0.055975 0.000000 0.000000 0.000000 0.032444 0.000000 0.000000 0.000000 0.022323 0.00000 0.00000 0.00000 Schroth, G.P. Kagawa, T.F. Shing Ho, P. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 17.865 30.822 44.797 C10 H16 N3 O7 P 321.224 n 5-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 C10 H15 N3 O4 241.244 n 5-METHYL-2'-DEOXYCYTIDINE DNA linking N 1 N N N 2 N C N 3 N N N 4 N C N 5 N C N 6 N C N 7 N C N 8 N O N 9 N N N 10 R C N 11 N C N 12 S C N 13 R C N 14 N O N 15 N O N 16 N C N 17 N O N 18 N P N 19 N O N 20 N O 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 112 N N N 113 N C N 114 N N N 115 N C N 116 N C N 117 N C N 118 N O N 119 N N N 120 R C N 121 N C N 122 S C N 123 R C N 124 N O N 125 N O N 126 N C N 127 N O N 128 N C N 129 N H N 130 N H N 131 N H N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N doub N 6 N doub N 7 N sing N 8 N sing N 9 N sing N 10 N doub 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 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 doub 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 N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N doub N 120 N doub N 121 N sing N 122 N sing N 123 N doub N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 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 N 146 N sing N 147 N sing US Biochemistry BICHAW 0033 0006-2960 32 13381 13392 10.1021/bi00212a002 8257675 Structure and thermodynamics of nonalternating C.G base pairs in Z-DNA: the 1.3-A crystal structure of the asymmetric hexanucleotide d(m5CGGGm5CG).d(m5CGCCm5CG). 1993 UK Nucleic Acids Res. NARHAD 0389 0305-1048 10 7879 7892 Molecular Structure of (m5dC-dG)3: The Role of the Methyl Group on 5-Methyl Cytosine in Stabilizing Z-DNA 1982 10.2210/pdb145d/pdb pdb_0000145d 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 SIEMENS SINGLE WAVELENGTH M x-ray 1 1.0 ROTATING ANODE SIEMENS 1798.303 DNA (5'-D(*(MCY)P*GP*GP*GP*(5CM)P*G)-3') 1 syn polymer 1718.255 DNA (5'-D(*(MCY)P*GP*CP*CP*(5CM)P*G)-3') 2 syn polymer 1878.283 DNA (5'-D(*(5CM)P*DGP*DGP*DGP*(5CM)P*DG)-3') 1 syn polymer 18.015 water 48 nat water no yes (MCY)(DG)(DG)(DG)(5CM)(DG) CGGGCG A polydeoxyribonucleotide no yes (MCY)(DG)(DC)(DC)(5CM)(DG) CGCCCG B,C polydeoxyribonucleotide no yes (5CM)(DG)(DG)(DG)(5CM)(DG) CGGGCG D polydeoxyribonucleotide n n n n n n n n n n n n n n n n n n VAPOR DIFFUSION 7.00 pH 7.00, VAPOR DIFFUSION ROOM TEMPERATURE WATER 1 MPD 1 MGCL2 1 SPERMIDINE 1 WATER 2 MPD 2 3.039 1 19 A 1 B 12 -1.153 A_MCY1:DG12_B 1 0.768 -0.403 0.007 -0.109 -2.423 1 19 A 2 B 11 2.615 A_DG2:5CM11_B 2 0.384 0.431 0.112 -0.291 13.709 1 19 A 3 B 10 3.019 A_DG3:DC10_B 3 0.078 0.033 0.617 -0.119 -6.824 1 19 A 4 B 9 3.078 A_DG4:DC9_B 4 0.879 0.378 -0.014 -0.154 4.290 1 19 A 5 B 8 1.472 A_5CM5:DG8_B 5 -3.670 -0.302 -0.015 -0.100 -3.420 1 19 A 6 B 7 2.757 A_DG6:MCY7_B 6 -3.102 0.190 -0.096 -0.124 3.819 -10.042 A A 1 2 1.192 B B 12 11 3.703 -0.208 0.190 5.575 AA_MCY1DG2:5CM11DG12_BB 1 -0.992 -5.676 -9.990 -31.407 -1.039 3.126 -49.786 A A 2 3 -1.043 B B 11 10 3.106 0.878 0.210 -0.906 AA_DG2DG3:DC105CM11_BB 2 -2.247 -2.670 -49.732 1.015 0.093 5.116 -11.547 A A 3 4 12.069 B B 10 9 4.272 -2.366 -0.004 5.727 AA_DG3DG4:DC9DC10_BB 3 3.763 19.195 -10.660 -23.507 7.863 3.368 -50.458 A A 4 5 -0.201 B B 9 8 3.360 0.171 -0.358 -1.026 AA_DG45CM5:DG8DC9_BB 4 0.772 0.905 -50.452 1.191 -0.364 5.422 -11.659 A A 5 6 21.952 B B 8 7 3.675 -4.344 0.096 5.494 AA_5CM5DG6:MCY7DG8_BB 5 1.191 6.017 -10.756 -18.395 2.843 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_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id BNL Y NDB 1993-11-11 REL REL HOH water HOH 31 4 HOH HOH 31 A HOH 37 4 HOH HOH 37 A HOH 41 4 HOH HOH 41 A HOH 44 4 HOH HOH 44 A HOH 53 4 HOH HOH 53 A HOH 58 4 HOH HOH 58 A HOH 67 4 HOH HOH 67 A HOH 70 4 HOH HOH 70 A HOH 71 4 HOH HOH 71 A HOH 72 4 HOH HOH 72 A HOH 25 4 HOH HOH 25 B HOH 34 4 HOH HOH 34 B HOH 38 4 HOH HOH 38 B HOH 40 4 HOH HOH 40 B HOH 42 4 HOH HOH 42 B HOH 45 4 HOH HOH 45 B HOH 46 4 HOH HOH 46 B HOH 47 4 HOH HOH 47 B HOH 50 4 HOH HOH 50 B HOH 52 4 HOH HOH 52 B HOH 55 4 HOH HOH 55 B HOH 26 4 HOH HOH 26 C HOH 27 4 HOH HOH 27 C HOH 29 4 HOH HOH 29 C HOH 32 4 HOH HOH 32 C HOH 35 4 HOH HOH 35 C HOH 39 4 HOH HOH 39 C HOH 43 4 HOH HOH 43 C HOH 48 4 HOH HOH 48 C HOH 51 4 HOH HOH 51 C HOH 54 4 HOH HOH 54 C HOH 60 4 HOH HOH 60 C HOH 61 4 HOH HOH 61 C HOH 62 4 HOH HOH 62 C HOH 64 4 HOH HOH 64 C HOH 66 4 HOH HOH 66 C HOH 28 4 HOH HOH 28 D HOH 30 4 HOH HOH 30 D HOH 33 4 HOH HOH 33 D HOH 36 4 HOH HOH 36 D HOH 49 4 HOH HOH 49 D HOH 56 4 HOH HOH 56 D HOH 57 4 HOH HOH 57 D HOH 59 4 HOH HOH 59 D HOH 63 4 HOH HOH 63 D HOH 65 4 HOH HOH 65 D HOH 68 4 HOH HOH 68 D HOH 69 4 HOH HOH 69 D MCY 1 n 1 MCY 1 A DG 2 n 2 DG 2 A DG 3 n 3 DG 3 A DG 4 n 4 DG 4 A 5CM 5 n 5 5CM 5 A DG 6 n 6 DG 6 A MCY 7 n 1 MCY 7 B DG 8 n 2 DG 8 B DC 9 n 3 DC 9 B DC 10 n 4 DC 10 B 5CM 11 n 5 5CM 11 B DG 12 n 6 DG 12 B MCY 13 n 1 MCY 13 C DG 14 n 2 DG 14 C DC 15 n 3 DC 15 C DC 16 n 4 DC 16 C 5CM 17 n 5 5CM 17 C DG 18 n 6 DG 18 C MCY 19 n 1 5CM 19 D DG 20 n 2 DG 20 D DG 21 n 3 DG 21 D DG 22 n 4 DG 22 D 5CM 23 n 5 5CM 23 D DG 24 n 6 DG 24 D author_defined_assembly 2 dimeric author_defined_assembly 2 dimeric A MCY 1 5-METHYL-2'-DEOXYCYTIDINE A MCY 1 DC A 5CM 5 A 5CM 5 DC B MCY 7 5-METHYL-2'-DEOXYCYTIDINE B MCY 1 DC B 5CM 11 B 5CM 5 DC C MCY 13 5-METHYL-2'-DEOXYCYTIDINE C MCY 1 DC C 5CM 17 C 5CM 5 DC D 5CM 19 D 5CM 1 DC D 5CM 23 D 5CM 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 B B O H2 HOH HOH 25 46 1.44 1 D D H2 O HOH HOH 56 57 1.45 1 A C H2 O HOH HOH 53 54 1.56 1 A DG 2 A 0.063 SIDE CHAIN 1 3.04 0.50 113.10 116.14 A A A N7 C8 N9 DG DG DG 2 2 2 A A A N 1 8.08 1.20 119.70 127.78 A A A C3' O3' P DG DG DG 2 2 3 A A A Y 1 -5.59 0.70 108.00 102.41 A A A O4' C1' N9 DG DG DG 4 4 4 A A A N 1 3.79 0.60 106.00 109.79 A A A O4' C4' C3' DG DG DG 6 6 6 A A A N 1 -4.71 0.70 102.20 97.49 A A A C4' C3' C2' DG DG DG 6 6 6 A A A N 1 3.55 0.50 113.10 116.65 A A A N7 C8 N9 DG DG DG 6 6 6 A A A N 1 3.45 0.50 106.80 110.25 B B B O4' C1' C2' DG DG DG 8 8 8 A A A N 1 8.65 1.20 119.70 128.35 B B B C3' O3' P 5CM 5CM DG 11 11 12 A A A Y 1 3.50 0.50 113.10 116.60 C C C N7 C8 N9 DG DG DG 14 14 14 B B B N 1 2.38 0.30 108.30 110.68 C C C O4' C1' N1 DC DC DC 15 15 15 B B B N 1 3.53 0.30 108.30 111.83 C C C O4' C1' N1 DC DC DC 16 16 16 B B B N 1 8.60 1.20 119.70 128.30 D D D C3' O3' P 5CM 5CM DG 19 19 20 B B B Y 1 2.41 0.30 108.30 110.71 D D D O4' C1' N9 DG DG DG 20 20 20 B B B N 1 3.00 0.50 113.10 116.10 D D D N7 C8 N9 DG DG DG 20 20 20 B B B N 1 3.27 0.50 113.10 116.37 D D D N7 C8 N9 DG DG DG 21 21 21 B B B N 1 3.47 0.50 113.10 116.57 D D D N7 C8 N9 DG DG DG 22 22 22 B B B N 1 A A C8 N9 DG DG 4 4 -0.046 0.007 1.374 1.328 A A N 0.193 1.250 8.000 5029 1 1.500 1.250 8.000 144 920 0 776 0 refinement NUCLSQ Structure and thermodynamics of nonalternating C/G base pairs in Z-DNA: the 1.3 angstroms crystal structure of the asymmetric hexanucleotide D(M(5)CGGGM(5) CG)/D(M(5)CGCCM(5)CG) 1 N N 2 N N 2 N N 3 N N 4 N N 4 N N 4 N N 4 N N covale 1.601 both A A A MCY 1 A O3' MCY 1 1_555 A DG 2 A P DG 2 1_555 covale 1.619 both A A A DG 4 A O3' DG 4 1_555 A 5CM 5 A P 5CM 5 1_555 covale 1.610 both A A A 5CM 5 A O3' 5CM 5 1_555 A DG 6 A P DG 6 1_555 covale 1.579 both A A B MCY 7 B O3' MCY 1 1_555 B DG 8 B P DG 2 1_555 covale 1.619 both A A B DC 10 B O3' DC 4 1_555 B 5CM 11 B P 5CM 5 1_555 covale 1.609 both A A B 5CM 11 B O3' 5CM 5 1_555 B DG 12 B P DG 6 1_555 covale 1.611 both B B C MCY 13 C O3' MCY 1 1_555 C DG 14 C P DG 2 1_555 covale 1.641 both B B C DC 16 C O3' DC 4 1_555 C 5CM 17 C P 5CM 5 1_555 covale 1.585 both B B C 5CM 17 C O3' 5CM 5 1_555 C DG 18 C P DG 6 1_555 covale 1.622 both B B D 5CM 19 D O3' 5CM 1 1_555 D DG 20 D P DG 2 1_555 covale 1.603 both B B D DG 22 D O3' DG 4 1_555 D 5CM 23 D P 5CM 5 1_555 covale 1.615 both B B D 5CM 23 D O3' 5CM 5 1_555 D DG 24 D P DG 6 1_555 hydrog WATSON-CRICK A A A MCY 1 A N3 MCY 1 1_555 B DG 12 B N1 DG 6 1_555 hydrog WATSON-CRICK A A A MCY 1 A N4 MCY 1 1_555 B DG 12 B O6 DG 6 1_555 hydrog WATSON-CRICK A A A MCY 1 A O2 MCY 1 1_555 B DG 12 B N2 DG 6 1_555 hydrog WATSON-CRICK A A A DG 2 A N1 DG 2 1_555 B 5CM 11 B N3 5CM 5 1_555 hydrog WATSON-CRICK A A A DG 2 A N2 DG 2 1_555 B 5CM 11 B O2 5CM 5 1_555 hydrog WATSON-CRICK A A A DG 2 A O6 DG 2 1_555 B 5CM 11 B N4 5CM 5 1_555 hydrog WATSON-CRICK A A A DG 3 A N1 DG 3 1_555 B DC 10 B N3 DC 4 1_555 hydrog WATSON-CRICK A A A DG 3 A N2 DG 3 1_555 B DC 10 B O2 DC 4 1_555 hydrog WATSON-CRICK A A A DG 3 A O6 DG 3 1_555 B DC 10 B N4 DC 4 1_555 hydrog WATSON-CRICK A A A DG 4 A N1 DG 4 1_555 B DC 9 B N3 DC 3 1_555 hydrog WATSON-CRICK A A A DG 4 A N2 DG 4 1_555 B DC 9 B O2 DC 3 1_555 hydrog WATSON-CRICK A A A DG 4 A O6 DG 4 1_555 B DC 9 B N4 DC 3 1_555 hydrog WATSON-CRICK A A A 5CM 5 A N3 5CM 5 1_555 B DG 8 B N1 DG 2 1_555 hydrog WATSON-CRICK A A A 5CM 5 A N4 5CM 5 1_555 B DG 8 B O6 DG 2 1_555 hydrog WATSON-CRICK A A A 5CM 5 A O2 5CM 5 1_555 B DG 8 B N2 DG 2 1_555 hydrog WATSON-CRICK A A A DG 6 A N1 DG 6 1_555 B MCY 7 B N3 MCY 1 1_555 hydrog WATSON-CRICK A A A DG 6 A N2 DG 6 1_555 B MCY 7 B O2 MCY 1 1_555 hydrog WATSON-CRICK A A A DG 6 A O6 DG 6 1_555 B MCY 7 B N4 MCY 1 1_555 DNA Z-DNA, DOUBLE HELIX, MODIFIED, DNA 145D PDB 1 145D 145D PDB 2 145D 145D PDB 3 145D 1 6 145D 1 6 145D A 1 1 6 7 12 145D 7 12 145D B 2 1 6 13 18 145D 13 18 145D C 2 1 6 19 24 145D 19 24 145D D 3 1 6 19 P 21 21 21