0.055935 0.000000 0.000000 0.000000 0.032289 0.000000 0.000000 0.000000 0.023039 0.00000 0.00000 0.00000 Venkadesh, S. Mandal, P.K. Kannan, R. Gautham, N. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 17.878 30.970 43.405 C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C9 H14 N3 O7 P 307.197 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE non-polymer 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 Mn 2 54.938 MANGANESE (II) ION 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 N N 36 N C N 37 N N N 38 N C N 39 N C N 40 N C N 41 N O N 42 N N N 43 R C N 44 N C N 45 S C N 46 R C N 47 N O N 48 N O N 49 N C N 50 N O N 51 N P N 52 N O N 53 N O N 54 N O N 55 N H N 56 N H N 57 N H 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 O N 70 N P N 71 N O N 72 N O N 73 N O N 74 N C N 75 R C N 76 N O N 77 S C N 78 N O N 79 N C N 80 R C Y 81 N N Y 82 N C Y 83 N N Y 84 N C N 85 N C N 86 N O N 87 N N N 88 N C N 89 N N N 90 N N Y 91 N C 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 O N 107 N P N 108 N O N 109 N O N 110 N O N 111 N C N 112 R C N 113 N O N 114 S C N 115 N O N 116 N C N 117 R C N 118 N N N 119 N C N 120 N O N 121 N N N 122 N C N 123 N O N 124 N C N 125 N C N 126 N C N 127 N H N 128 N H 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 O N 143 N H N 144 N H N 145 N MN 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 sing N 39 N sing N 40 N doub N 41 N doub N 42 N sing N 43 N sing N 44 N doub 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 sing 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 sing N 72 N sing N 73 N doub 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 Y 94 N sing Y 95 N sing Y 96 N doub N 97 N sing Y 98 N sing N 99 N sing Y 100 N doub N 101 N doub N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N doub N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N doub 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 sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing 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 doub N 136 N sing N 137 N sing N 138 N sing N 139 N doub N 140 N sing N 141 N sing N 142 N doub N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N sing To be Published 0353 Crystal studies of d(CACGCG).d(CGCGTG) grown with various counter ions 10.2210/pdb3g2r/pdb pdb_00003g2r 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 mirrors IMAGE PLATE 2008-11-20 MARRESEARCH mirror SINGLE WAVELENGTH M x-ray 1 1.54 1.0 1.54 ROTATING ANODE BRUKER AXS MICROSTAR 1825.216 5'-D(*CP*GP*TP*GP*CP*G)-3' 1 syn polymer 307.197 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE 1 syn non-polymer 54.938 MANGANESE (II) ION 1 syn non-polymer 18.015 water 6 nat water no no (DC)(DG)(DT)(DG)(DC)(DG) CGTGCG A polydeoxyribonucleotide n n n n n n 1 VAPOR DIFFUSION, HANGING DROP 6.99 50mM Sodium cacodylate, 5mM MnCl2, 1mM Spermine, 50% methyl pentane diol, pH 6.99, VAPOR DIFFUSION, HANGING DROP, temperature 293K 293 Sodium cacoldylate 1 MnCl2 1 Spermine 1 MPD 1 Sodium cacoldylate 2 MnCl2 2 MPD 2 -7.096 1 19 A 1 A 4 -1.170 A_DC1:DG4_A 1 6.716 -1.227 -0.037 -0.099 11.528 A 2 A 3 4.713 A_DG2:DT3_A 2 -5.397 0.396 0.857 -0.051 -11.528 A 3 A 2 4.713 A_DT3:DG2_A 3 -5.397 -0.396 0.857 -0.051 7.096 1 19 A 4 A 1 -1.170 A_DG4:DC1_A 4 6.716 1.227 -0.037 -0.099 0.208 -9.167 A A 1 2 -23.696 A A 4 3 3.333 3.270 0.040 5.122 AA_DC1DG2:DT3DG4_AA 1 -6.557 -47.514 -5.512 -36.978 -9.637 4.502 -48.812 A A 2 3 -6.507 A A 3 2 4.351 5.368 0.000 -1.688 AA_DG2DT3:DG2DT3_AA 2 0.000 0.000 -48.534 1.488 0.000 0.208 -9.167 A A 3 4 -23.696 A A 2 1 3.333 3.270 -0.040 5.122 AA_DT3DG4:DC1DG2_AA 3 6.557 47.514 -5.512 -36.978 9.637 chem_comp_atom chem_comp_bond database_2 struct_site repository Initial release Version format compliance Data collection Database references Derived calculations 1 0 2009-03-03 1 1 2011-07-13 1 2 2024-03-20 _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 Crystal structure of d(CACGCG)d(CGCGTG) grown in presence of MnCl2 RCSB Y PDBJ 2009-02-01 REL REL DCM 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE MN MANGANESE (II) ION HOH water C 7 2 DCM DCM 7 A MN 1 3 MN MN 8 A HOH 1 4 HOH HOH 9 A HOH 2 4 HOH HOH 10 A HOH 3 4 HOH HOH 11 A HOH 4 4 HOH HOH 12 A HOH 5 4 HOH HOH 13 A HOH 7 4 HOH HOH 14 A C 1 n 1 DC 1 A G 2 n 2 DG 2 A T 3 n 3 DT 3 A G 4 n 4 DG 4 A C 5 n 5 DC 5 A G 6 n 6 DG 6 A software_defined_assembly PISA 2 dimeric 480 -9 2520 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 4_565 x,-y+1,-z crystal symmetry operation 0.0000000000 30.9700000000 0.0000000000 1 A MN 8 C MN 1 A N1 DCM 7 B N1 DCM 1 1 N 1 A C2 DCM 7 B C2 DCM 1 1 N 1 A N3 DCM 7 B N3 DCM 1 1 N 1 A C4 DCM 7 B C4 DCM 1 1 N 1 A C5 DCM 7 B C5 DCM 1 1 N 1 A C6 DCM 7 B C6 DCM 1 1 N 1 A O2 DCM 7 B O2 DCM 1 1 N 1 A N4 DCM 7 B N4 DCM 1 1 N 1 A C1' DCM 7 B C1' DCM 1 1 N 1 A C2' DCM 7 B C2' DCM 1 1 N 1 A C3' DCM 7 B C3' DCM 1 1 N 1 A C4' DCM 7 B C4' DCM 1 1 N 1 A O4' DCM 7 B O4' DCM 1 1 N 1 A O3' DCM 7 B O3' DCM 1 1 N 1 A C5' DCM 7 B C5' DCM 1 1 N 1 A O5' DCM 7 B O5' DCM 1 1 N 1 A O3P DCM 7 B O3P DCM 1 1 N 1 A A O3' P DG DCM 6 7 1.89 1 -5.55 0.80 102.40 96.85 A A A C3' C2' C1' DC DC DC 1 1 1 N 1 -10.24 0.70 108.00 97.76 A A A O4' C1' N1 DC DC DC 1 1 1 N 1 -18.67 1.60 120.90 102.23 A A A P O5' C5' DG DG DG 2 2 2 N 1 4.89 0.60 106.00 110.89 A A A O4' C4' C3' DG DG DG 2 2 2 N 1 -9.71 0.70 108.00 98.29 A A A O4' C1' N9 DG DG DG 2 2 2 N 1 3.75 0.50 111.90 115.65 A A A C2 N3 C4 DG DG DG 2 2 2 N 1 -3.30 0.50 128.60 125.30 A A A N3 C4 C5 DG DG DG 2 2 2 N 1 -4.24 0.40 110.80 106.56 A A A C4 C5 N7 DG DG DG 2 2 2 N 1 3.72 0.50 104.30 108.02 A A A C5 N7 C8 DG DG DG 2 2 2 N 1 3.97 0.60 130.40 134.37 A A A C6 C5 N7 DG DG DG 2 2 2 N 1 -6.18 0.60 119.90 113.72 A A A N1 C6 O6 DG DG DG 2 2 2 N 1 4.88 0.60 128.60 133.48 A A A C5 C6 O6 DG DG DG 2 2 2 N 1 3.35 0.30 108.30 111.65 A A A O4' C1' N1 DT DT DT 3 3 3 N 1 -5.15 0.40 104.50 99.35 A A A O4' C4' C3' DG DG DG 4 4 4 N 1 8.14 1.20 119.70 127.84 A A A C3' O3' P DG DG DC 4 4 5 Y 1 -3.24 0.40 104.50 101.26 A A A O4' C4' C3' DC DC DC 5 5 5 N 1 8.57 1.40 114.30 122.87 A A A N1 C1' C2' DC DC DC 5 5 5 N 1 -14.13 0.70 108.00 93.87 A A A O4' C1' N1 DC DC DC 5 5 5 N 1 3.47 0.50 119.90 123.37 A A A C2 N3 C4 DC DC DC 5 5 5 N 1 6.47 0.60 118.90 125.37 A A A N1 C2 O2 DC DC DC 5 5 5 N 1 -12.73 1.90 104.00 91.27 A A A O3' P O5' DC DG DG 5 6 6 Y 1 9.04 1.20 110.70 119.74 A A A O5' P OP1 DG DG DG 6 6 6 N 1 -11.82 1.60 120.90 109.08 A A A P O5' C5' DG DG DG 6 6 6 N 1 -5.39 0.40 104.50 99.11 A A A O4' C4' C3' DG DG DG 6 6 6 N 1 -3.50 0.50 128.60 125.10 A A A N3 C4 C5 DG DG DG 6 6 6 N 1 -3.36 0.50 111.50 108.14 A A A C5 C6 N1 DG DG DG 6 6 6 N 1 -4.65 0.40 110.80 106.15 A A A C4 C5 N7 DG DG DG 6 6 6 N 1 3.88 0.50 104.30 108.18 A A A C5 N7 C8 DG DG DG 6 6 6 N 1 2.45 0.40 105.40 107.85 A A A N9 C4 C5 DG DG DG 6 6 6 N 1 6.07 0.60 128.60 134.67 A A A C5 C6 O6 DG DG DG 6 6 6 N 1 A A C6 O6 DG DG 6 6 0.063 0.009 1.237 1.300 N 30.334 -1.12 0.00 0.00 -0.45 0.00 1.57 0.934 0.950 0.27015 0.26859 0.26870 2.15 14.70 41 694 693 5.6 99.73 7.295 0.188 RANDOM 1 isotropic THROUGHOUT MOLECULAR REPLACEMENT 0.390 0.258 0.80 0.80 1.20 MAXIMUM LIKELIHOOD MASK 2.15 14.70 6 131 4 121 0 0.021 0.021 138 4.056 3.000 211 0.128 0.200 23 0.017 0.020 64 0.227 0.200 53 0.345 0.200 74 0.451 0.200 3 0.459 0.200 22 0.688 0.200 3 0.066 0.358 2.208 1 55 55 20 100.00 40.616 2.15 15 3G2R 751 742 0.0410 0.0383 1 8.0 3.83 98.8 0.2377 2.15 2.23 2.0 82 0.2162 3.87 100 data collection MAR345dtb phasing AMoRE refinement REFMAC 5.2.0019 data reduction AUTOMAR data scaling SCALEPACK N Crystal structure of d(CACGCG).d(CGCGTG) cocrystallized with MnCl2 1 N N 2 N N 3 N N 4 N N The author states that there is no possible quaternary structure metalc 2.439 A DG 2 A O6 DG 2 1_555 A MN 8 C MN MN 1_555 hydrog WATSON-CRICK A DC 1 A N3 DC 1 1_555 A DG 4 A N1 DG 4 4_565 hydrog WATSON-CRICK A DC 1 A N4 DC 1 1_555 A DG 4 A O6 DG 4 4_565 hydrog WATSON-CRICK A DC 1 A O2 DC 1 1_555 A DG 4 A N2 DG 4 4_565 hydrog DG-DT MISPAIR A DG 2 A N2 DG 2 1_555 A DT 3 A O2 DT 3 4_565 hydrog DT-DG MISPAIR A DT 3 A N3 DT 3 1_555 A DG 2 A O6 DG 2 4_565 hydrog WATSON-CRICK A DG 4 A N1 DG 4 1_555 A DC 1 A N3 DC 1 4_565 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 A DC 1 A O2 DC 1 4_565 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 A DC 1 A N4 DC 1 4_565 DNA duplex Z-form DNA with Watson-Crick base pairing, DNA 3G2R PDB 1 3G2R 1 6 3G2R 1 6 3G2R A 1 1 6 BINDING SITE FOR RESIDUE DCM A 7 A DCM 7 Software 3 BINDING SITE FOR RESIDUE MN A 8 A MN 8 Software 3 A DC 1 A DC 1 3 2_565 A DG 4 A DG 4 3 7_455 A DG 6 A DG 6 3 1_555 A DG 2 A DG 2 3 1_555 A DT 3 A DT 3 3 1_555 A HOH 10 D HOH 3 1_555 20 C 2 2 21