 203 3 HOH HOH 203 A HOH 204 3 HOH HOH 204 A HOH 205 3 HOH HOH 205 A HOH 206 3 HOH HOH 206 B HOH 207 3 HOH HOH 207 B HOH 208 3 HOH HOH 208 B HOH 209 3 HOH HOH 209 B HOH 210 3 HOH HOH 210 B HOH 211 3 HOH HOH 211 C HOH 212 3 HOH HOH 212 C HOH 213 3 HOH HOH 213 C HOH 214 3 HOH HOH 214 C HOH 215 3 HOH HOH 215 C HOH 216 3 HOH HOH 216 D HOH 217 3 HOH HOH 217 D HOH 218 3 HOH HOH 218 D HOH 219 3 HOH HOH 219 D HOH 220 3 HOH HOH 220 D HOH 221 3 HOH HOH 221 E HOH 222 3 HOH HOH 222 E HOH 223 3 HOH HOH 223 E HOH 224 3 HOH HOH 224 E HOH 225 3 HOH HOH 225 E G 1 n 1 DG 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 C 6 n 6 DC 6 A G 7 n 1 DG 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 C 12 n 6 DC 12 B G 13 n 1 DG 13 C G 14 n 2 DG 14 C C 15 n 3 DC 15 C G 16 n 4 DG 16 C C 17 n 5 DC 17 C C 18 n 6 DC 18 C G 19 n 1 DG 19 D G 20 n 2 DG 20 D C 21 n 3 DC 21 D G 22 n 4 DG 22 D C 23 n 5 DC 23 D C 24 n 6 DC 24 D G 25 n 1 DG 25 E G 26 n 2 DG 26 E C 27 n 3 DC 27 E G 28 n 4 DG 28 E C 29 n 5 DC 29 E C 30 n 6 DC 30 E author_defined_assembly 2 dimeric author_defined_assembly 2 dimeric author_defined_assembly 2 dimeric A DG 1 A N7 DG 1 1_555 A NI 101 F NI NI 1_555 A HOH 201 K O HOH 1_555 89.8 A DG 1 A N7 DG 1 1_555 A NI 101 F NI NI 1_555 A HOH 202 K O HOH 1_555 91.1 A HOH 201 K O HOH 1_555 A NI 101 F NI NI 1_555 A HOH 202 K O HOH 1_555 89.8 A DG 1 A N7 DG 1 1_555 A NI 101 F NI NI 1_555 A HOH 203 K O HOH 1_555 89.8 A HOH 201 K O HOH 1_555 A NI 101 F NI NI 1_555 A HOH 203 K O HOH 1_555 179.3 A HOH 202 K O HOH 1_555 A NI 101 F NI NI 1_555 A HOH 203 K O HOH 1_555 90.8 A DG 1 A N7 DG 1 1_555 A NI 101 F NI NI 1_555 A HOH 204 K O HOH 1_555 91.0 A HOH 201 K O HOH 1_555 A NI 101 F NI NI 1_555 A HOH 204 K O HOH 1_555 87.4 A HOH 202 K O HOH 1_555 A NI 101 F NI NI 1_555 A HOH 204 K O HOH 1_555 176.5 A HOH 203 K O HOH 1_555 A NI 101 F NI NI 1_555 A HOH 204 K O HOH 1_555 92.1 A DG 1 A N7 DG 1 1_555 A NI 101 F NI NI 1_555 A HOH 205 K O HOH 1_555 178.7 A HOH 201 K O HOH 1_555 A NI 101 F NI NI 1_555 A HOH 205 K O HOH 1_555 88.9 A HOH 202 K O HOH 1_555 A NI 101 F NI NI 1_555 A HOH 205 K O HOH 1_555 89.2 A HOH 203 K O HOH 1_555 A NI 101 F NI NI 1_555 A HOH 205 K O HOH 1_555 91.5 A HOH 204 K O HOH 1_555 A NI 101 F NI NI 1_555 A HOH 205 K O HOH 1_555 88.6 B DG 7 B N7 DG 1 1_555 B NI 102 G NI NI 1_555 B HOH 206 L O HOH 1_555 89.6 B DG 7 B N7 DG 1 1_555 B NI 102 G NI NI 1_555 B HOH 207 L O HOH 1_555 89.6 B HOH 206 L O HOH 1_555 B NI 102 G NI NI 1_555 B HOH 207 L O HOH 1_555 89.0 B DG 7 B N7 DG 1 1_555 B NI 102 G NI NI 1_555 B HOH 208 L O HOH 1_555 90.2 B HOH 206 L O HOH 1_555 B NI 102 G NI NI 1_555 B HOH 208 L O HOH 1_555 174.6 B HOH 207 L O HOH 1_555 B NI 102 G NI NI 1_555 B HOH 208 L O HOH 1_555 85.6 B DG 7 B N7 DG 1 1_555 B NI 102 G NI NI 1_555 B HOH 209 L O HOH 1_555 90.8 B HOH 206 L O HOH 1_555 B NI 102 G NI NI 1_555 B HOH 209 L O HOH 1_555 101.1 B HOH 207 L O HOH 1_555 B NI 102 G NI NI 1_555 B HOH 209 L O HOH 1_555 169.9 B HOH 208 L O HOH 1_555 B NI 102 G NI NI 1_555 B HOH 209 L O HOH 1_555 84.3 B DG 7 B N7 DG 1 1_555 B NI 102 G NI NI 1_555 B HOH 210 L O HOH 1_555 178.4 B HOH 206 L O HOH 1_555 B NI 102 G NI NI 1_555 B HOH 210 L O HOH 1_555 91.2 B HOH 207 L O HOH 1_555 B NI 102 G NI NI 1_555 B HOH 210 L O HOH 1_555 91.9 B HOH 208 L O HOH 1_555 B NI 102 G NI NI 1_555 B HOH 210 L O HOH 1_555 89.1 B HOH 209 L O HOH 1_555 B NI 102 G NI NI 1_555 B HOH 210 L O HOH 1_555 87.7 C DG 13 C N7 DG 1 1_555 C NI 103 H NI NI 1_555 C HOH 211 M O HOH 1_555 90.3 C DG 13 C N7 DG 1 1_555 C NI 103 H NI NI 1_555 C HOH 212 M O HOH 1_555 91.2 C HOH 211 M O HOH 1_555 C NI 103 H NI NI 1_555 C HOH 212 M O HOH 1_555 89.9 C DG 13 C N7 DG 1 1_555 C NI 103 H NI NI 1_555 C HOH 213 M O HOH 1_555 89.5 C HOH 211 M O HOH 1_555 C NI 103 H NI NI 1_555 C HOH 213 M O HOH 1_555 176.4 C HOH 212 M O HOH 1_555 C NI 103 H NI NI 1_555 C HOH 213 M O HOH 1_555 93.7 C DG 13 C N7 DG 1 1_555 C NI 103 H NI NI 1_555 C HOH 214 M O HOH 1_555 90.4 C HOH 211 M O HOH 1_555 C NI 103 H NI NI 1_555 C HOH 214 M O HOH 1_555 92.4 C HOH 212 M O HOH 1_555 C NI 103 H NI NI 1_555 C HOH 214 M O HOH 1_555 177.2 C HOH 213 M O HOH 1_555 C NI 103 H NI NI 1_555 C HOH 214 M O HOH 1_555 84.0 C DG 13 C N7 DG 1 1_555 C NI 103 H NI NI 1_555 C HOH 215 M O HOH 1_555 179.1 C HOH 211 M O HOH 1_555 C NI 103 H NI NI 1_555 C HOH 215 M O HOH 1_555 88.8 C HOH 212 M O HOH 1_555 C NI 103 H NI NI 1_555 C HOH 215 M O HOH 1_555 88.7 C HOH 213 M O HOH 1_555 C NI 103 H NI NI 1_555 C HOH 215 M O HOH 1_555 91.4 C HOH 214 M O HOH 1_555 C NI 103 H NI NI 1_555 C HOH 215 M O HOH 1_555 89.8 D DG 19 D N7 DG 1 1_555 D NI 104 I NI NI 1_555 D HOH 216 N O HOH 1_555 91.0 D DG 19 D N7 DG 1 1_555 D NI 104 I NI NI 1_555 D HOH 217 N O HOH 1_555 90.5 D HOH 216 N O HOH 1_555 D NI 104 I NI NI 1_555 D HOH 217 N O HOH 1_555 92.1 D DG 19 D N7 DG 1 1_555 D NI 104 I NI NI 1_555 D HOH 218 N O HOH 1_555 90.0 D HOH 216 N O HOH 1_555 D NI 104 I NI NI 1_555 D HOH 218 N O HOH 1_555 179.0 D HOH 217 N O HOH 1_555 D NI 104 I NI NI 1_555 D HOH 218 N O HOH 1_555 87.5 D DG 19 D N7 DG 1 1_555 D NI 104 I NI NI 1_555 D HOH 219 N O HOH 1_555 89.9 D HOH 216 N O HOH 1_555 D NI 104 I NI NI 1_555 D HOH 219 N O HOH 1_555 87.5 D HOH 217 N O HOH 1_555 D NI 104 I NI NI 1_555 D HOH 219 N O HOH 1_555 179.5 D HOH 218 N O HOH 1_555 D NI 104 I NI NI 1_555 D HOH 219 N O HOH 1_555 92.8 D DG 19 D N7 DG 1 1_555 D NI 104 I NI NI 1_555 D HOH 220 N O HOH 1_555 179.1 D HOH 216 N O HOH 1_555 D NI 104 I NI NI 1_555 D HOH 220 N O HOH 1_555 88.1 D HOH 217 N O HOH 1_555 D NI 104 I NI NI 1_555 D HOH 220 N O HOH 1_555 89.7 D HOH 218 N O HOH 1_555 D NI 104 I NI NI 1_555 D HOH 220 N O HOH 1_555 91.0 D HOH 219 N O HOH 1_555 D NI 104 I NI NI 1_555 D HOH 220 N O HOH 1_555 90.0 E DG 25 E N7 DG 1 1_555 E NI 105 J NI NI 1_555 E HOH 221 O O HOH 1_555 88.8 E DG 25 E N7 DG 1 1_555 E NI 105 J NI NI 1_555 E HOH 222 O O HOH 1_555 89.4 E HOH 221 O O HOH 1_555 E NI 105 J NI NI 1_555 E HOH 222 O O HOH 1_555 99.8 E DG 25 E N7 DG 1 1_555 E NI 105 J NI NI 1_555 E HOH 223 O O HOH 1_555 91.2 E HOH 221 O O HOH 1_555 E NI 105 J NI NI 1_555 E HOH 223 O O HOH 1_555 172.4 E HOH 222 O O HOH 1_555 E NI 105 J NI NI 1_555 E HOH 223 O O HOH 1_555 87.8 E DG 25 E N7 DG 1 1_555 E NI 105 J NI NI 1_555 E HOH 224 O O HOH 1_555 90.2 E HOH 221 O O HOH 1_555 E NI 105 J NI NI 1_555 E HOH 224 O O HOH 1_555 82.9 E HOH 222 O O HOH 1_555 E NI 105 J NI NI 1_555 E HOH 224 O O HOH 1_555 177.3 E HOH 223 O O HOH 1_555 E NI 105 J NI NI 1_555 E HOH 224 O O HOH 1_555 89.5 E DG 25 E N7 DG 1 1_555 E NI 105 J NI NI 1_555 E HOH 225 O O HOH 1_555 177.5 E HOH 221 O O HOH 1_555 E NI 105 J NI NI 1_555 E HOH 225 O O HOH 1_555 93.3 E HOH 222 O O HOH 1_555 E NI 105 J NI NI 1_555 E HOH 225 O O HOH 1_555 91.6 E HOH 223 O O HOH 1_555 E NI 105 J NI NI 1_555 E HOH 225 O O HOH 1_555 86.6 E HOH 224 O O HOH 1_555 E NI 105 J NI NI 1_555 E HOH 225 O O HOH 1_555 88.7 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_556 y,x,-z+1 crystal symmetry operation 0.0000000000 0.0000000000 56.1800000000 1 3.22 0.50 111.90 115.12 A A A C2 N3 C4 DG DG DG 1 1 1 N 1 3.63 0.50 113.10 116.73 A A A N7 C8 N9 DG DG DG 1 1 1 N 1 -2.96 0.40 106.40 103.44 A A A C8 N9 C4 DG DG DG 1 1 1 N 1 3.31 0.40 105.40 108.71 A A A N9 C4 C5 DG DG DG 1 1 1 N 1 3.31 0.50 113.10 116.41 A A A N7 C8 N9 DG DG DG 2 2 2 N 1 -9.63 1.60 120.90 111.27 A A A P O5' C5' DC DC DC 3 3 3 N 1 -5.07 0.80 105.90 100.83 A A A O4' C1' C2' DC DC DC 3 3 3 N 1 4.43 0.70 118.00 122.43 A A A N3 C4 N4 DC DC DC 3 3 3 N 1 -4.92 0.70 120.20 115.28 A A A C5 C4 N4 DC DC DC 3 3 3 N 1 9.78 1.20 119.70 129.48 A A A C3' O3' P DC DC DG 3 3 4 Y 1 -12.07 1.60 120.90 108.83 A A A P O5' C5' DG DG DG 4 4 4 N 1 -4.41 0.70 102.20 97.79 A A A C4' C3' C2' DG DG DG 4 4 4 N 1 -2.95 0.40 106.40 103.45 A A A C8 N9 C4 DG DG DG 4 4 4 N 1 8.21 1.20 119.70 127.91 A A A C3' O3' P DG DG DC 4 4 5 Y 1 8.15 1.20 110.70 118.85 A A A O5' P OP2 DC DC DC 5 5 5 N 1 5.91 0.30 108.30 114.21 A A A O4' C1' N1 DC DC DC 5 5 5 N 1 -10.68 1.60 120.90 110.22 A A A P O5' C5' DC DC DC 6 6 6 N 1 -4.31 0.70 102.20 97.89 A A A C4' C3' C2' DC DC DC 6 6 6 N 1 10.98 0.30 108.30 119.28 A A A O4' C1' N1 DC DC DC 6 6 6 N 1 5.66 0.60 118.90 124.56 A A A N1 C2 O2 DC DC DC 6 6 6 N 1 -5.84 0.70 121.90 116.06 A A A N3 C2 O2 DC DC DC 6 6 6 N 1 2.22 0.30 108.30 110.52 B B B O4' C1' N9 DG DG DG 7 7 7 N 1 -2.45 0.40 106.40 103.95 B B B C8 N9 C4 DG DG DG 7 7 7 N 1 7.37 1.20 119.70 127.07 B B B C3' O3' P DG DG DG 7 7 8 Y 1 6.47 0.30 108.30 114.77 B B B O4' C1' N9 DG DG DG 8 8 8 N 1 -2.57 0.40 106.40 103.83 B B B C8 N9 C4 DG DG DG 8 8 8 N 1 -4.00 0.60 128.60 124.60 B B B C5 C6 O6 DG DG DG 8 8 8 N 1 4.02 0.60 106.00 110.02 B B B O4' C4' C3' DC DC DC 9 9 9 N 1 -4.91 0.70 102.20 97.29 B B B C4' C3' C2' DC DC DC 9 9 9 N 1 5.44 0.30 108.30 113.74 B B B O4' C1' N1 DC DC DC 9 9 9 N 1 5.37 0.60 118.90 124.27 B B B N1 C2 O2 DC DC DC 9 9 9 N 1 -6.74 0.70 121.90 115.16 B B B N3 C2 O2 DC DC DC 9 9 9 N 1 3.72 0.50 113.10 116.82 B B B N7 C8 N9 DG DG DG 10 10 10 N 1 -2.63 0.40 106.40 103.77 B B B C8 N9 C4 DG DG DG 10 10 10 N 1 3.70 0.60 119.90 123.60 B B B N1 C6 O6 DG DG DG 10 10 10 N 1 -4.54 0.60 128.60 124.06 B B B C5 C6 O6 DG DG DG 10 10 10 N 1 4.04 0.60 118.90 122.94 B B B N1 C2 O2 DC DC DC 11 11 11 N 1 -4.42 0.70 121.90 117.48 B B B N3 C2 O2 DC DC DC 11 11 11 N 1 5.76 0.30 108.30 114.06 B B B O4' C1' N1 DC DC DC 12 12 12 N 1 4.09 0.60 118.90 122.99 B B B N1 C2 O2 DC DC DC 12 12 12 N 1 3.05 0.30 108.30 111.35 C C C O4' C1' N9 DG DG DG 13 13 13 N 1 3.82 0.50 113.10 116.92 C C C N7 C8 N9 DG DG DG 13 13 13 N 1 -3.48 0.40 106.40 102.92 C C C C8 N9 C4 DG DG DG 13 13 13 N 1 3.03 0.30 108.30 111.33 C C C O4' C1' N9 DG DG DG 14 14 14 N 1 2.49 0.40 110.80 113.29 C C C C4 C5 N7 DG DG DG 14 14 14 N 1 -4.66 0.50 104.30 99.64 C C C C5 N7 C8 DG DG DG 14 14 14 N 1 4.28 0.50 113.10 117.38 C C C N7 C8 N9 DG DG DG 14 14 14 N 1 -3.39 0.40 106.40 103.01 C C C C8 N9 C4 DG DG DG 14 14 14 N 1 -3.84 0.60 130.40 126.56 C C C C6 C5 N7 DG DG DG 14 14 14 N 1 6.00 0.60 119.90 125.90 C C C N1 C6 O6 DG DG DG 14 14 14 N 1 -6.62 0.60 128.60 121.98 C C C C5 C6 O6 DG DG DG 14 14 14 N 1 12.23 0.30 108.30 120.53 C C C O4' C1' N1 DC DC DC 15 15 15 N 1 9.66 0.30 108.30 117.96 C C C O4' C1' N9 DG DG DG 16 16 16 N 1 4.27 0.50 113.10 117.37 C C C N7 C8 N9 DG DG DG 16 16 16 N 1 -4.23 0.40 106.40 102.17 C C C C8 N9 C4 DG DG DG 16 16 16 N 1 -9.88 1.60 120.90 111.02 C C C P O5' C5' DC DC DC 17 17 17 N 1 2.66 0.30 108.30 110.96 C C C O4' C1' N1 DC DC DC 17 17 17 N 1 4.04 0.30 108.30 112.34 C C C O4' C1' N1 DC DC DC 18 18 18 N 1 -5.89 0.70 108.00 102.11 D D D O4' C1' N9 DG DG DG 19 19 19 N 1 -12.04 1.60 120.90 108.86 D D D P O5' C5' DC DC DC 21 21 21 N 1 3.76 0.30 108.30 112.06 D D D O4' C1' N1 DC DC DC 21 21 21 N 1 2.48 0.40 120.30 122.78 D D D C6 N1 C2 DC DC DC 21 21 21 N 1 -11.56 1.80 114.10 102.54 D D D C5' C4' C3' DG DG DG 22 22 22 N 1 -5.30 0.70 102.20 96.90 D D D C4' C3' C2' DG DG DG 22 22 22 N 1 19.10 0.30 108.30 127.40 D D D O4' C1' N9 DG DG DG 22 22 22 N 1 -3.42 0.50 104.30 100.88 D D D C5 N7 C8 DG DG DG 22 22 22 N 1 4.51 0.50 113.10 117.61 D D D N7 C8 N9 DG DG DG 22 22 22 N 1 -2.53 0.40 106.40 103.87 D D D C8 N9 C4 DG DG DG 22 22 22 N 1 -3.74 0.60 130.40 126.66 D D D C6 C5 N7 DG DG DG 22 22 22 N 1 3.72 0.60 118.90 122.62 D D D N1 C2 O2 DC DC DC 23 23 23 N 1 -5.11 0.70 121.90 116.79 D D D N3 C2 O2 DC DC DC 23 23 23 N 1 6.26 0.60 118.90 125.16 D D D N1 C2 O2 DC DC DC 24 24 24 N 1 -5.67 0.70 121.90 116.23 D D D N3 C2 O2 DC DC DC 24 24 24 N 1 3.57 0.50 113.10 116.67 E E E N7 C8 N9 DG DG DG 25 25 25 N 1 2.75 0.40 110.80 113.55 E E E C4 C5 N7 DG DG DG 26 26 26 N 1 -5.22 0.50 104.30 99.08 E E E C5 N7 C8 DG DG DG 26 26 26 N 1 4.12 0.50 113.10 117.22 E E E N7 C8 N9 DG DG DG 26 26 26 N 1 -2.82 0.40 106.40 103.58 E E E C8 N9 C4 DG DG DG 26 26 26 N 1 4.38 0.60 119.90 124.28 E E E N1 C6 O6 DG DG DG 26 26 26 N 1 -6.05 0.60 128.60 122.55 E E E C5 C6 O6 DG DG DG 26 26 26 N 1 -12.67 1.60 120.90 108.23 E E E P O5' C5' DC DC DC 27 27 27 N 1 5.56 0.30 108.30 113.86 E E E O4' C1' N1 DC DC DC 27 27 27 N 1 -11.75 1.60 120.90 109.15 E E E P O5' C5' DG DG DG 28 28 28 N 1 12.50 0.30 108.30 120.80 E E E O4' C1' N9 DG DG DG 28 28 28 N 1 -3.50 0.50 104.30 100.80 E E E C5 N7 C8 DG DG DG 28 28 28 N 1 3.10 0.50 113.10 116.20 E E E N7 C8 N9 DG DG DG 28 28 28 N 1 4.45 0.60 118.90 123.35 E E E N1 C2 O2 DC DC DC 29 29 29 N 1 -11.45 1.60 120.90 109.45 E E E P O5' C5' DC DC DC 30 30 30 N 1 13.45 0.30 108.30 121.75 E E E O4' C1' N1 DC DC DC 30 30 30 N 1 A A C5' C4' DG DG 1 1 0.073 0.007 1.512 1.585 N 1 A A P O5' DC DC 6 6 0.076 0.010 1.593 1.669 N 1 B B C4 C5 DC DC 11 11 0.049 0.008 1.425 1.474 N 1 D D C2 N3 DG DG 22 22 0.054 0.008 1.323 1.377 N 1 E E C8 N9 DG DG 25 25 -0.088 0.007 1.374 1.286 N 1 E E C5 C6 DG DG 26 26 -0.073 0.010 1.419 1.346 N 29.4 0.276 0.223 0.2281 0.228 2.90 15. 261 2924 2706 9.0 random 1 Grouped B-values THROUGHOUT 2.0 MOLECULAR REPLACEMENT NDB ENTRY BD0040 2.90 15. 25 970 5 940 0 0.016 3.996 32.665 1.305 47.9 2.90 26. 1P25 3217 3217 0.0 0.0 0.09 1 22.0 8.9 96.9 2.90 3.00 1.8 0.6 4.9 80.6 data reduction DENZO data scaling SCALEPACK model building X-PLOR refinement X-PLOR 3.851 phasing X-PLOR Crystal structure of nickel(II)-d(GGCGCC)2 1 N N 1 N N 1 N N 1 N N 1 N N 2 N N 2 N N 2 N N 2 N N 2 N N 3 N N 3 N N 3 N N 3 N N 3 N N metalc 2.120 A DG 1 A N7 DG 1 1_555 A NI 101 F NI NI 1_555 metalc 2.069 A NI 101 F NI NI 1_555 A HOH 201 K O HOH 1_555 metalc 2.082 A NI 101 F NI NI 1_555 A HOH 202 K O HOH 1_555 metalc 2.082 A NI 101 F NI NI 1_555 A HOH 203 K O HOH 1_555 metalc 2.079 A NI 101 F NI NI 1_555 A HOH 204 K O HOH 1_555 metalc 2.076 A NI 101 F NI NI 1_555 A HOH 205 K O HOH 1_555 metalc 2.061 B DG 7 B N7 DG 1 1_555 B NI 102 G NI NI 1_555 metalc 2.090 B NI 102 G NI NI 1_555 B HOH 206 L O HOH 1_555 metalc 2.080 B NI 102 G NI NI 1_555 B HOH 207 L O HOH 1_555 metalc 2.071 B NI 102 G NI NI 1_555 B HOH 208 L O HOH 1_555 metalc 2.073 B NI 102 G NI NI 1_555 B HOH 209 L O HOH 1_555 metalc 2.087 B NI 102 G NI NI 1_555 B HOH 210 L O HOH 1_555 metalc 2.096 C DG 13 C N7 DG 1 1_555 C NI 103 H NI NI 1_555 metalc 2.068 C NI 103 H NI NI 1_555 C HOH 211 M O HOH 1_555 metalc 2.092 C NI 103 H NI NI 1_555 C HOH 212 M O HOH 1_555 metalc 2.092 C NI 103 H NI NI 1_555 C HOH 213 M O HOH 1_555 metalc 2.078 C NI 103 H NI NI 1_555 C HOH 214 M O HOH 1_555 metalc 2.081 C NI 103 H NI NI 1_555 C HOH 215 M O HOH 1_555 metalc 2.074 D DG 19 D N7 DG 1 1_555 D NI 104 I NI NI 1_555 metalc 2.070 D NI 104 I NI NI 1_555 D HOH 216 N O HOH 1_555 metalc 2.077 D NI 104 I NI NI 1_555 D HOH 217 N O HOH 1_555 metalc 2.091 D NI 104 I NI NI 1_555 D HOH 218 N O HOH 1_555 metalc 2.082 D NI 104 I NI NI 1_555 D HOH 219 N O HOH 1_555 metalc 2.080 D NI 104 I NI NI 1_555 D HOH 220 N O HOH 1_555 metalc 2.113 E DG 25 E N7 DG 1 1_555 E NI 105 J NI NI 1_555 metalc 2.104 E NI 105 J NI NI 1_555 E HOH 221 O O HOH 1_555 metalc 2.080 E NI 105 J NI NI 1_555 E HOH 222 O O HOH 1_555 metalc 2.081 E NI 105 J NI NI 1_555 E HOH 223 O O HOH 1_555 metalc 2.094 E NI 105 J NI NI 1_555 E HOH 224 O O HOH 1_555 metalc 2.069 E NI 105 J NI NI 1_555 E HOH 225 O O HOH 1_555 hydrog WATSON-CRICK B DG 7 B N1 DG 1 1_555 C DC 18 C N3 DC 6 1_555 hydrog WATSON-CRICK B DG 7 B N2 DG 1 1_555 C DC 18 C O2 DC 6 1_555 hydrog WATSON-CRICK B DG 7 B O6 DG 1 1_555 C DC 18 C N4 DC 6 1_555 hydrog WATSON-CRICK B DG 8 B N1 DG 2 1_555 C DC 17 C N3 DC 5 1_555 hydrog WATSON-CRICK B DG 8 B N2 DG 2 1_555 C DC 17 C O2 DC 5 1_555 hydrog WATSON-CRICK B DG 8 B O6 DG 2 1_555 C DC 17 C N4 DC 5 1_555 hydrog WATSON-CRICK B DC 9 B N3 DC 3 1_555 C DG 16 C N1 DG 4 1_555 hydrog WATSON-CRICK B DC 9 B N4 DC 3 1_555 C DG 16 C O6 DG 4 1_555 hydrog WATSON-CRICK B DC 9 B O2 DC 3 1_555 C DG 16 C N2 DG 4 1_555 hydrog WATSON-CRICK B DG 10 B N1 DG 4 1_555 C DC 15 C N3 DC 3 1_555 hydrog WATSON-CRICK B DG 10 B N2 DG 4 1_555 C DC 15 C O2 DC 3 1_555 hydrog WATSON-CRICK B DG 10 B O6 DG 4 1_555 C DC 15 C N4 DC 3 1_555 hydrog WATSON-CRICK B DC 11 B N3 DC 5 1_555 C DG 14 C N1 DG 2 1_555 hydrog WATSON-CRICK B DC 11 B N4 DC 5 1_555 C DG 14 C O6 DG 2 1_555 hydrog WATSON-CRICK B DC 11 B O2 DC 5 1_555 C DG 14 C N2 DG 2 1_555 hydrog WATSON-CRICK B DC 12 B N3 DC 6 1_555 C DG 13 C N1 DG 1 1_555 hydrog WATSON-CRICK B DC 12 B N4 DC 6 1_555 C DG 13 C O6 DG 1 1_555 hydrog WATSON-CRICK B DC 12 B O2 DC 6 1_555 C DG 13 C N2 DG 1 1_555 hydrog WATSON-CRICK D DG 19 D N1 DG 1 1_555 E DC 30 E N3 DC 6 1_555 hydrog WATSON-CRICK D DG 19 D N2 DG 1 1_555 E DC 30 E O2 DC 6 1_555 hydrog WATSON-CRICK D DG 19 D O6 DG 1 1_555 E DC 30 E N4 DC 6 1_555 hydrog WATSON-CRICK D DG 20 D N1 DG 2 1_555 E DC 29 E N3 DC 5 1_555 hydrog WATSON-CRICK D DG 20 D N2 DG 2 1_555 E DC 29 E O2 DC 5 1_555 hydrog WATSON-CRICK D DG 20 D O6 DG 2 1_555 E DC 29 E N4 DC 5 1_555 hydrog WATSON-CRICK D DC 21 D N3 DC 3 1_555 E DG 28 E N1 DG 4 1_555 hydrog WATSON-CRICK D DC 21 D N4 DC 3 1_555 E DG 28 E O6 DG 4 1_555 hydrog WATSON-CRICK D DC 21 D O2 DC 3 1_555 E DG 28 E N2 DG 4 1_555 hydrog WATSON-CRICK D DG 22 D N1 DG 4 1_555 E DC 27 E N3 DC 3 1_555 hydrog WATSON-CRICK D DG 22 D N2 DG 4 1_555 E DC 27 E O2 DC 3 1_555 hydrog WATSON-CRICK D DG 22 D O6 DG 4 1_555 E DC 27 E N4 DC 3 1_555 hydrog WATSON-CRICK D DC 23 D N3 DC 5 1_555 E DG 26 E N1 DG 2 1_555 hydrog WATSON-CRICK D DC 23 D N4 DC 5 1_555 E DG 26 E O6 DG 2 1_555 hydrog WATSON-CRICK D DC 23 D O2 DC 5 1_555 E DG 26 E N2 DG 2 1_555 hydrog WATSON-CRICK D DC 24 D N3 DC 6 1_555 E DG 25 E N1 DG 1 1_555 hydrog WATSON-CRICK D DC 24 D N4 DC 6 1_555 E DG 25 E O6 DG 1 1_555 hydrog WATSON-CRICK D DC 24 D O2 DC 6 1_555 E DG 25 E N2 DG 1 1_555 hydrog WATSON-CRICK A DG 1 A N1 DG 1 1_555 A DC 6 A N3 DC 6 7_556 hydrog WATSON-CRICK A DG 1 A N2 DG 1 1_555 A DC 6 A O2 DC 6 7_556 hydrog WATSON-CRICK A DG 1 A O6 DG 1 1_555 A DC 6 A N4 DC 6 7_556 hydrog WATSON-CRICK A DG 2 A N1 DG 2 1_555 A DC 5 A N3 DC 5 7_556 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 A DC 5 A O2 DC 5 7_556 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 A DC 5 A N4 DC 5 7_556 hydrog WATSON-CRICK A DC 3 A N3 DC 3 1_555 A DG 4 A N1 DG 4 7_556 hydrog WATSON-CRICK A DC 3 A N4 DC 3 1_555 A DG 4 A O6 DG 4 7_556 hydrog WATSON-CRICK A DC 3 A O2 DC 3 1_555 A DG 4 A N2 DG 4 7_556 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 A DC 3 A N3 DC 3 7_556 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 A DC 3 A O2 DC 3 7_556 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 A DC 3 A N4 DC 3 7_556 hydrog WATSON-CRICK A DC 5 A N3 DC 5 1_555 A DG 2 A N1 DG 2 7_556 hydrog WATSON-CRICK A DC 5 A N4 DC 5 1_555 A DG 2 A O6 DG 2 7_556 hydrog WATSON-CRICK A DC 5 A O2 DC 5 1_555 A DG 2 A N2 DG 2 7_556 hydrog WATSON-CRICK A DC 6 A N3 DC 6 1_555 A DG 1 A N1 DG 1 7_556 hydrog WATSON-CRICK A DC 6 A N4 DC 6 1_555 A DG 1 A O6 DG 1 7_556 hydrog WATSON-CRICK A DC 6 A O2 DC 6 1_555 A DG 1 A N2 DG 1 7_556 DNA B-DNA, nickel binding, DNA 1P25 PDB 1 1P25 1 6 1P25 1 6 1P25 A 1 1 6 7 12 1P25 7 12 1P25 B 1 1 6 13 18 1P25 13 18 1P25 C 1 1 6 19 24 1P25 19 24 1P25 D 1 1 6 25 30 1P25 25 30 1P25 E 1 1 6 BINDING SITE FOR RESIDUE NI A 101 A NI 101 Software 6 BINDING SITE FOR RESIDUE NI B 102 B NI 102 Software 6 BINDING SITE FOR RESIDUE NI C 103 C NI 103 Software 6 BINDING SITE FOR RESIDUE NI D 104 D NI 104 Software 7 BINDING SITE FOR RESIDUE NI E 105 E NI 105 Software 7 A DG 1 A DG 1 6 1_555 A HOH 201 K HOH 6 1_555 A HOH 202 K HOH 6 1_555 A HOH 203 K HOH 6 1_555 A HOH 204 K HOH 6 1_555 A HOH 205 K HOH 6 1_555 B DG 7 B DG 1 6 1_555 B HOH 206 L HOH 6 1_555 B HOH 207 L HOH 6 1_555 B HOH 208 L HOH 6 1_555 B HOH 209 L HOH 6 1_555 B HOH 210 L HOH 6 1_555 C DG 13 C DG 1 6 1_555 C HOH 211 M HOH 6 1_555 C HOH 212 M HOH 6 1_555 C HOH 213 M HOH 6 1_555 C HOH 214 M HOH 6 1_555 C HOH 215 M HOH 6 1_555 A DC 5 A DC 5 7 3_555 D DG 19 D DG 1 7 1_555 D HOH 216 N HOH 7 1_555 D HOH 217 N HOH 7 1_555 D HOH 218 N HOH 7 1_555 D HOH 219 N HOH 7 1_555 D HOH 220 N HOH 7 1_555 A DC 3 A DC 3 7 3_555 E DG 25 E DG 1 7 1_555 E HOH 221 O HOH 7 1_555 E HOH 222 O HOH 7 1_555 E HOH 223 O HOH 7 1_555 E HOH 224 O HOH 7 1_555 E HOH 225 O HOH 7 1_555 92 tetragonal P 41 21 2