0.055525 0.000000 0.000000 0.000000 0.032383 0.000000 0.000000 0.000000 0.022341 0.00000 0.00000 0.00000 ATOM HOH 1 IS PROBABLY A SODIUM ION. Chevrier, B. Dock, A.C. Hartmann, B. Leng, M. Moras, D. Thuong, M.T. Westhof, E. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 18.010 30.880 44.760 C9 H13 Br N3 O7 P 386.093 n 5-BROMO-2'-DEOXY-CYTIDINE-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 BR N 2 N P N 3 N O N 4 N O N 5 N O N 6 N N N 7 N C N 8 N C N 9 N O N 10 N N N 11 N C N 12 N N N 13 N C N 14 N C N 15 N C N 16 R C N 17 N O N 18 R C N 19 S C 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 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 1 N sing N 2 N doub 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 doub N 12 N sing N 13 N doub N 14 N sing N 15 N doub 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 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 UK J.Mol.Biol. JMOBAK 0070 0022-2836 188 707 719 10.1016/S0022-2836(86)80016-X 3735433 Solvation of the left-handed hexamer d(5BrC-G-5BrC-G-5 BrC-G) in crystals grown at two temperatures. 1986 10.2210/pdb1dn4/pdb pdb_00001dn4 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 291.00 1 DIFFRACTOMETER ENRAF-NONIUS CAD4 x-ray 1 1.0 2046.893 DNA (5'-D(*(CBR)P*GP*(CBR)P*GP*(CBR)P*G)-3') 2 syn polymer 18.015 water 61 nat water no yes (CBR)(DG)(CBR)(DG)(CBR)(DG) CGCGCG A,B polydeoxyribonucleotide n n n n n n VAPOR DIFFUSION VAPOR DIFFUSION, temperature 291.00K 291.00 WATER 1 MPD 1 NACL 1 NA CACODYLATE 1 WATER 2 MPD 2 14.210 1 19 A 1 B 12 1.617 A_CBR1:DG12_B 1 2.881 -0.175 -0.190 0.100 1.411 1 19 A 2 B 11 1.933 A_DG2:CBR11_B 2 3.734 0.368 0.570 -0.117 -2.619 1 19 A 3 B 10 1.453 A_CBR3:DG10_B 3 -4.437 -0.246 -0.010 -0.057 -12.785 1 19 A 4 B 9 0.206 A_DG4:CBR9_B 4 -1.705 0.413 -0.088 -0.174 6.284 1 19 A 5 B 8 0.830 A_CBR5:DG8_B 5 3.421 -0.466 0.173 -0.106 -2.341 1 19 A 6 B 7 1.085 A_DG6:CBR7_B 6 -3.295 0.250 0.092 -0.219 3.804 -12.726 A A 1 2 1.221 B B 12 11 4.006 -0.263 0.016 5.711 AA_CBR1DG2:CBR11DG12_BB 1 -5.043 -23.392 -11.685 -25.387 -7.182 3.546 -48.556 A A 2 3 3.928 B B 11 10 3.633 -3.225 -0.019 -1.144 AA_DG2CBR3:DG10CBR11_BB 2 3.777 4.600 -48.317 1.664 0.297 4.885 -9.178 A A 3 4 14.606 B B 10 9 3.658 -2.312 0.034 5.350 AA_CBR3DG4:CBR9DG10_BB 3 0.031 0.194 -8.882 -26.616 0.304 2.995 -50.467 A A 4 5 4.856 B B 9 8 3.087 -4.137 -0.231 -1.105 AA_DG4CBR5:DG8CBR9_BB 4 0.401 0.471 -50.307 1.569 -0.244 4.081 -11.751 A A 5 6 3.295 B B 8 7 3.789 -0.673 -0.015 5.544 AA_CBR5DG6:CBR7DG8_BB 5 1.222 5.981 -11.668 -25.980 1.923 diffrn_detector chem_comp_atom chem_comp_bond database_2 struct_conn repository Initial release Version format compliance Version format compliance Data collection Data collection Database references Derived calculations 1 0 1987-04-16 1 1 2008-05-22 1 2 2011-07-13 1 3 2018-04-18 1 4 2024-02-07 _diffrn_detector.detector _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag BNL Y BNL 1986-12-01 REL REL HOH water HOH 14 2 HOH HOH 14 A HOH 16 2 HOH HOH 16 A HOH 17 2 HOH HOH 17 A HOH 19 2 HOH HOH 19 A HOH 20 2 HOH HOH 20 A HOH 22 2 HOH HOH 22 A HOH 24 2 HOH HOH 24 A HOH 25 2 HOH HOH 25 A HOH 28 2 HOH HOH 28 A HOH 29 2 HOH HOH 29 A HOH 30 2 HOH HOH 30 A HOH 32 2 HOH HOH 32 A HOH 33 2 HOH HOH 33 A HOH 35 2 HOH HOH 35 A HOH 36 2 HOH HOH 36 A HOH 37 2 HOH HOH 37 A HOH 38 2 HOH HOH 38 A HOH 40 2 HOH HOH 40 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 45 2 HOH HOH 45 A HOH 46 2 HOH HOH 46 A HOH 47 2 HOH HOH 47 A HOH 48 2 HOH HOH 48 A HOH 49 2 HOH HOH 49 A HOH 51 2 HOH HOH 51 A HOH 52 2 HOH HOH 52 A HOH 53 2 HOH HOH 53 A HOH 56 2 HOH HOH 56 A HOH 58 2 HOH HOH 58 A HOH 59 2 HOH HOH 59 A HOH 61 2 HOH HOH 61 A HOH 63 2 HOH HOH 63 A HOH 64 2 HOH HOH 64 A HOH 65 2 HOH HOH 65 A HOH 67 2 HOH HOH 67 A HOH 68 2 HOH HOH 68 A HOH 70 2 HOH HOH 70 A HOH 71 2 HOH HOH 71 A HOH 13 2 HOH HOH 13 B HOH 15 2 HOH HOH 15 B HOH 18 2 HOH HOH 18 B HOH 21 2 HOH HOH 21 B HOH 23 2 HOH HOH 23 B HOH 26 2 HOH HOH 26 B HOH 27 2 HOH HOH 27 B HOH 31 2 HOH HOH 31 B HOH 34 2 HOH HOH 34 B HOH 39 2 HOH HOH 39 B HOH 50 2 HOH HOH 50 B HOH 54 2 HOH HOH 54 B HOH 55 2 HOH HOH 55 B HOH 57 2 HOH HOH 57 B HOH 60 2 HOH HOH 60 B HOH 62 2 HOH HOH 62 B HOH 66 2 HOH HOH 66 B HOH 69 2 HOH HOH 69 B HOH 72 2 HOH HOH 72 B HOH 73 2 HOH HOH 73 B C 1 n 1 CBR 1 A G 2 n 2 DG 2 A C 3 n 3 CBR 3 A G 4 n 4 DG 4 A C 5 n 5 CBR 5 A G 6 n 6 DG 6 A C 7 n 1 CBR 7 B G 8 n 2 DG 8 B C 9 n 3 CBR 9 B G 10 n 4 DG 10 B C 11 n 5 CBR 11 B G 12 n 6 DG 12 B author_defined_assembly 2 dimeric A CBR 1 A CBR 1 DC A CBR 3 A CBR 3 DC A CBR 5 A CBR 5 DC B CBR 7 B CBR 1 DC B CBR 9 B CBR 3 DC B CBR 11 B CBR 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 -10.14 0.90 105.70 95.56 A A A O5' P OP1 DG DG DG 2 2 2 N 1 7.71 1.20 110.70 118.41 A A A O5' P OP2 DG DG DG 2 2 2 N 1 -5.06 0.60 125.10 120.04 A A A C6 N1 C2 DG DG DG 2 2 2 N 1 4.27 0.50 111.90 116.17 A A A C2 N3 C4 DG DG DG 2 2 2 N 1 3.85 0.50 111.50 115.35 A A A C5 C6 N1 DG DG DG 2 2 2 N 1 -2.96 0.40 110.80 107.84 A A A C4 C5 N7 DG DG DG 2 2 2 N 1 4.32 0.70 119.90 124.22 A A A N3 C2 N2 DG DG DG 2 2 2 N 1 -5.71 0.60 119.90 114.19 A A A N1 C6 O6 DG DG DG 2 2 2 N 1 9.27 1.20 119.70 128.97 A A A C3' O3' P CBR CBR DG 3 3 4 Y 1 -6.21 0.60 123.90 117.69 A A A N1 C2 N3 DG DG DG 4 4 4 N 1 7.71 0.50 111.90 119.61 A A A C2 N3 C4 DG DG DG 4 4 4 N 1 -4.66 0.50 128.60 123.94 A A A N3 C4 C5 DG DG DG 4 4 4 N 1 3.40 0.50 111.50 114.90 A A A C5 C6 N1 DG DG DG 4 4 4 N 1 5.93 0.60 126.00 131.93 A A A N3 C4 N9 DG DG DG 4 4 4 N 1 -5.15 0.60 128.60 123.45 A A A C5 C6 O6 DG DG DG 4 4 4 N 1 18.73 1.10 110.50 129.23 A A A O3' P OP1 CBR DG DG 5 6 6 Y 1 -8.75 0.90 105.70 96.95 A A A O5' P OP2 DG DG DG 6 6 6 N 1 -9.59 0.80 109.40 99.81 A A A O5' C5' C4' DG DG DG 6 6 6 N 1 8.02 0.60 106.00 114.02 A A A O4' C4' C3' DG DG DG 6 6 6 N 1 -9.26 1.00 110.10 100.84 A A A C1' O4' C4' DG DG DG 6 6 6 N 1 5.24 0.50 106.80 112.04 A A A O4' C1' C2' DG DG DG 6 6 6 N 1 -7.12 0.60 125.10 117.98 A A A C6 N1 C2 DG DG DG 6 6 6 N 1 4.09 0.60 123.90 127.99 A A A N1 C2 N3 DG DG DG 6 6 6 N 1 -3.70 0.50 128.60 124.90 A A A N3 C4 C5 DG DG DG 6 6 6 N 1 3.29 0.50 111.50 114.79 A A A C5 C6 N1 DG DG DG 6 6 6 N 1 4.39 0.60 126.00 130.39 A A A N3 C4 N9 DG DG DG 6 6 6 N 1 -3.97 0.60 128.60 124.63 A A A C5 C6 O6 DG DG DG 6 6 6 N 1 7.62 1.20 110.70 118.32 B B B O5' P OP2 DG DG DG 8 8 8 N 1 -3.90 0.60 123.90 120.00 B B B N1 C2 N3 DG DG DG 8 8 8 N 1 -3.67 0.40 105.40 101.73 B B B N9 C4 C5 DG DG DG 8 8 8 N 1 5.15 0.60 126.00 131.15 B B B N3 C4 N9 DG DG DG 8 8 8 N 1 4.78 0.60 119.90 124.68 B B B N1 C6 O6 DG DG DG 8 8 8 N 1 -5.26 0.60 128.60 123.34 B B B C5 C6 O6 DG DG DG 8 8 8 N 1 14.37 1.20 119.70 134.07 B B B C3' O3' P DG DG CBR 8 8 9 Y 1 -10.35 1.50 119.60 109.25 B B B OP1 P OP2 DG DG DG 10 10 10 N 1 -6.31 0.80 109.40 103.09 B B B O5' C5' C4' DG DG DG 10 10 10 N 1 -4.72 0.50 111.90 107.18 B B B C2 N3 C4 DG DG DG 10 10 10 N 1 4.85 0.50 113.10 117.95 B B B N7 C8 N9 DG DG DG 10 10 10 N 1 -4.05 0.40 106.40 102.35 B B B C8 N9 C4 DG DG DG 10 10 10 N 1 7.38 0.90 116.20 123.58 B B B N1 C2 N2 DG DG DG 10 10 10 N 1 -10.35 0.70 119.90 109.55 B B B N3 C2 N2 DG DG DG 10 10 10 N 1 14.52 1.20 119.70 134.22 B B B C3' O3' P DG DG CBR 10 10 11 Y 1 -11.36 1.20 119.70 108.34 B B B C3' O3' P CBR CBR DG 11 11 12 Y 1 15.84 1.50 119.60 135.44 B B B OP1 P OP2 DG DG DG 12 12 12 N 1 -13.28 1.60 120.90 107.62 B B B P O5' C5' DG DG DG 12 12 12 N 1 -5.73 0.40 110.80 105.07 B B B C4 C5 N7 DG DG DG 12 12 12 N 1 5.97 0.50 104.30 110.27 B B B C5 N7 C8 DG DG DG 12 12 12 N 1 -5.56 0.50 113.10 107.54 B B B N7 C8 N9 DG DG DG 12 12 12 N 1 2.73 0.40 106.40 109.13 B B B C8 N9 C4 DG DG DG 12 12 12 N 1 A A O3' P CBR DG 1 2 0.117 0.012 1.607 1.724 Y 1 A A O4' C4' DG DG 4 4 -0.099 0.010 1.446 1.347 N 1 A A C6 N1 DG DG 4 4 -0.044 0.007 1.391 1.347 N 1 A A P OP1 DG DG 6 6 -0.130 0.017 1.485 1.355 N 1 A A P OP2 DG DG 6 6 0.143 0.017 1.485 1.628 N 1 A A P O5' DG DG 6 6 0.135 0.010 1.593 1.728 N 1 A A N7 C8 DG DG 6 6 -0.051 0.006 1.305 1.254 N 1 B B O4' C4' DG DG 8 8 -0.101 0.010 1.446 1.345 N 1 B B C2 N3 DG DG 8 8 0.056 0.008 1.323 1.379 N 1 B B N7 C8 DG DG 8 8 -0.055 0.006 1.305 1.250 N 1 B B O3' P CBR DG 9 10 -0.105 0.012 1.607 1.502 Y 1 B B P OP2 DG DG 10 10 -0.104 0.017 1.485 1.381 N 1 B B P O5' DG DG 10 10 0.096 0.010 1.593 1.689 N 1 B B O4' C1' DG DG 10 10 0.075 0.011 1.420 1.495 N 1 B B N3 C4 DG DG 10 10 0.045 0.007 1.350 1.395 N 1 B B C6 N1 DG DG 10 10 -0.046 0.007 1.391 1.345 N 1 B B C5 N7 DG DG 10 10 0.043 0.006 1.388 1.431 N 1 B B N7 C8 DG DG 10 10 -0.055 0.006 1.305 1.250 N 1 B B P OP2 DG DG 12 12 -0.127 0.017 1.485 1.358 N 0.1327 1.600 10.000 3195 1.0 0.44 1 3.000 TR isotropic TR isotropic 1.600 10.000 61 307 6 240 0 fix ref 1.600 10.000 1DN4 3195 2919 3.000 1 refinement NUCLSQ SOLVATION OF THE LEFT-HANDED HEXAMER D(5BRC-G-5BRC-G-5BRC-G) IN CRYSTALS GROWN AT TWO TEMPERATURES 1 N N 1 N N 2 N N 2 N N covale 1.724 both A CBR 1 A O3' CBR 1 1_555 A DG 2 A P DG 2 1_555 covale 1.582 both A DG 2 A O3' DG 2 1_555 A CBR 3 A P CBR 3 1_555 covale 1.601 both A CBR 3 A O3' CBR 3 1_555 A DG 4 A P DG 4 1_555 covale 1.636 both A DG 4 A O3' DG 4 1_555 A CBR 5 A P CBR 5 1_555 covale 1.567 both A CBR 5 A O3' CBR 5 1_555 A DG 6 A P DG 6 1_555 covale 1.651 both B CBR 7 B O3' CBR 1 1_555 B DG 8 B P DG 2 1_555 covale 1.631 both B DG 8 B O3' DG 2 1_555 B CBR 9 B P CBR 3 1_555 covale 1.502 both B CBR 9 B O3' CBR 3 1_555 B DG 10 B P DG 4 1_555 covale 1.602 both B DG 10 B O3' DG 4 1_555 B CBR 11 B P CBR 5 1_555 covale 1.632 both B CBR 11 B O3' CBR 5 1_555 B DG 12 B P DG 6 1_555 hydrog WATSON-CRICK A CBR 1 A N3 CBR 1 1_555 B DG 12 B N1 DG 6 1_555 hydrog WATSON-CRICK A CBR 1 A N4 CBR 1 1_555 B DG 12 B O6 DG 6 1_555 hydrog WATSON-CRICK A CBR 1 A O2 CBR 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 CBR 11 B N3 CBR 5 1_555 hydrog WATSON-CRICK A DG 2 A N2 DG 2 1_555 B CBR 11 B O2 CBR 5 1_555 hydrog WATSON-CRICK A DG 2 A O6 DG 2 1_555 B CBR 11 B N4 CBR 5 1_555 hydrog WATSON-CRICK A CBR 3 A N3 CBR 3 1_555 B DG 10 B N1 DG 4 1_555 hydrog WATSON-CRICK A CBR 3 A N4 CBR 3 1_555 B DG 10 B O6 DG 4 1_555 hydrog WATSON-CRICK A CBR 3 A O2 CBR 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 CBR 9 B N3 CBR 3 1_555 hydrog WATSON-CRICK A DG 4 A N2 DG 4 1_555 B CBR 9 B O2 CBR 3 1_555 hydrog WATSON-CRICK A DG 4 A O6 DG 4 1_555 B CBR 9 B N4 CBR 3 1_555 hydrog WATSON-CRICK A CBR 5 A N3 CBR 5 1_555 B DG 8 B N1 DG 2 1_555 hydrog WATSON-CRICK A CBR 5 A N4 CBR 5 1_555 B DG 8 B O6 DG 2 1_555 hydrog WATSON-CRICK A CBR 5 A O2 CBR 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 CBR 7 B N3 CBR 1 1_555 hydrog WATSON-CRICK A DG 6 A N2 DG 6 1_555 B CBR 7 B O2 CBR 1 1_555 hydrog WATSON-CRICK A DG 6 A O6 DG 6 1_555 B CBR 7 B N4 CBR 1 1_555 DNA Z-DNA, DOUBLE HELIX, MODIFIED, DNA 1DN4 PDB 1 1DN4 1 6 1DN4 1 6 1DN4 A 1 1 6 7 12 1DN4 7 12 1DN4 B 1 1 6 19 P 21 21 21