0.022717 0.000000 0.000000 0.000000 0.018212 0.000000 0.000000 0.000000 0.029682 0.000000 0.000000 0.000000 Campbell, N.H. Abd Karim, N.H. Parkinson, G.N. Vilar, R. Neidle, S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.000 90.000 90.000 44.020 54.909 33.691 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 C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking H2 O 18.015 WATER non-polymer K 1 39.098 POTASSIUM ION non-polymer C34 H38 F2 N4 Ni O4 663.380 [2,2'-{(4,5-difluorobenzene-1,2-diyl)bis[(nitrilo-kappaN)methylylidene]}bis{5-[2-(piperidin-1-yl)ethoxy]phenolato-kappa O}(2-)]nickel (II) N,N-Bis[4-[[1-(2-ethyl)piperidine]oxy]salicylidene]-4,5-difluoro-1,2-phenylenediamine-Nickel (II) 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 Y 49 N N Y 50 N C Y 51 N N Y 52 N C N 53 N C N 54 N O N 55 N N N 56 N C N 57 N N N 58 N N Y 59 N C 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 H N 73 N H N 74 N O N 75 N P N 76 N O N 77 N O N 78 N O N 79 N C N 80 R C N 81 N O N 82 S C N 83 N O N 84 N C N 85 R C N 86 N N N 87 N C N 88 N O N 89 N N N 90 N C N 91 N O N 92 N C N 93 N C N 94 N C 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 H N 109 N H N 110 N O N 111 N H N 112 N H N 113 N K Y 114 N C N 115 N F N 116 N N N 117 N O N 118 N NI Y 119 N C N 120 N F N 121 N N N 122 N O Y 123 N C N 124 N N N 125 N O Y 126 N C N 127 N N N 128 N O Y 129 N C Y 130 N C N 131 N C Y 132 N C Y 133 N C Y 134 N C Y 135 N C Y 136 N C Y 137 N C N 138 N C Y 139 N C Y 140 N C Y 141 N C Y 142 N C Y 143 N C Y 144 N C N 145 N C N 146 N C N 147 N C N 148 N C N 149 N C N 150 N C N 151 N C N 152 N C N 153 N C N 154 N C N 155 N C N 156 N C N 157 N C N 158 N C 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 184 N H N 185 N H N 186 N H N 187 N H N 188 N H N 189 N H N 190 N H N 191 N H N 192 N H N 193 N H N 194 N H N 195 N H N 196 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 Y 62 N sing Y 63 N sing Y 64 N doub N 65 N sing Y 66 N sing N 67 N sing Y 68 N doub N 69 N doub N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N doub N 75 N sing N 76 N sing N 77 N sing N 78 N sing N 79 N sing N 80 N doub 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 N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N doub N 104 N sing N 105 N sing N 106 N sing N 107 N doub 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 Y 118 N doub Y 119 N sing N 120 N sing N 121 N sing N 122 N doub N 123 N sing N 124 N sing N 125 N sing N 126 N sing Y 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N doub N 132 N sing N 133 N sing Y 134 N doub N 135 N sing N 136 N sing N 137 N sing N 138 N sing Y 139 N sing N 140 N sing N 141 N sing N 142 N sing N 143 N sing N 144 N sing N 145 N sing Y 146 N doub N 147 N sing N 148 N sing N 149 N sing Y 150 N doub Y 151 N sing Y 152 N sing N 153 N sing Y 154 N doub Y 155 N sing Y 156 N doub N 157 N sing N 158 N sing N 159 N sing Y 160 N doub Y 161 N sing Y 162 N sing N 163 N sing Y 164 N doub N 165 N sing Y 166 N sing Y 167 N doub 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 N 189 N sing N 190 N sing N 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N sing N 204 N sing N 205 N sing N 206 N sing US J.Med.Chem. JMCMAR 0151 0022-2623 55 209 222 10.1021/jm201140v 22112241 Molecular basis of structure-activity relationships between salphen metal complexes and human telomeric DNA quadruplexes. 2012 10.2210/pdb3qsf/pdb pdb_00003qsf 105 1 CCD 2010-06-28 ADSC QUANTUM 315r SINGLE WAVELENGTH M x-ray 1 1.48660 1.0 I03 Diamond 1.48660 SYNCHROTRON DIAMOND BEAMLINE I03 Human telomeric G-quadruplex DNA 3773.462 5'-D(*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*T)-3' 1 syn polymer 39.098 POTASSIUM ION 3 syn non-polymer 663.380 [2,2'-{(4,5-difluorobenzene-1,2-diyl)bis[(nitrilo-kappaN)methylylidene]}bis{5-[2-(piperidin-1-yl)ethoxy]phenolato-kappa O}(2-)]nickel (II) 1 syn non-polymer 18.015 water 20 nat water no no (DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT) AGGGTTAGGGTT X polydeoxyribonucleotide n n n n n n n n n n n n 1 2.70 54.40 VAPOR DIFFUSION, HANGING DROP 7.0 Initial conditions in the 3 ul drop were: 1.25mM quadruplex DNA, 1.25mM ligand, 0.83% PEG (w/v) 10 000, 16.7mM potassium chloride, 16.7mM sodium chloride, 16.7mM lithium sulphate and 20 mM potassium cacodylate buffer at pH 7.0. This was equilibrated against a reservoir well solution of 50% (w/v) PEG 10000 , VAPOR DIFFUSION, HANGING DROP, temperature 293.15K 293.15 -8.706 3 6 X 1002 X 1008 -93.042 X_DG1002:DG1008_X 1 -7.726 1.348 0.122 3.418 -14.223 3 6 X 1003 X 1009 -87.185 X_DG1003:DG1009_X 2 3.740 1.570 0.444 3.537 2.844 3 6 X 1004 X 1010 -83.727 X_DG1004:DG1010_X 3 -3.448 1.839 -0.205 3.721 3.494 33.244 X X 1002 1003 0.732 X X 1008 1009 3.492 0.419 -0.559 -1.113 XX_DG1002DG1003:DG1009DG1008_XX 1 -1.083 1.893 33.224 -2.020 0.784 2.988 25.982 X X 1003 1004 5.615 X X 1009 1010 3.159 2.512 -0.551 -0.423 XX_DG1003DG1004:DG1010DG1009_XX 2 3.891 -8.700 25.573 -1.596 2.241 chem_comp chem_comp_atom chem_comp_bond database_2 entity pdbx_entity_nonpoly pdbx_initial_refinement_model pdbx_struct_conn_angle struct_conn struct_site repository Initial release Database references Data collection Database references Derived calculations Refinement description Structure summary 1 0 2011-12-07 1 1 2012-04-18 1 2 2023-09-13 _chem_comp.name _database_2.pdbx_DOI _database_2.pdbx_database_accession _entity.pdbx_description _pdbx_entity_nonpoly.name _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id The same human telomeric G-quadruplex bound to a similar metal-containing ligand (a copper complex). The same human telomeric G-quadruplex bound to an acridine ligand (Braco19) The same human telomeric G-quadruplex bound to a naphthalene diimide ligand. The same human telomeric G-quadruplex bound to a naphthalene diimide ligand. The same human telomeric G-quadruplex in its native (ligand-free) form. The same human telomeric G-quadruplex in its native (ligand-free) form. The same human telomeric G-quadruplex bound to a porphyrin ligand. RCSB Y RCSB 2011-02-21 REL REL K POTASSIUM ION NUF [2,2'-{(4,5-difluorobenzene-1,2-diyl)bis[(nitrilo-kappaN)methylylidene]}bis{5-[2-(piperidin-1-yl)ethoxy]phenolato-kappa O}(2-)]nickel (II) HOH water This sequence occurs naturally in humans sample 3QSC PDB experimental model K 2013 2 K K 2013 X K 2014 2 K K 2014 X K 2015 2 K K 2015 X NUF 3016 3 NUF NUF 3016 X HOH 1 4 HOH HOH 1 X HOH 2 4 HOH HOH 2 X HOH 3 4 HOH HOH 3 X HOH 4 4 HOH HOH 4 X HOH 5 4 HOH HOH 5 X HOH 6 4 HOH HOH 6 X HOH 7 4 HOH HOH 7 X HOH 8 4 HOH HOH 8 X HOH 9 4 HOH HOH 9 X HOH 10 4 HOH HOH 10 X HOH 11 4 HOH HOH 11 X HOH 12 4 HOH HOH 12 X HOH 13 4 HOH HOH 13 X HOH 14 4 HOH HOH 14 X HOH 15 4 HOH HOH 15 X HOH 16 4 HOH HOH 16 X HOH 17 4 HOH HOH 17 X HOH 18 4 HOH HOH 18 X HOH 19 4 HOH HOH 19 X HOH 20 4 HOH HOH 20 X 36.360 2.500 2.500 22.010 22.010 Phaser MODE: MR_AUTO A 1001 n 1 DA 1001 X G 1002 n 2 DG 1002 X G 1003 n 3 DG 1003 X G 1004 n 4 DG 1004 X T 1005 n 5 DT 1005 X T 1006 n 6 DT 1006 X A 1007 n 7 DA 1007 X G 1008 n 8 DG 1008 X G 1009 n 9 DG 1009 X G 1010 n 10 DG 1010 X T 1011 n 11 DT 1011 X n 12 1012 X author_and_software_defined_assembly PISA 2 dimeric 1730 -1 4770 X DG 1002 A O6 DG 2 1_555 X K 2014 C K K 1_555 X DG 1003 A O6 DG 3 1_555 78.9 X DG 1002 A O6 DG 2 1_555 X K 2014 C K K 1_555 X DG 1008 A O6 DG 8 1_555 66.1 X DG 1003 A O6 DG 3 1_555 X K 2014 C K K 1_555 X DG 1008 A O6 DG 8 1_555 91.1 X DG 1002 A O6 DG 2 1_555 X K 2014 C K K 1_555 X DG 1009 A O6 DG 9 1_555 135.5 X DG 1003 A O6 DG 3 1_555 X K 2014 C K K 1_555 X DG 1009 A O6 DG 9 1_555 68.4 X DG 1008 A O6 DG 8 1_555 X K 2014 C K K 1_555 X DG 1009 A O6 DG 9 1_555 84.6 X DG 1002 A O6 DG 2 1_555 X K 2015 D K K 1_555 X DG 1008 A O6 DG 8 1_555 77.6 X DG 1003 A O6 DG 3 1_555 X K 2013 B K K 1_555 X DG 1004 A O6 DG 4 1_555 68.2 X DG 1003 A O6 DG 3 1_555 X K 2013 B K K 1_555 X DG 1009 A O6 DG 9 1_555 70.8 X DG 1004 A O6 DG 4 1_555 X K 2013 B K K 1_555 X DG 1009 A O6 DG 9 1_555 93.8 X DG 1003 A O6 DG 3 1_555 X K 2013 B K K 1_555 X DG 1010 A O6 DG 10 1_555 133.7 X DG 1004 A O6 DG 4 1_555 X K 2013 B K K 1_555 X DG 1010 A O6 DG 10 1_555 83.6 X DG 1009 A O6 DG 9 1_555 X K 2013 B K K 1_555 X DG 1010 A O6 DG 10 1_555 75.4 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 2_665 -x+1,-y+1,z crystal symmetry operation 44.0200000000 54.9090000000 0.0000000000 1 X K 2013 B K 1 X K 2014 C K 1 X K 2015 D K 1 X HOH 20 F HOH 1 X DT 1012 A DT 12 1 Y 1 3.16 0.30 108.30 111.46 X X X O4' C1' N9 DG DG DG 1004 1004 1004 N 1 3.70 0.30 108.30 112.00 X X X O4' C1' N9 DG DG DG 1008 1008 1008 N 1 2.48 0.30 108.30 110.78 X X X O4' C1' N9 DG DG DG 1010 1010 1010 N 1 3.10 0.30 108.30 111.40 X X X O4' C1' N1 DT DT DT 1011 1011 1011 N 1 3.60 0.60 119.90 123.50 X X X N3 C4 O4 DT DT DT 1011 1011 1011 N 1 X X O3' C3' DT DT 1005 1005 -0.058 0.006 1.419 1.361 N 1 X X O3' C3' DA DA 1007 1007 -0.046 0.006 1.419 1.373 N 68.950 34.0311 4.510 0.7300 0.0000 0.0000 -0.0700 0.0000 -0.6600 0.9360 0.8720 0.3203 0.2369 0.2404 2.4000 15.0000 77 1684 1684 4.6000 97.0000 0.3649 0.2714 1.000 0.250 0.7240 9.9490 0.2110 0.4976 0.3403 RANDOM 1 THROUGHOUT 0.000 MOLECULAR REPLACEMENT 0.3400 0.8000 0.8000 1.4000 3QSC MAXIMUM LIKELIHOOD MASK 2.4000 15.0000 20 299 48 231 0 0.014 0.021 312 1.608 3.000 478 0.059 0.200 45 0.021 0.020 169 2.864 3.000 312 4.428 4.500 478 0.3470 0.3810 2.4610 5 114 119 20 92.9700 2.308 22.010 3QSF 1888 1888 0.053 1 15.100 3.500 97.400 0.153 2.310 2.430 4.600 658 242 0.153 1 2.700 89.800 0.110 2.430 2.580 6.100 981 263 0.110 1 3.700 99.200 0.082 2.580 2.760 6.700 919 245 0.082 1 3.800 100.000 0.074 2.760 2.980 8.700 863 228 0.074 1 3.800 100.000 0.053 2.980 3.260 10.700 829 219 0.053 1 3.800 99.700 0.052 3.260 3.650 7.500 675 185 0.052 1 3.600 98.500 0.058 3.650 4.210 9.800 634 179 0.058 1 3.500 100.000 0.040 4.210 5.160 14.900 531 150 0.040 1 3.500 99.600 0.045 5.160 7.290 12.100 389 118 0.045 1 3.300 96.100 0.043 7.290 22.010 14.800 183 59 0.043 1 3.100 80.500 data scaling Phil R. Evans pre@mrc-lmb.cam.ac.uk 2010/01/06 Fortran_77 http://www.ccp4.ac.uk/dist/html/scala.html SCALA other 3.3.16 phasing Randy J. Read cimr-phaser@lists.cam.ac.uk Wed Jun 24 14:00:05 2009 http://www-structmed.cimr.cam.ac.uk/phaser/ PHASER program 2.1.4 refinement Garib N. Murshudov garib@ysbl.york.ac.uk Fortran_77 http://www.ccp4.ac.uk/dist/html/refmac5.html REFMAC program data extraction PDB deposit@deposit.rcsb.org June 10, 2010 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.10 data collection ADSC Quantum data reduction XDS The first crystal structure of a human telomeric G-quadruplex DNA bound to a metal-containing ligand (a nickel complex) 1 N N 2 N N 2 N N 2 N N 3 N N 4 N N metalc 2.721 X DG 1002 A O6 DG 2 1_555 X K 2014 C K K 1_555 metalc 2.353 X DG 1002 A O6 DG 2 1_555 X K 2015 D K K 1_555 metalc 2.882 X DG 1003 A O6 DG 3 1_555 X K 2013 B K K 1_555 metalc 2.951 X DG 1003 A O6 DG 3 1_555 X K 2014 C K K 1_555 metalc 2.876 X DG 1004 A O6 DG 4 1_555 X K 2013 B K K 1_555 metalc 2.750 X DG 1008 A O6 DG 8 1_555 X K 2014 C K K 1_555 metalc 2.411 X DG 1008 A O6 DG 8 1_555 X K 2015 D K K 1_555 metalc 2.739 X DG 1009 A O6 DG 9 1_555 X K 2013 B K K 1_555 metalc 2.842 X DG 1009 A O6 DG 9 1_555 X K 2014 C K K 1_555 metalc 2.582 X DG 1010 A O6 DG 10 1_555 X K 2013 B K K 1_555 hydrog TYPE_6_PAIR X DG 1002 A N1 DG 2 1_555 X DG 1008 A O6 DG 8 1_555 hydrog TYPE_6_PAIR X DG 1002 A N2 DG 2 1_555 X DG 1008 A N7 DG 8 1_555 hydrog TYPE_6_PAIR X DG 1003 A N1 DG 3 1_555 X DG 1009 A O6 DG 9 1_555 hydrog TYPE_6_PAIR X DG 1003 A N2 DG 3 1_555 X DG 1009 A N7 DG 9 1_555 hydrog TYPE_6_PAIR X DG 1004 A N1 DG 4 1_555 X DG 1010 A O6 DG 10 1_555 hydrog TYPE_6_PAIR X DG 1004 A N2 DG 4 1_555 X DG 1010 A N7 DG 10 1_555 DNA Parallel, telomere, nickel, drug, DNA, metal complex 3QSF PDB 1 3QSF 1001 1012 3QSF 1001 1012 3QSF X 1 1 12 BINDING SITE FOR RESIDUE K X 2013 X K 2013 Software 10 BINDING SITE FOR RESIDUE K X 2014 X K 2014 Software 12 BINDING SITE FOR RESIDUE K X 2015 X K 2015 Software 10 BINDING SITE FOR RESIDUE NUF X 3016 X NUF 3016 Software 8 X DG 1003 A DG 3 10 1_555 X DG 1003 A DG 3 10 2_665 X DG 1004 A DG 4 10 1_555 X DG 1004 A DG 4 10 2_665 X DG 1009 A DG 9 10 2_665 X DG 1009 A DG 9 10 1_555 X DG 1010 A DG 10 10 2_665 X DG 1010 A DG 10 10 1_555 X K 2014 C K 10 2_665 X K 2014 C K 10 1_555 X DG 1002 A DG 2 12 1_555 X DG 1002 A DG 2 12 2_665 X DG 1003 A DG 3 12 2_665 X DG 1003 A DG 3 12 1_555 X DG 1008 A DG 8 12 2_665 X DG 1008 A DG 8 12 1_555 X DG 1009 A DG 9 12 1_555 X DG 1009 A DG 9 12 2_665 X K 2013 B K 12 2_665 X K 2013 B K 12 1_555 X K 2015 D K 12 2_665 X K 2015 D K 12 1_555 X DG 1002 A DG 2 10 1_555 X DG 1002 A DG 2 10 2_665 X DG 1002 A DG 2 10 3_656 X DG 1002 A DG 2 10 4_566 X DG 1008 A DG 8 10 1_555 X DG 1008 A DG 8 10 2_665 X DG 1008 A DG 8 10 3_656 X DG 1008 A DG 8 10 4_566 X K 2014 C K 10 2_665 X K 2014 C K 10 1_555 X DG 1004 A DG 4 8 1_555 X DG 1004 A DG 4 8 2_665 X DT 1005 A DT 5 8 1_555 X DG 1010 A DG 10 8 1_555 X DG 1010 A DG 10 8 2_665 X DT 1011 A DT 11 8 4_565 X DT 1011 A DT 11 8 1_555 X DT 1011 A DT 11 8 2_665 21 C 2 2 2