0.054333 0.000000 0.000000 0.000000 0.032501 0.000000 0.000000 0.000000 0.023174 0.00000 0.00000 0.00000 Egli, M. Williams, L.D. Gao, Q. Rich, A. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 18.405 30.768 43.152 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 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 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 N N 76 N C N 77 N C N 78 N C N 79 N N N 80 N C N 81 N C N 82 N C N 83 N C N 84 N N N 85 N C N 86 N C N 87 N C N 88 N N 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 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 H N 111 N H N 112 N H N 113 N H N 114 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 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 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 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 sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing N 115 N sing US Biochemistry BICHAW 0033 0006-2960 30 11388 11402 10.1021/bi00112a005 1742278 Structure of the pure-spermine form of Z-DNA (magnesium free) at 1-A resolution. 1991 10.2210/pdb1d48/pdb pdb_00001d48 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 ROOM TEMPERATURE 1 DIFFRACTOMETER RIGAKU AFC-5R x-ray 1 1.0 ROTATING ANODE 1810.205 DNA (5'-D(*CP*GP*CP*GP*CP*G)-3') 2 syn polymer 202.340 SPERMINE 1 syn non-polymer 18.015 water 47 nat water no no (DC)(DG)(DC)(DG)(DC)(DG) CGCGCG A,B polydeoxyribonucleotide n n n n n n 1.69 27.11 VAPOR DIFFUSION, SITTING DROP 7.00 pH 7.00, VAPOR DIFFUSION, SITTING DROP ROOM TEMPERATURE WATER 1 SPERMINE 1 WATER 2 MPD 2 4.165 1 19 A 1 B 12 1.246 A_DC1:DG12_B 1 -1.134 -0.251 0.188 -0.116 -4.993 1 19 A 2 B 11 1.442 A_DG2:DC11_B 2 -0.272 0.324 -0.017 -0.188 2.909 1 19 A 3 B 10 1.732 A_DC3:DG10_B 3 3.257 -0.255 -0.044 -0.126 -6.176 1 19 A 4 B 9 2.665 A_DG4:DC9_B 4 4.605 0.272 0.104 -0.177 2.638 1 19 A 5 B 8 1.782 A_DC5:DG8_B 5 -4.592 -0.245 0.047 -0.179 -3.530 1 19 A 6 B 7 1.557 A_DG6:DC7_B 6 3.052 0.262 0.079 -0.161 4.376 -9.925 A A 1 2 9.649 B B 12 11 3.733 -1.639 0.209 5.513 AA_DC1DG2:DC11DG12_BB 1 2.816 16.581 -9.376 -27.899 8.029 3.171 -52.548 A A 2 3 7.144 B B 11 10 3.247 -6.311 0.546 -0.435 AA_DG2DC3:DG10DC11_BB 2 0.677 0.767 -52.190 0.898 0.661 3.217 -9.482 A A 3 4 -2.721 B B 10 9 3.680 0.444 -0.277 5.418 AA_DC3DG4:DC9DG10_BB 3 -2.521 -15.438 -9.131 -33.770 -7.314 3.353 -50.438 A A 4 5 1.285 B B 9 8 3.364 -1.095 -0.495 -1.032 AA_DG4DC5:DG8DC9_BB 4 1.259 1.478 -50.412 1.291 -0.489 2.032 -9.459 A A 5 6 -15.469 B B 8 7 3.713 2.503 0.040 5.550 AA_DC5DG6:DC7DG8_BB 5 1.861 11.502 -8.931 -38.390 3.764 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 1992-04-15 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 NDB 1991-09-11 REL SPM SPERMINE HOH water SPM 13 2 SPM SPM 13 A HOH 14 3 HOH HOH 14 A HOH 15 3 HOH HOH 15 A HOH 18 3 HOH HOH 18 A HOH 19 3 HOH HOH 19 A HOH 20 3 HOH HOH 20 A HOH 21 3 HOH HOH 21 A HOH 24 3 HOH HOH 24 A HOH 26 3 HOH HOH 26 A HOH 28 3 HOH HOH 28 A HOH 29 3 HOH HOH 29 A HOH 33 3 HOH HOH 33 A HOH 34 3 HOH HOH 34 A HOH 35 3 HOH HOH 35 A HOH 41 3 HOH HOH 41 A HOH 42 3 HOH HOH 42 A HOH 43 3 HOH HOH 43 A HOH 44 3 HOH HOH 44 A HOH 46 3 HOH HOH 46 A HOH 56 3 HOH HOH 56 A HOH 57 3 HOH HOH 57 A HOH 16 3 HOH HOH 16 B HOH 17 3 HOH HOH 17 B HOH 22 3 HOH HOH 22 B HOH 23 3 HOH HOH 23 B HOH 25 3 HOH HOH 25 B HOH 27 3 HOH HOH 27 B HOH 30 3 HOH HOH 30 B HOH 31 3 HOH HOH 31 B HOH 32 3 HOH HOH 32 B HOH 36 3 HOH HOH 36 B HOH 37 3 HOH HOH 37 B HOH 38 3 HOH HOH 38 B HOH 39 3 HOH HOH 39 B HOH 40 3 HOH HOH 40 B HOH 45 3 HOH HOH 45 B HOH 47 3 HOH HOH 47 B HOH 48 3 HOH HOH 48 B HOH 49 3 HOH HOH 49 B HOH 50 3 HOH HOH 50 B HOH 51 3 HOH HOH 51 B HOH 52 3 HOH HOH 52 B HOH 53 3 HOH HOH 53 B HOH 54 3 HOH HOH 54 B HOH 55 3 HOH HOH 55 B HOH 58 3 HOH HOH 58 B HOH 59 3 HOH HOH 59 B HOH 60 3 HOH HOH 60 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 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 4.58 0.50 119.90 124.48 A A A C2 N3 C4 DC DC DC 1 1 1 N 1 -5.33 0.40 121.90 116.57 A A A N3 C4 C5 DC DC DC 1 1 1 N 1 6.22 0.60 118.90 125.12 A A A N1 C2 O2 DC DC DC 1 1 1 N 1 4.91 0.70 120.20 125.11 A A A C5 C4 N4 DC DC DC 1 1 1 N 1 -5.77 0.60 125.10 119.33 A A A C6 N1 C2 DG DG DG 2 2 2 N 1 4.42 0.60 123.90 128.32 A A A N1 C2 N3 DG DG DG 2 2 2 N 1 6.59 0.50 111.50 118.09 A A A C5 C6 N1 DG DG DG 2 2 2 N 1 -8.87 0.70 119.90 111.03 A A A N3 C2 N2 DG DG DG 2 2 2 N 1 -6.98 0.60 128.60 121.62 A A A C5 C6 O6 DG DG DG 2 2 2 N 1 -2.70 0.40 121.90 119.20 A A A N3 C4 C5 DC DC DC 3 3 3 N 1 4.16 0.60 118.90 123.06 A A A N1 C2 O2 DC DC DC 3 3 3 N 1 3.69 0.60 123.90 127.59 A A A N1 C2 N3 DG DG DG 4 4 4 N 1 3.96 0.50 111.50 115.46 A A A C5 C6 N1 DG DG DG 4 4 4 N 1 -6.32 0.70 119.90 113.58 A A A N3 C2 N2 DG DG DG 4 4 4 N 1 -4.14 0.60 128.60 124.46 A A A C5 C6 O6 DG DG DG 4 4 4 N 1 6.54 0.50 119.90 126.44 A A A C2 N3 C4 DC DC DC 5 5 5 N 1 -5.55 0.40 121.90 116.35 A A A N3 C4 C5 DC DC DC 5 5 5 N 1 5.08 0.60 118.90 123.98 A A A N1 C2 O2 DC DC DC 5 5 5 N 1 -4.18 0.60 125.10 120.92 A A A C6 N1 C2 DG DG DG 6 6 6 N 1 5.42 0.50 111.50 116.92 A A A C5 C6 N1 DG DG DG 6 6 6 N 1 3.51 0.40 110.80 114.31 A A A C4 C5 N7 DG DG DG 6 6 6 N 1 -6.71 0.70 119.90 113.19 A A A N3 C2 N2 DG DG DG 6 6 6 N 1 -4.90 0.60 128.60 123.70 A A A C5 C6 O6 DG DG DG 6 6 6 N 1 -3.45 0.40 121.90 118.45 B B B N3 C4 C5 DC DC DC 7 7 7 N 1 -6.76 0.80 109.40 102.64 B B B O5' C5' C4' DG DG DG 8 8 8 N 1 -5.12 0.60 125.10 119.98 B B B C6 N1 C2 DG DG DG 8 8 8 N 1 5.11 0.60 123.90 129.01 B B B N1 C2 N3 DG DG DG 8 8 8 N 1 -3.33 0.50 111.90 108.57 B B B C2 N3 C4 DG DG DG 8 8 8 N 1 5.65 0.50 111.50 117.15 B B B C5 C6 N1 DG DG DG 8 8 8 N 1 -7.39 0.70 119.90 112.51 B B B N3 C2 N2 DG DG DG 8 8 8 N 1 -5.62 0.60 128.60 122.98 B B B C5 C6 O6 DG DG DG 8 8 8 N 1 3.10 0.50 119.90 123.00 B B B C2 N3 C4 DC DC DC 9 9 9 N 1 -3.21 0.40 121.90 118.69 B B B N3 C4 C5 DC DC DC 9 9 9 N 1 5.80 0.60 118.90 124.70 B B B N1 C2 O2 DC DC DC 9 9 9 N 1 -5.40 0.80 109.40 104.00 B B B O5' C5' C4' DG DG DG 10 10 10 N 1 -4.53 0.60 125.10 120.57 B B B C6 N1 C2 DG DG DG 10 10 10 N 1 5.70 0.50 111.50 117.20 B B B C5 C6 N1 DG DG DG 10 10 10 N 1 5.82 0.90 116.20 122.02 B B B N1 C2 N2 DG DG DG 10 10 10 N 1 -8.81 0.70 119.90 111.09 B B B N3 C2 N2 DG DG DG 10 10 10 N 1 -6.04 0.60 128.60 122.56 B B B C5 C6 O6 DG DG DG 10 10 10 N 1 -4.97 0.80 102.40 97.43 B B B C3' C2' C1' DC DC DC 11 11 11 N 1 4.13 0.50 119.90 124.03 B B B C2 N3 C4 DC DC DC 11 11 11 N 1 -3.99 0.40 121.90 117.91 B B B N3 C4 C5 DC DC DC 11 11 11 N 1 4.42 0.60 118.90 123.32 B B B N1 C2 O2 DC DC DC 11 11 11 N 1 4.70 0.70 120.20 124.90 B B B C5 C4 N4 DC DC DC 11 11 11 N 1 -4.57 0.60 125.10 120.53 B B B C6 N1 C2 DG DG DG 12 12 12 N 1 4.97 0.60 123.90 128.87 B B B N1 C2 N3 DG DG DG 12 12 12 N 1 -3.19 0.50 111.90 108.71 B B B C2 N3 C4 DG DG DG 12 12 12 N 1 4.30 0.50 111.50 115.80 B B B C5 C6 N1 DG DG DG 12 12 12 N 1 -6.97 0.70 119.90 112.93 B B B N3 C2 N2 DG DG DG 12 12 12 N 1 -5.46 0.60 128.60 123.14 B B B C5 C6 O6 DG DG DG 12 12 12 N 1 A A O3' C3' DC DC 1 1 -0.052 0.006 1.419 1.367 N 1 A A N3 C4 DC DC 1 1 0.043 0.007 1.335 1.378 N 1 A A P OP2 DG DG 2 2 -0.114 0.017 1.485 1.371 N 1 A A C3' C2' DG DG 2 2 -0.061 0.008 1.516 1.455 N 1 A A O4' C4' DG DG 2 2 -0.072 0.010 1.446 1.374 N 1 A A C6 N1 DG DG 2 2 -0.048 0.007 1.391 1.343 N 1 A A C2 N2 DG DG 2 2 -0.091 0.010 1.341 1.250 N 1 A A C6 O6 DG DG 2 2 0.057 0.009 1.237 1.294 N 1 A A C2' C1' DC DC 3 3 0.069 0.010 1.519 1.588 N 1 A A N3 C4 DC DC 3 3 0.048 0.007 1.335 1.383 N 1 A A C2' C1' DG DG 4 4 0.077 0.010 1.519 1.596 N 1 A A C6 N1 DG DG 4 4 -0.054 0.007 1.391 1.337 N 1 A A C5 N7 DG DG 4 4 -0.038 0.006 1.388 1.350 N 1 A A C8 N9 DG DG 4 4 -0.042 0.007 1.374 1.332 N 1 A A C2 N2 DG DG 4 4 -0.075 0.010 1.341 1.266 N 1 A A C6 N1 DG DG 6 6 -0.069 0.007 1.391 1.322 N 1 A A C2 N2 DG DG 6 6 -0.093 0.010 1.341 1.248 N 1 B B N3 C4 DC DC 7 7 0.045 0.007 1.335 1.380 N 1 B B C5' C4' DG DG 8 8 0.059 0.007 1.512 1.571 N 1 B B C6 N1 DG DG 8 8 -0.048 0.007 1.391 1.343 N 1 B B N7 C8 DG DG 8 8 0.040 0.006 1.305 1.345 N 1 B B C8 N9 DG DG 8 8 -0.046 0.007 1.374 1.328 N 1 B B C2 N2 DG DG 8 8 -0.088 0.010 1.341 1.253 N 1 B B C2' C1' DC DC 9 9 0.080 0.010 1.519 1.599 N 1 B B N3 C4 DC DC 9 9 0.045 0.007 1.335 1.380 N 1 B B P O5' DG DG 10 10 0.061 0.010 1.593 1.654 N 1 B B C6 N1 DG DG 10 10 -0.053 0.007 1.391 1.338 N 1 B B C2 N2 DG DG 10 10 -0.090 0.010 1.341 1.251 N 1 B B N3 C4 DC DC 11 11 0.046 0.007 1.335 1.381 N 1 B B C6 N1 DG DG 12 12 -0.049 0.007 1.391 1.342 N 1 B B C2 N2 DG DG 12 12 -0.079 0.010 1.341 1.262 N 0.1850000 1.000 8183 1 2.000 TR isotropic TR isotropic 1.000 47 301 14 240 0 fix fix 1.000 1D48 10900 8200 2.000 1 refinement PROLSQ (MODIFIED BY G.J.QUIGLEY) refinement MODIFIED BY G.J.QUIGLEY STRUCTURE OF THE PURE-SPERMINE FORM OF Z-DNA (MAGNESIUM FREE) AT 1 ANGSTROM RESOLUTION 1 N N 1 N N 2 N N 3 N N 3 N N 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, DOUBLE HELIX, DNA 1D48 PDB 1 1D48 1 6 1D48 1 6 1D48 A 1 1 6 7 12 1D48 7 12 1D48 B 1 1 6 BINDING SITE FOR RESIDUE SPM A 13 A SPM 13 Software 11 A DG 2 A DG 2 11 1_555 A DC 3 A DC 3 11 1_555 A DG 4 A DG 4 11 1_555 A HOH 21 D HOH 11 1_555 A HOH 29 D HOH 11 4_566 B DG 8 B DG 2 11 1_555 B DC 9 B DC 3 11 4_556 B DG 10 B DG 4 11 1_655 B DG 10 B DG 4 11 4_556 B DC 11 B DC 5 11 1_655 B DG 12 B DG 6 11 1_655 19 P 21 21 21