1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Junker, H.-D. Hoehn, S.T. Bunt, R.C. Marathius, V. Chen, J. Turner, C.J. Stubbe, J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 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 C2 H5 O6 P 156.031 2-PHOSPHOGLYCOLIC ACID non-polymer UK Nucleic Acids Res. NARHAD 0389 0305-1048 30 5497 5508 10.1093/nar/gkf681 12490718 Synthesis, Characterization and Solution Structure of Tethered Oligonucleotides Containing an Internal 3'-Phosphoglycolate, 5'-Phosphate Gapped Lesion 2002 10.2210/pdb1n0k/pdb pdb_00001n0k 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M 1 1.0 1818.231 5'-D(*CP*CP*AP*AP*GP*G)-3' 1 syn polymer 1840.227 5'-D(P*CP*TP*TP*GP*GP*G)-3' 1 syn polymer 3952.574 5'-D(*CP*CP*CP*AP*AP*GP*GP*CP*CP*TP*TP*GP*G)-3' 1 syn polymer 156.031 2-PHOSPHOGLYCOLIC ACID 1 man non-polymer no no (DC)(DC)(DA)(DA)(DG)(DG) CCAAGG A polydeoxyribonucleotide no no (DC)(DT)(DT)(DG)(DG)(DG) CTTGGG B polydeoxyribonucleotide no no (DC)(DC)(DC)(DA)(DA)(DG)(DG)(DC)(DC)(DT)(DT)(DG)(DG) CCCAAGGCCTTGG C polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n n n -0.681 1 22 A 1 C 26 -8.103 A_DC1:DG26_C 1 2.223 -0.702 -0.261 -1.437 -7.719 1 19 A 2 C 25 -1.150 A_DC2:DG25_C 2 -0.272 0.408 0.003 -0.204 -1.591 1 20 A 3 C 24 -4.763 A_DA3:DT24_C 3 -15.103 0.188 -0.237 -0.136 1.925 1 20 A 4 C 23 -1.861 A_DA4:DT23_C 4 -11.139 -0.205 0.395 -0.259 3.992 1 19 A 5 C 22 -0.420 A_DG5:DC22_C 5 -8.669 -0.526 0.164 -0.225 -9.570 1 19 A 6 C 21 -2.837 A_DG6:DC21_C 6 3.861 -0.163 -0.414 -0.200 -1.438 1 19 B 8 C 19 -4.880 B_DC8:DG19_C 7 -1.044 0.635 0.437 -0.361 5.622 1 20 B 9 C 18 -3.007 B_DT9:DA18_C 8 -6.228 0.195 0.409 -0.240 -4.145 1 20 B 10 C 17 -7.367 B_DT10:DA17_C 9 -7.672 -0.115 0.535 -0.413 11.291 1 19 B 11 C 16 -8.188 B_DG11:DC16_C 10 -17.548 -0.111 0.632 -0.392 -6.773 1 19 B 12 C 15 -6.810 B_DG12:DC15_C 11 -17.724 0.058 0.374 -0.319 -19.415 1 19 B 13 C 14 -17.920 B_DG13:DC14_C 12 -12.084 -1.015 -0.455 -0.780 4.185 58.590 A A 1 2 -34.604 C C 26 25 4.826 -32.266 0.323 -0.102 AA_DC1DC2:DG25DG26_CC 1 -0.597 0.641 49.573 2.452 -0.377 3.047 38.319 A A 2 3 5.485 C C 25 24 3.358 3.548 -0.313 -0.865 AA_DC2DA3:DT24DG25_CC 2 11.024 -17.042 36.590 -1.763 1.862 2.894 35.023 A A 3 4 -1.208 C C 24 23 2.966 -0.722 0.069 -0.026 AA_DA3DA4:DT23DT24_CC 3 -7.115 11.902 34.308 0.055 -1.084 3.342 34.957 A A 4 5 -7.905 C C 23 22 3.289 -4.733 0.188 -0.727 AA_DA4DG5:DC22DT23_CC 4 -1.930 3.224 34.593 -0.483 -0.610 3.869 34.642 A A 5 6 -4.652 C C 22 21 3.742 -2.758 0.399 -1.534 AA_DG5DG6:DC21DC22_CC 5 4.911 -8.282 34.194 -2.080 0.214 6.990 83.833 A B 6 8 -1.364 C C 21 19 6.963 -1.823 1.367 -0.467 AB_DG6DC8:DG19DC21_CC 6 1.583 -1.185 83.804 -0.257 -0.943 3.362 32.547 B B 8 9 -18.452 C C 19 18 3.293 -10.169 0.483 -0.662 BB_DC8DT9:DA18DG19_CC 7 2.195 -3.982 30.882 0.675 -0.462 3.489 36.366 B B 9 10 8.817 C C 18 17 3.595 5.482 -0.589 -0.294 BB_DT9DT10:DA17DA18_CC 8 1.410 -2.268 35.938 -1.303 1.158 2.952 38.196 B B 10 11 -2.494 C C 17 16 3.022 -1.625 -0.177 0.125 BB_DT10DG11:DC16DA17_CC 9 6.010 -9.223 37.703 0.380 0.967 3.840 44.092 B B 11 12 -1.560 C C 16 15 3.794 -1.167 0.710 0.526 BB_DG11DG12:DC15DC16_CC 10 6.168 -8.242 43.665 0.830 -0.266 3.353 41.878 B B 12 13 -14.754 C C 15 14 3.504 -10.400 -1.625 1.093 BB_DG12DG13:DC14DC15_CC 11 -6.834 9.696 40.066 2.695 1.507 database_2 pdbx_struct_assembly pdbx_struct_oper_list struct_conn struct_site repository Initial release Version format compliance Version format compliance Database references Derived calculations 1 0 2003-01-07 1 1 2008-04-28 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id This entry is the ensemble model for PDB ENTRY 1N0K ENSEMBLE: 1G5K is the structure of the oligonucleotide containing the phosphoglycolate lesion without the bleomycin bound. Minimized average structure: NMR STRUCTURE OF AN OLIGONUCLEOTIDE CONTAINING A PHOSPHOGLYCOLATE LESION RCSB Y RCSB 2002-10-14 REL PGA 2-PHOSPHOGLYCOLIC ACID minimum rmsd and nmr constraints violation 10 1 PECOSY TOCSY NOESY HSQC GE-HSQC 40 mM NaH2PO4 6.9 1 atm 293.15 K conjugate gradient minimized average structure 1.4 mM oligonucleotide Brunger refinement XPLOR 3.851 Brunger structure solution XPLOR 3.851 500 custom build 600 custom build 750 custom build C 7 4 PGA PGA 7 A C 1 n 1 DC 1 A C 2 n 2 DC 2 A A 3 n 3 DA 3 A A 4 n 4 DA 4 A G 5 n 5 DG 5 A G 6 n 6 DG 6 A C 7 n 1 DC 8 B T 9 n 2 DT 9 B T 10 n 3 DT 10 B G 11 n 4 DG 11 B G 12 n 5 DG 12 B G 13 n 6 DG 13 B C 14 n 1 DC 14 C C 15 n 2 DC 15 C C 16 n 3 DC 16 C A 17 n 4 DA 17 C A 18 n 5 DA 18 C G 19 n 6 DG 19 C G 20 n 7 DG 20 C C 21 n 8 DC 21 C C 22 n 9 DC 22 C T 23 n 10 DT 23 C T 24 n 11 DT 24 C G 25 n 12 DG 25 C G 26 n 13 DG 26 C author_defined_assembly 3 trimeric 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 C H41 O6 DC DG 1 26 0.69 1 A C N3 H1 DC DG 1 26 0.76 1 A C O2 H21 DC DG 1 26 1.02 1 A C H41 C6 DC DG 1 26 1.19 1 A C N4 O6 DC DG 1 26 1.38 1 A C C4 H1 DC DG 1 26 1.39 1 B C O4 H61 DT DA 10 17 1.55 1 A C C2 H21 DC DG 1 26 1.59 1 B C O6 H41 DG DC 13 14 1.60 1 A C H42 O6 DC DG 1 26 1.60 1 A C N3 N1 DC DG 1 26 1.66 1 A C O2 N2 DC DG 1 26 1.72 1 A C N4 C6 DC DG 1 26 2.03 1 A DA 3 0.162 SIDE CHAIN 1 A DG 6 0.053 SIDE CHAIN 1 B DT 9 0.080 SIDE CHAIN 1 B DT 10 0.074 SIDE CHAIN 1 B DG 11 0.075 SIDE CHAIN 1 C DC 15 0.118 SIDE CHAIN 1 C DC 16 0.188 SIDE CHAIN 1 C DA 17 0.056 SIDE CHAIN 1 C DG 19 0.060 SIDE CHAIN 1 C DT 23 0.154 SIDE CHAIN 1 3.08 0.30 108.30 111.38 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 -3.41 0.40 120.30 116.89 A A A C6 N1 C2 DC DC DC 1 1 1 N 1 3.40 0.50 117.40 120.80 A A A C4 C5 C6 DC DC DC 1 1 1 N 1 -4.76 0.70 121.90 117.14 A A A N3 C2 O2 DC DC DC 1 1 1 N 1 2.44 0.30 108.30 110.74 A A A O4' C1' N1 DC DC DC 2 2 2 N 1 7.27 1.20 119.70 126.97 A A A C3' O3' P DC DC DA 2 2 3 Y 1 10.68 1.20 119.70 130.38 A A A C3' O3' P DA DA DA 3 3 4 Y 1 12.67 1.60 120.90 133.57 B B B P O5' C5' DC DC DC 8 8 8 N 1 3.76 0.30 108.30 112.06 B B B O4' C1' N1 DC DC DC 8 8 8 N 1 4.68 0.60 118.90 123.58 B B B N1 C2 O2 DC DC DC 8 8 8 N 1 9.60 1.20 119.70 129.30 B B B C3' O3' P DC DC DT 8 8 9 Y 1 5.18 0.30 108.30 113.48 B B B O4' C1' N1 DT DT DT 9 9 9 N 1 -4.16 0.60 122.30 118.14 B B B N3 C2 O2 DT DT DT 9 9 9 N 1 15.54 1.60 120.90 136.44 B B B P O5' C5' DT DT DT 10 10 10 N 1 4.36 0.70 110.30 114.66 B B B C1' O4' C4' DT DT DT 10 10 10 N 1 -4.59 0.60 122.30 117.71 B B B N3 C2 O2 DT DT DT 10 10 10 N 1 -4.94 0.60 119.00 114.06 B B B C4 C5 C7 DT DT DT 10 10 10 N 1 1.98 0.30 108.30 110.28 B B B O4' C1' N9 DG DG DG 11 11 11 N 1 5.11 0.70 119.90 125.01 B B B N3 C2 N2 DG DG DG 11 11 11 N 1 12.99 1.60 120.90 133.89 B B B P O5' C5' DG DG DG 12 12 12 N 1 1.85 0.30 108.30 110.15 B B B O4' C1' N9 DG DG DG 12 12 12 N 1 5.76 0.70 119.90 125.66 B B B N3 C2 N2 DG DG DG 12 12 12 N 1 6.18 0.70 110.30 116.48 B B B C1' O4' C4' DG DG DG 13 13 13 N 1 2.77 0.30 108.30 111.07 B B B O4' C1' N9 DG DG DG 13 13 13 N 1 3.39 0.50 111.90 115.29 B B B C2 N3 C4 DG DG DG 13 13 13 N 1 -3.34 0.50 128.60 125.26 B B B N3 C4 C5 DG DG DG 13 13 13 N 1 -6.17 0.90 116.20 110.03 B B B N1 C2 N2 DG DG DG 13 13 13 N 1 8.46 0.70 119.90 128.36 B B B N3 C2 N2 DG DG DG 13 13 13 N 1 4.63 0.60 118.90 123.53 C C C N1 C2 O2 DC DC DC 14 14 14 N 1 -3.49 0.40 120.30 116.81 C C C C6 N1 C2 DC DC DC 15 15 15 N 1 7.28 1.20 119.70 126.98 C C C C3' O3' P DC DC DC 15 15 16 Y 1 -2.73 0.40 120.30 117.57 C C C C6 N1 C2 DC DC DC 16 16 16 N 1 10.02 1.20 119.70 129.72 C C C C3' O3' P DC DC DA 16 16 17 Y 1 9.45 1.20 119.70 129.15 C C C C3' O3' P DA DA DA 17 17 18 Y 1 4.13 0.60 118.60 122.73 C C C N1 C6 N6 DA DA DA 18 18 18 N 1 9.00 1.20 119.70 128.70 C C C C3' O3' P DA DA DG 18 18 19 Y 1 1.83 0.30 108.30 110.13 C C C O4' C1' N9 DG DG DG 19 19 19 N 1 5.26 0.70 119.90 125.16 C C C N3 C2 N2 DG DG DG 19 19 19 N 1 8.40 1.20 119.70 128.10 C C C C3' O3' P DG DG DG 19 19 20 Y 1 5.40 0.70 110.30 115.70 C C C C1' O4' C4' DG DG DG 20 20 20 N 1 9.30 1.20 102.50 111.80 C C C C3' C2' C1' DG DG DG 20 20 20 N 1 2.21 0.30 108.30 110.51 C C C O4' C1' N9 DG DG DG 20 20 20 N 1 4.94 0.70 119.90 124.84 C C C N3 C2 N2 DG DG DG 20 20 20 N 1 7.42 1.20 119.70 127.12 C C C C3' O3' P DC DC DC 21 21 22 Y 1 7.72 1.20 119.70 127.42 C C C C3' O3' P DC DC DT 22 22 23 Y 1 2.87 0.30 108.30 111.17 C C C O4' C1' N1 DT DT DT 23 23 23 N 1 8.58 1.20 119.70 128.28 C C C C3' O3' P DT DT DG 24 24 25 Y 1 3.03 0.50 111.90 114.93 C C C C2 N3 C4 DG DG DG 26 26 26 N 1 4.72 0.70 119.90 124.62 C C C N3 C2 N2 DG DG DG 26 26 26 N 1 A A C2 O2 DC DC 1 1 -0.057 0.009 1.240 1.183 N 1 A A N1 C6 DC DC 1 1 -0.047 0.006 1.367 1.320 N 1 A A N3 C4 DC DC 1 1 -0.067 0.007 1.335 1.268 N 1 A A N9 C4 DA DA 4 4 0.037 0.006 1.374 1.411 N 1 B B P OP1 DC DC 8 8 0.124 0.017 1.485 1.609 N 1 B B P OP2 DC DC 8 8 0.125 0.017 1.485 1.610 N 1 B B P O5' DC DC 8 8 -0.153 0.010 1.593 1.440 N 1 B B O3' C3' DC DC 8 8 -0.055 0.006 1.419 1.364 N 1 B B O3' P DC DT 8 9 -0.127 0.012 1.607 1.480 Y 1 B B P OP1 DT DT 9 9 -0.121 0.017 1.485 1.364 N 1 B B P OP2 DT DT 9 9 -0.108 0.017 1.485 1.377 N 1 B B C6 N1 DT DT 9 9 0.044 0.007 1.378 1.422 N 1 B B P O5' DT DT 10 10 -0.086 0.010 1.593 1.507 N 1 B B O4' C1' DT DT 10 10 -0.073 0.012 1.418 1.345 N 1 B B O3' C3' DT DT 10 10 -0.044 0.006 1.419 1.375 N 1 B B C5 C7 DT DT 10 10 -0.038 0.006 1.496 1.458 N 1 B B O3' P DT DG 10 11 -0.090 0.012 1.607 1.517 Y 1 B B C4' C3' DG DG 13 13 -0.064 0.010 1.521 1.457 N 1 B B O3' C3' DG DG 13 13 -0.077 0.006 1.419 1.342 N 1 C C O5' C5' DC DC 14 14 -0.231 0.025 1.418 1.187 N 1 C C O3' P DC DC 14 15 -0.090 0.012 1.607 1.517 Y 1 C C P O5' DC DC 15 15 -0.070 0.010 1.593 1.523 N 1 C C O3' P DC DC 15 16 -0.075 0.012 1.607 1.532 Y 1 C C O5' C5' DC DC 21 21 -0.167 0.025 1.418 1.251 N 1 C C C2' C1' DC DC 21 21 0.066 0.010 1.519 1.585 N 1 C C N1 C2 DT DT 24 24 0.055 0.008 1.376 1.431 N minimized average NMR Structure of duplex DNA d(CCAAGGXCTTGGG), X is a 3' phosphoglycolate, 5'phosphate gapped lesion 1 N N 2 N N 3 N N 4 N N covale 1.621 one A DG 6 A O3' DG 6 1_555 A PGA 7 D P PGA 1_555 hydrog REVERSED WATSON-CRICK A DC 1 A N3 DC 1 1_555 C DG 26 C N2 DG 13 1_555 hydrog REVERSED WATSON-CRICK A DC 1 A O2 DC 1 1_555 C DG 26 C N1 DG 13 1_555 hydrog WATSON-CRICK A DC 2 A N3 DC 2 1_555 C DG 25 C N1 DG 12 1_555 hydrog WATSON-CRICK A DC 2 A N4 DC 2 1_555 C DG 25 C O6 DG 12 1_555 hydrog WATSON-CRICK A DC 2 A O2 DC 2 1_555 C DG 25 C N2 DG 12 1_555 hydrog WATSON-CRICK A DA 3 A N1 DA 3 1_555 C DT 24 C N3 DT 11 1_555 hydrog WATSON-CRICK A DA 3 A N6 DA 3 1_555 C DT 24 C O4 DT 11 1_555 hydrog WATSON-CRICK A DA 4 A N1 DA 4 1_555 C DT 23 C N3 DT 10 1_555 hydrog WATSON-CRICK A DA 4 A N6 DA 4 1_555 C DT 23 C O4 DT 10 1_555 hydrog WATSON-CRICK A DG 5 A N1 DG 5 1_555 C DC 22 C N3 DC 9 1_555 hydrog WATSON-CRICK A DG 5 A N2 DG 5 1_555 C DC 22 C O2 DC 9 1_555 hydrog WATSON-CRICK A DG 5 A O6 DG 5 1_555 C DC 22 C N4 DC 9 1_555 hydrog WATSON-CRICK A DG 6 A N1 DG 6 1_555 C DC 21 C N3 DC 8 1_555 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 C DC 21 C O2 DC 8 1_555 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 C DC 21 C N4 DC 8 1_555 hydrog WATSON-CRICK B DC 8 B N3 DC 1 1_555 C DG 19 C N1 DG 6 1_555 hydrog WATSON-CRICK B DC 8 B N4 DC 1 1_555 C DG 19 C O6 DG 6 1_555 hydrog WATSON-CRICK B DC 8 B O2 DC 1 1_555 C DG 19 C N2 DG 6 1_555 hydrog WATSON-CRICK B DT 9 B N3 DT 2 1_555 C DA 18 C N1 DA 5 1_555 hydrog WATSON-CRICK B DT 9 B O4 DT 2 1_555 C DA 18 C N6 DA 5 1_555 hydrog DT-DC MISPAIR B DT 10 B O4 DT 3 1_555 C DC 16 C N4 DC 3 1_555 hydrog WATSON-CRICK B DT 10 B N3 DT 3 1_555 C DA 17 C N1 DA 4 1_555 hydrog WATSON-CRICK B DT 10 B O4 DT 3 1_555 C DA 17 C N6 DA 4 1_555 hydrog WATSON-CRICK B DG 11 B N1 DG 4 1_555 C DC 16 C N3 DC 3 1_555 hydrog WATSON-CRICK B DG 11 B N2 DG 4 1_555 C DC 16 C O2 DC 3 1_555 hydrog WATSON-CRICK B DG 11 B O6 DG 4 1_555 C DC 16 C N4 DC 3 1_555 hydrog WATSON-CRICK B DG 12 B N1 DG 5 1_555 C DC 15 C N3 DC 2 1_555 hydrog WATSON-CRICK B DG 12 B N2 DG 5 1_555 C DC 15 C O2 DC 2 1_555 hydrog WATSON-CRICK B DG 12 B O6 DG 5 1_555 C DC 15 C N4 DC 2 1_555 hydrog WATSON-CRICK B DG 13 B N1 DG 6 1_555 C DC 14 C N3 DC 1 1_555 hydrog WATSON-CRICK B DG 13 B N2 DG 6 1_555 C DC 14 C O2 DC 1 1_555 hydrog WATSON-CRICK B DG 13 B O6 DG 6 1_555 C DC 14 C N4 DC 1 1_555 DNA DNA, bleomycin, phosphoglycolate 1N0K PDB 1 1N0K 1N0K PDB 2 1N0K 1N0K PDB 3 1N0K 1 6 1N0K 1 6 1N0K A 1 1 6 8 13 1N0K 8 13 1N0K B 2 1 6 14 26 1N0K 14 26 1N0K C 3 1 13 BINDING SITE FOR RESIDUE PGA A 7 A PGA 7 Software 1 A DG 6 A DG 6 1 1_555