0.055617 0.000000 0.000000 0.000000 0.032499 0.000000 0.000000 0.000000 0.022341 0.00000 0.00000 0.00000 Cervi, A.R. Guy, A. Leonard, G.A. Teoule, R. Hunter, W.N. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 17.980 30.770 44.760 C10 H16 N3 O7 P 321.224 n N4-METHYL-2'-DEOXY-CYTIDINE-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 H2 O 18.015 WATER non-polymer N 1 N P N 2 N O 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 R C N 10 N N N 11 N C N 12 N C N 13 N O N 14 N N N 15 N C N 16 N N N 17 N C N 18 N C N 19 N C N 20 S C N 21 N O 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 H N 36 N H N 37 N H N 38 N O N 39 N P N 40 N O N 41 N O N 42 N O N 43 N C N 44 R C N 45 N O N 46 S C N 47 N O N 48 N C N 49 R C N 50 N N N 51 N C N 52 N O N 53 N N N 54 N C N 55 N N N 56 N C N 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 P N 74 N O N 75 N O N 76 N O N 77 N C N 78 R C N 79 N O N 80 S C N 81 N O N 82 N C N 83 R C Y 84 N N Y 85 N C Y 86 N N Y 87 N C N 88 N C N 89 N O N 90 N N N 91 N C N 92 N N N 93 N N Y 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 O N 110 N H N 111 N H N 1 N doub 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 doub N 21 N sing N 22 N doub N 23 N sing N 24 N doub N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing 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 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 N 62 N sing N 63 N sing N 64 N doub N 65 N sing 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 doub 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 Y 97 N sing Y 98 N sing Y 99 N doub N 100 N sing Y 101 N sing N 102 N sing Y 103 N doub N 104 N doub N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N doub N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N sing UK Nucleic Acids Res. NARHAD 0389 0305-1048 21 5623 5629 10.1093/nar/21.24.5623 8284207 The crystal structure of N4-methylcytosine.guanosine base-pairs in the synthetic hexanucleotide d(CGCGm4CG). 1993 10.2210/pdb133d/pdb pdb_0000133d 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 295.00 1 DIFFRACTOMETER RIGAKU AFC-5 x-ray 1 1.0 ROTATING ANODE RIGAKU RU200 1824.232 DNA (5'-D(*CP*GP*CP*GP*(C34)P*G)-3') 2 syn polymer 18.015 water 49 nat water no yes (DC)(DG)(DC)(DG)(C34)(DG) CGCGCG A,B polydeoxyribonucleotide n n n n n n 1.70 27.51 VAPOR DIFFUSION 6.50 pH 6.50, VAPOR DIFFUSION, temperature 277.00K 277.00 WATER 1 MPD 1 NA CACODYLATE 1 MGCL2 1 SPERMINE_HCL 1 WATER 2 MPD 2 3.579 1 19 A 1 B 12 2.750 A_DC1:DG12_B 1 -2.919 -0.567 0.473 -0.438 0.205 1 19 A 2 B 11 6.091 A_DG2:C3411_B 2 0.691 0.513 0.125 -0.393 1.897 1 19 A 3 B 10 -0.082 A_DC3:DG10_B 3 -3.169 -0.048 0.101 -0.242 -7.509 1 19 A 4 B 9 6.510 A_DG4:DC9_B 4 2.953 0.372 0.059 -0.212 1.441 1 19 A 5 B 8 0.065 A_C345:DG8_B 5 -2.156 -0.320 0.108 -0.511 -11.755 1 19 A 6 B 7 0.482 A_DG6:DC7_B 6 6.155 0.525 -0.206 0.039 2.449 -8.594 A A 1 2 -9.837 B B 12 11 3.825 1.426 0.349 5.211 AA_DC1DG2:C3411DG12_BB 1 3.429 23.658 -7.752 -38.423 11.097 3.405 -50.684 A A 2 3 4.038 B B 11 10 3.484 -3.454 -0.350 -1.181 AA_DG2DC3:DG10C3411_BB 2 0.523 0.611 -50.572 1.637 -0.370 4.624 -8.277 A A 3 4 9.788 B B 10 9 3.850 -1.402 0.348 5.336 AA_DC3DG4:DC9DG10_BB 3 1.028 7.174 -8.093 -31.948 6.089 3.275 -55.853 A A 4 5 5.845 B B 9 8 3.365 -5.468 -0.292 -0.886 AA_DG4C345:DG8DC9_BB 4 0.891 0.952 -55.599 1.266 -0.260 3.402 -7.355 A A 5 6 -0.889 B B 8 7 3.732 0.112 0.245 5.581 AA_C345DG6:DC7DG8_BB 5 2.202 17.430 -7.017 -43.939 10.422 chem_comp_atom chem_comp_bond database_2 struct_conn repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 1994-01-15 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_conn.pdbx_leaving_atom_flag BNL Y NDB 1993-07-29 REL REL HOH water HOH 14 2 HOH HOH 14 A HOH 15 2 HOH HOH 15 A HOH 16 2 HOH HOH 16 A HOH 19 2 HOH HOH 19 A HOH 20 2 HOH HOH 20 A HOH 24 2 HOH HOH 24 A HOH 26 2 HOH HOH 26 A HOH 27 2 HOH HOH 27 A HOH 28 2 HOH HOH 28 A HOH 29 2 HOH HOH 29 A HOH 33 2 HOH HOH 33 A HOH 34 2 HOH HOH 34 A HOH 35 2 HOH HOH 35 A HOH 38 2 HOH HOH 38 A HOH 41 2 HOH HOH 41 A HOH 42 2 HOH HOH 42 A HOH 43 2 HOH HOH 43 A HOH 44 2 HOH HOH 44 A HOH 49 2 HOH HOH 49 A HOH 50 2 HOH HOH 50 A HOH 52 2 HOH HOH 52 A HOH 53 2 HOH HOH 53 A HOH 56 2 HOH HOH 56 A HOH 57 2 HOH HOH 57 A HOH 58 2 HOH HOH 58 A HOH 59 2 HOH HOH 59 A HOH 61 2 HOH HOH 61 A HOH 13 2 HOH HOH 13 B HOH 17 2 HOH HOH 17 B HOH 18 2 HOH HOH 18 B HOH 21 2 HOH HOH 21 B HOH 22 2 HOH HOH 22 B HOH 23 2 HOH HOH 23 B HOH 25 2 HOH HOH 25 B HOH 30 2 HOH HOH 30 B HOH 31 2 HOH HOH 31 B HOH 32 2 HOH HOH 32 B HOH 36 2 HOH HOH 36 B HOH 37 2 HOH HOH 37 B HOH 39 2 HOH HOH 39 B HOH 40 2 HOH HOH 40 B HOH 45 2 HOH HOH 45 B HOH 46 2 HOH HOH 46 B HOH 47 2 HOH HOH 47 B HOH 48 2 HOH HOH 48 B HOH 51 2 HOH HOH 51 B HOH 54 2 HOH HOH 54 B HOH 55 2 HOH HOH 55 B HOH 60 2 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 C34 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 C34 11 B G 12 n 6 DG 12 B author_defined_assembly 2 dimeric A C34 5 A C34 5 DC B C34 11 B C34 5 DC 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 34 52 2.10 1 7.54 1.20 115.70 123.24 A A A C5' C4' C3' DC DC DC 1 1 1 N 1 5.75 0.30 108.30 114.05 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 -2.65 0.40 121.90 119.25 A A A N3 C4 C5 DC DC DC 1 1 1 N 1 -10.53 0.80 109.40 98.87 A A A O5' C5' C4' DG DG DG 2 2 2 N 1 4.93 0.60 106.00 110.93 A A A O4' C4' C3' DG DG DG 2 2 2 N 1 -3.93 0.60 125.10 121.17 A A A C6 N1 C2 DG DG DG 2 2 2 N 1 3.44 0.50 111.50 114.94 A A A C5 C6 N1 DG DG DG 2 2 2 N 1 12.99 1.20 119.70 132.69 A A A C3' O3' P DG DG DC 2 2 3 Y 1 -9.75 1.50 119.60 109.85 A A A OP1 P OP2 DC DC DC 3 3 3 N 1 4.43 0.30 108.30 112.73 A A A O4' C1' N1 DC DC DC 3 3 3 N 1 -8.04 0.80 109.40 101.36 A A A O5' C5' C4' DG DG DG 4 4 4 N 1 3.16 0.50 111.50 114.66 A A A C5 C6 N1 DG DG DG 4 4 4 N 1 10.57 1.20 119.70 130.27 A A A C3' O3' P DG DG C34 4 4 5 Y 1 -6.44 0.80 109.40 102.96 A A A O5' C5' C4' DG DG DG 6 6 6 N 1 1.97 0.30 108.30 110.27 A A A O4' C1' N9 DG DG DG 6 6 6 N 1 -5.61 0.90 116.20 110.59 A A A N1 C2 N2 DG DG DG 6 6 6 N 1 4.72 0.70 119.90 124.62 A A A N3 C2 N2 DG DG DG 6 6 6 N 1 -4.57 0.60 119.90 115.33 A A A N1 C6 O6 DG DG DG 6 6 6 N 1 -6.44 0.80 109.40 102.96 B B B O5' C5' C4' DG DG DG 8 8 8 N 1 -11.30 1.60 120.90 109.60 B B B P O5' C5' DG DG DG 8 8 8 N 1 1.95 0.30 108.30 110.25 B B B O4' C1' N9 DG DG DG 8 8 8 N 1 -4.26 0.60 125.10 120.84 B B B C6 N1 C2 DG DG DG 8 8 8 N 1 4.28 0.50 111.50 115.78 B B B C5 C6 N1 DG DG DG 8 8 8 N 1 15.81 1.20 119.70 135.51 B B B C3' O3' P DG DG DC 8 8 9 Y 1 -10.48 1.50 119.60 109.12 B B B OP1 P OP2 DC DC DC 9 9 9 N 1 -9.63 0.80 109.40 99.77 B B B O5' C5' C4' DC DC DC 9 9 9 N 1 -9.48 0.80 105.90 96.42 B B B O4' C1' C2' DC DC DC 9 9 9 N 1 3.45 0.30 108.30 111.75 B B B O4' C1' N1 DC DC DC 9 9 9 N 1 -10.11 1.20 119.70 109.59 B B B C3' O3' P DC DC DG 9 9 10 Y 1 7.63 1.20 110.70 118.33 B B B O5' P OP2 DG DG DG 10 10 10 N 1 3.75 0.30 108.30 112.05 B B B O4' C1' N9 DG DG DG 10 10 10 N 1 3.16 0.50 111.50 114.66 B B B C5 C6 N1 DG DG DG 10 10 10 N 1 -3.98 0.60 119.90 115.92 B B B N1 C6 O6 DG DG DG 10 10 10 N 1 -12.25 0.80 109.40 97.15 B B B O5' C5' C4' DG DG DG 12 12 12 N 1 -5.42 0.70 102.20 96.78 B B B C4' C3' C2' DG DG DG 12 12 12 N 1 8.41 0.30 108.30 116.71 B B B O4' C1' N9 DG DG DG 12 12 12 N 1 -5.65 0.60 125.10 119.45 B B B C6 N1 C2 DG DG DG 12 12 12 N 1 3.86 0.60 123.90 127.76 B B B N1 C2 N3 DG DG DG 12 12 12 N 1 4.65 0.50 111.50 116.15 B B B C5 C6 N1 DG DG DG 12 12 12 N 1 A A O4' C1' DG DG 2 2 0.085 0.011 1.420 1.505 N 1 B B P O5' DG DG 8 8 0.070 0.010 1.593 1.663 N 1 A A O O HOH HOH 28 61 2.00 1_555 2_664 1 B A OP1 O DG HOH 8 43 2.19 1_555 3_756 0.189 1.800 8.000 1495 1 1.000 TR isotropic TR isotropic 1.800 8.000 49 291 2 240 0 0.019 0.025 0.028 0.029 fix fix 1.500 133D 2994 1 refinement NUCLSQ refinement X-PLOR THE CRYSTAL STRUCTURE OF N4-METHYLCYTOSINE.GUANOSIN BASE-PAIRS IN THE SYNTHETIC HEXANUCLEOTIDE D(CGCGM(4)CG) 1 N N 1 N N 2 N N 2 N N covale 1.578 both A DG 4 A O3' DG 4 1_555 A C34 5 A P C34 5 1_555 covale 1.609 both A C34 5 A O3' C34 5 1_555 A DG 6 A P DG 6 1_555 covale 1.629 both B DG 10 B O3' DG 4 1_555 B C34 11 B P C34 5 1_555 covale 1.642 both B C34 11 B O3' C34 5 1_555 B DG 12 B P DG 6 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 C34 11 B N3 C34 5 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B C34 11 B O2 C34 5 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B C34 11 B N4 C34 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 C34 5 A N3 C34 5 1_555 B DG 8 B N1 DG 2 1_555 hydrog WATSON-CRICK A C34 5 A N4 C34 5 1_555 B DG 8 B O6 DG 2 1_555 hydrog WATSON-CRICK A C34 5 A O2 C34 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, MODIFIED, DNA 133D PDB 1 133D 1 6 133D 1 6 133D A 1 1 6 7 12 133D 7 12 133D B 1 1 6 19 P 21 21 21