0.014995 0.008657 0.000000 0.000000 0.017315 0.000000 0.000000 0.000000 0.007116 0.00000 0.00000 0.00000 Dunham, C.M. Murray, J.B. Scott, W.G. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.00 90.00 120.00 66.689 66.689 140.528 C10 H14 N5 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA linking C9 H14 N3 O8 P 323.197 y CYTIDINE-5'-MONOPHOSPHATE RNA linking Co 2 58.933 COBALT (II) ION non-polymer C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking 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 R C N 12 N O N 13 R C Y 14 N N Y 15 N C Y 16 N N Y 17 N C Y 18 N C N 19 N N Y 20 N N Y 21 N C Y 22 N N Y 23 N C 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 R C N 49 N O N 50 R C N 51 N N N 52 N C N 53 N O N 54 N N N 55 N C N 56 N N N 57 N C N 58 N C 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 H N 73 N CO N 74 N O N 75 N P N 76 N O N 77 N O N 78 N O N 79 N C N 80 R C N 81 N O N 82 S C N 83 N O N 84 R C N 85 N O N 86 R C Y 87 N N Y 88 N C Y 89 N N Y 90 N C N 91 N C N 92 N O N 93 N N N 94 N C N 95 N N N 96 N N Y 97 N C 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 O N 113 N P N 114 N O N 115 N O N 116 N O N 117 N C N 118 R C N 119 N O N 120 S C N 121 N O N 122 R C N 123 N O N 124 R C N 125 N N N 126 N C N 127 N O N 128 N N N 129 N C N 130 N O N 131 N C N 132 N C 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 144 N H N 145 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 Y 25 N sing Y 26 N sing Y 27 N doub N 28 N sing Y 29 N sing Y 30 N sing Y 31 N doub N 32 N sing Y 33 N doub N 34 N sing N 35 N sing Y 36 N sing Y 37 N doub N 38 N sing Y 39 N sing N 40 N sing N 41 N sing N 42 N doub 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 sing N 65 N sing N 66 N doub N 67 N sing N 68 N doub 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 doub 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 Y 100 N sing Y 101 N sing Y 102 N doub N 103 N sing Y 104 N sing N 105 N sing Y 106 N doub N 107 N doub 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 doub 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 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 doub N 143 N sing N 144 N sing N 145 N sing N 146 N doub N 147 N sing N 148 N doub N 149 N sing N 150 N sing UK J.Mol.Biol. JMOBAK 0070 0022-2836 332 327 336 10.1016/S0022-2836(03)00843-X 12948485 A helical twist-induced conformational switch activates cleavage in the hammerhead ribozyme. 2003 10.2210/pdb1q29/pdb pdb_00001q29 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 CCD SINGLE WAVELENGTH M x-ray 1 1.0 5.0.2 ALS SYNCHROTRON ALS BEAMLINE 5.0.2 5515.309 5'-R(*GP*GP*UP*GP*GP*UP*CP*UP*GP*AP*UP*GP*AP*GP*GP*CP*C)-3' 1 syn polymer 7674.670 Ribozyme 1 syn polymer 58.933 COBALT (II) ION 5 syn non-polymer no no GGUGGUCUGAUGAGGCC GGUGGUCUGAUGAGGCC A polyribonucleotide no no GCCGAAACUCGUAAGAGUCACCAC GCCGAAACUCGUAAGAGUCACCAC B polyribonucleotide n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n 6.84 82.02 15.266 1 19 A 10 A 26 -2.138 A_G10:C26_A 1 -18.011 -0.132 0.299 0.079 6.452 1 19 B 102 A 25 -4.787 B_G102:C25_A 2 -8.451 -0.509 0.433 0.099 3.562 1 19 B 103 A 24 -1.864 B_C103:G24_A 3 -15.645 -0.207 0.069 -0.112 2.261 1 19 B 104 A 23 5.665 B_C104:G23_A 4 -13.455 0.177 0.064 0.076 9.922 10 11 B 105 A 22 -5.210 B_G105:A22_A 5 -15.934 6.942 -0.075 -4.443 -24.878 10 11 B 106 A 21 1.176 B_A106:G21_A 6 18.921 -6.882 0.097 -4.357 14.159 5 B 107 A 20 45.065 B_A107:U20_A 7 -2.005 -6.458 0.130 -0.645 -0.418 1 19 B 109 B 118 -5.250 B_C109:G118_B 8 -19.246 0.664 0.456 0.021 5.680 1 20 B 110 B 117 5.179 B_U110:A117_B 9 -9.031 -0.702 0.226 0.133 15.951 1 19 B 111 B 116 4.291 B_C111:G116_B 10 -8.879 0.748 -0.224 -0.178 -2.885 B 112 B 115 -43.914 B_G112:A115_B 11 -18.874 7.501 0.309 -5.611 -3.760 1 A 11 B 125 1.135 A_G11:C125_B 12 -23.123 0.350 0.160 0.460 4.806 A 12 B 124 5.882 A_U12:A124_B 13 -12.952 0.288 0.273 0.424 3.544 1 19 A 13 B 123 -0.101 A_G13:C123_B 14 -11.667 0.249 0.369 -0.082 -10.734 1 19 A 14 B 122 3.641 A_G14:C122_B 15 -17.890 0.192 -0.120 -0.061 -10.552 1 20 A 15 B 121 0.429 A_U15:A121_B 16 -8.295 0.408 0.465 -0.009 2.410 31.075 A B 10 102 23.634 A A 26 25 3.388 12.283 0.390 -1.599 AB_G10G102:C25C26_AA 1 -4.580 8.813 28.236 -5.178 -1.547 3.302 35.006 B B 102 103 -1.301 A A 25 24 3.250 -0.782 0.171 -2.238 BB_G102C103:G24C25_AA 2 1.611 -2.679 34.962 -3.603 -0.042 2.942 30.205 B B 103 104 9.125 A A 24 23 3.289 4.736 0.190 -1.980 BB_C103C104:G23G24_AA 3 -0.622 1.199 29.834 -4.721 -0.486 3.396 58.254 B B 104 105 3.184 A A 23 22 3.431 3.099 -0.875 -0.516 BB_C104G105:A22G23_AA 4 0.389 -0.400 58.178 -0.701 0.920 3.151 -10.609 B B 105 106 -1.034 A A 22 21 3.929 0.185 1.016 -1.192 BB_G105A106:G21A22_AA 5 4.498 25.120 -9.609 6.098 13.993 -0.177 37.391 B B 106 107 17.781 A A 21 20 2.021 10.667 2.911 -1.073 BB_A106A107:U20G21_AA 6 -19.873 33.126 30.018 -2.117 -5.367 6.648 110.509 B B 107 109 2.314 A B 20 118 6.694 3.798 -0.177 -1.567 BB_A107C109:G118U20_BA 7 -13.419 8.175 109.916 -1.047 -0.224 3.206 27.213 B B 109 110 -3.027 B B 118 117 3.190 -1.419 0.236 -1.575 BB_C109U110:A117G118_BB 8 -3.705 7.901 26.927 -2.998 -1.415 2.865 42.514 B B 110 111 6.079 B B 117 116 2.987 4.400 0.068 -1.093 BB_U110C111:G116A117_BB 9 1.659 -2.293 42.265 -1.908 0.056 2.785 52.984 B B 111 112 24.809 B B 116 115 4.123 21.532 -4.857 -1.273 BB_C111G112:A115G116_BB 10 5.981 -6.892 48.353 -2.968 5.872 2.778 37.331 A A 11 12 6.827 B B 125 124 2.950 4.359 -0.163 -1.395 AA_G11U12:A124C125_BB 11 -1.798 2.817 37.042 -2.685 0.046 2.952 33.547 A A 12 13 7.907 B B 124 123 3.182 4.546 -0.105 -1.404 AA_U12G13:C123A124_BB 12 2.643 -4.597 33.144 -3.136 0.592 2.606 29.972 A A 13 14 19.189 B B 123 122 3.483 9.710 0.629 -2.362 AA_G13G14:C122C123_BB 13 4.719 -9.326 28.002 -6.498 -0.279 3.103 31.790 A A 14 15 2.908 B B 122 121 3.119 1.585 -0.825 -2.152 AA_G14U15:A121C122_BB 14 -5.335 9.788 31.311 -4.206 0.569 pdbx_validate_polymer_linkage software struct_conn chem_comp_atom chem_comp_bond database_2 struct_conn struct_site pdbx_initial_refinement_model repository Initial release Version format compliance Version format compliance Advisory Data collection Derived calculations Refinement description Data collection Database references Derived calculations Refinement description 1 0 2004-02-24 1 1 2008-04-29 1 2 2011-07-13 1 3 2019-07-24 1 4 2024-02-14 1 5 2024-04-03 _software.classification _software.name _software.version _struct_conn.pdbx_leaving_atom_flag _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_seq_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Crosslinked Hammerhead Ribozyme Initial State RCSB Y RCSB 2003-07-23 REL CO COBALT (II) ION 299D NDB entry urx057 PDB experimental model CO 1 3 CO CO 1 A CO 2 3 CO CO 2 A CO 5 3 CO CO 5 A CO 3 3 CO CO 3 B CO 4 3 CO CO 4 B G 500 n 1 G 10 A G 11 n 2 G 11 A U 12 n 3 U 12 A G 13 n 4 G 13 A G 14 n 5 G 14 A U 15 n 6 U 15 A C 16 n 7 C 16 A U 17 n 8 U 17 A G 18 n 9 G 18 A A 19 n 10 A 19 A U 20 n 11 U 20 A G 21 n 12 G 21 A A 22 n 13 A 22 A G 23 n 14 G 23 A G 24 n 15 G 24 A C 25 n 16 C 25 A C 26 n 17 C 26 A G 102 n 1 G 102 B C 103 n 2 C 103 B C 104 n 3 C 104 B G 105 n 4 G 105 B A 106 n 5 A 106 B A 107 n 6 A 107 B A 108 n 7 A 108 B C 109 n 8 C 109 B U 110 n 9 U 110 B C 111 n 10 C 111 B G 112 n 11 G 112 B U 113 n 12 U 113 B A 114 n 13 A 114 B A 115 n 14 A 115 B G 116 n 15 G 116 B A 117 n 16 A 117 B G 118 n 17 G 118 B U 119 n 18 U 119 B C 120 n 19 C 120 B A 121 n 20 A 121 B C 122 n 21 C 122 B C 123 n 22 C 123 B A 124 n 23 A 124 B C 125 n 24 C 125 B author_defined_assembly 2 dimeric A A 22 A OP2 A 13 1_555 A CO 5 E CO CO 1_555 A G 23 A N7 G 14 1_555 84.3 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 N2 G 18 A N2 G 9 1 Y 1 B B O2' OP1 C A 120 121 1.72 1 -8.91 1.20 109.10 100.19 A A A C5' C4' O4' G G G 11 11 11 N 1 4.60 0.70 108.50 113.10 A A A O4' C1' N9 G G G 13 13 13 N 1 -8.79 1.00 102.60 93.81 A A A C4' C3' C2' U U U 17 17 17 N 1 -10.92 0.90 105.70 94.78 A A A O5' P OP2 G G G 18 18 18 N 1 -4.29 0.60 125.10 120.81 A A A C6 N1 C2 G G G 18 18 18 N 1 8.47 0.50 111.90 120.37 A A A C2 N3 C4 G G G 18 18 18 N 1 -8.30 0.50 128.60 120.30 A A A N3 C4 C5 G G G 18 18 18 N 1 7.51 0.50 111.50 119.01 A A A C5 C6 N1 G G G 18 18 18 N 1 -2.92 0.40 110.80 107.88 A A A C4 C5 N7 G G G 18 18 18 N 1 4.66 0.50 104.30 108.96 A A A C5 N7 C8 G G G 18 18 18 N 1 -4.30 0.50 113.10 108.80 A A A N7 C8 N9 G G G 18 18 18 N 1 6.87 0.60 126.00 132.87 A A A N3 C4 N9 G G G 18 18 18 N 1 -7.89 0.60 128.60 120.71 A A A C5 C6 O6 G G G 18 18 18 N 1 8.22 1.20 110.70 118.92 B B B O5' P OP2 U U U 110 110 110 N 1 8.03 1.30 114.00 122.03 B B B N9 C1' C2' A A A 114 114 114 N 1 -12.04 1.90 104.00 91.96 B B B O3' P O5' G A A 116 117 117 Y 1 7.91 1.20 110.70 118.61 B B B O5' P OP2 A A A 117 117 117 N 1 -3.91 0.60 119.90 115.99 B B B N1 C6 O6 G G G 118 118 118 N 1 12.01 1.60 116.00 128.01 B B B C5' C4' C3' C C C 120 120 120 N 1 -7.80 0.70 109.70 101.90 B B B C1' O4' C4' C C C 120 120 120 N 1 -19.20 2.20 109.50 90.30 B B B C2' C3' O3' C C C 120 120 120 N 1 -11.03 1.00 102.60 91.57 B B B C4' C3' C2' C C C 120 120 120 N 1 -16.05 1.00 102.60 86.55 B B B C4' C3' C2' A A A 121 121 121 N 1 9.67 0.70 108.50 118.17 B B B O4' C1' N9 A A A 121 121 121 N 1 -4.31 0.70 121.90 117.59 B B B N3 C2 O2 C C C 122 122 122 N 1 A A C5' C4' G G 11 11 0.233 0.012 1.509 1.742 N 1 A A C5 N7 G G 18 18 -0.045 0.006 1.388 1.343 N 1 A A N7 C8 G G 18 18 0.043 0.006 1.305 1.348 N 1 B B O3' C3' C C 109 109 -0.085 0.014 1.417 1.332 N 1 B B C4' C3' A A 121 121 0.115 0.011 1.527 1.642 N 1 B B O4' C1' A A 121 121 -0.181 0.013 1.412 1.231 N 77.623 0.19 0.09 0.00 0.19 0.00 -0.28 0.944 0.924 0.27914 0.24196 0.24559 3.00 19.80 744 6872 9.8 99.30 17.927 0.310 RANDOM 1 THROUGHOUT 0 MOLECULAR REPLACEMENT 0.385 0.310 0.80 0.80 1.40 NDB entry urx057 BABINET MODEL WITH MASK 3.00 19.80 0 877 5 872 0 0.011 975 .021 2.077 1512 3.0 0.092 164 .20 0.006 427 .02 0.196 396 .20 0.212 14 .20 0.195 25 .20 0.173 4 .20 1.087 975 3.0 1.728 1512 4.5 0.412 0.438 3.077 55 474 20 refinement REFMAC 5.1 data scaling SCALA refinement CNS data reduction MOSFLM data scaling CCP4 (SCALA) phasing CNS Hammerhead Ribozyme with 5'-5' G-G linkage: Conformational change experiment 1 N N 2 N N 3 N N 3 N N 3 N N 3 N N 3 N N Hammerhead Ribozyme with 5'-5' G-G linkage at 5' end of enzyme strand covale 1.591 one A G 10 A O5' G 1 1_555 A G 11 A P G 2 1_555 metalc 2.560 A CO 2 D CO CO 1_555 A G 18 A N7 G 9 1_555 metalc 2.326 A CO 5 E CO CO 1_555 A A 22 A OP2 A 13 1_555 metalc 2.348 A CO 5 E CO CO 1_555 A G 23 A N7 G 14 1_555 metalc 2.583 B CO 3 F CO CO 1_555 B G 116 B N7 G 15 1_555 metalc 1.996 B CO 4 G CO CO 1_555 B G 118 B N7 G 17 1_555 hydrog WATSON-CRICK A G 10 A N1 G 1 1_555 A C 26 A N3 C 17 1_555 hydrog WATSON-CRICK A G 10 A N2 G 1 1_555 A C 26 A O2 C 17 1_555 hydrog WATSON-CRICK A G 10 A O6 G 1 1_555 A C 26 A N4 C 17 1_555 hydrog G-C PAIR A G 11 A N1 G 2 1_555 B C 125 B N3 C 24 1_555 hydrog U-A PAIR A U 12 A N3 U 3 1_555 B A 124 B N1 A 23 1_555 hydrog WATSON-CRICK A G 13 A N1 G 4 1_555 B C 123 B N3 C 22 1_555 hydrog WATSON-CRICK A G 13 A N2 G 4 1_555 B C 123 B O2 C 22 1_555 hydrog WATSON-CRICK A G 13 A O6 G 4 1_555 B C 123 B N4 C 22 1_555 hydrog WATSON-CRICK A G 14 A N1 G 5 1_555 B C 122 B N3 C 21 1_555 hydrog WATSON-CRICK A G 14 A N2 G 5 1_555 B C 122 B O2 C 21 1_555 hydrog WATSON-CRICK A G 14 A O6 G 5 1_555 B C 122 B N4 C 21 1_555 hydrog WATSON-CRICK A U 15 A N3 U 6 1_555 B A 121 B N1 A 20 1_555 hydrog WATSON-CRICK A U 15 A O4 U 6 1_555 B A 121 B N6 A 20 1_555 hydrog U-A PAIR A U 20 A O2 U 11 1_555 B A 107 B N6 A 6 1_555 hydrog TYPE_11_PAIR A G 21 A N2 G 12 1_555 B A 106 B N7 A 5 1_555 hydrog TYPE_11_PAIR A G 21 A N3 G 12 1_555 B A 106 B N6 A 5 1_555 hydrog TYPE_11_PAIR A A 22 A N6 A 13 1_555 B G 105 B N3 G 4 1_555 hydrog TYPE_11_PAIR A A 22 A N7 A 13 1_555 B G 105 B N2 G 4 1_555 hydrog WATSON-CRICK A G 23 A N1 G 14 1_555 B C 104 B N3 C 3 1_555 hydrog WATSON-CRICK A G 23 A N2 G 14 1_555 B C 104 B O2 C 3 1_555 hydrog WATSON-CRICK A G 23 A O6 G 14 1_555 B C 104 B N4 C 3 1_555 hydrog WATSON-CRICK A G 24 A N1 G 15 1_555 B C 103 B N3 C 2 1_555 hydrog WATSON-CRICK A G 24 A N2 G 15 1_555 B C 103 B O2 C 2 1_555 hydrog WATSON-CRICK A G 24 A O6 G 15 1_555 B C 103 B N4 C 2 1_555 hydrog WATSON-CRICK A C 25 A N3 C 16 1_555 B G 102 B N1 G 1 1_555 hydrog WATSON-CRICK A C 25 A N4 C 16 1_555 B G 102 B O6 G 1 1_555 hydrog WATSON-CRICK A C 25 A O2 C 16 1_555 B G 102 B N2 G 1 1_555 hydrog WATSON-CRICK B C 109 B N3 C 8 1_555 B G 118 B N1 G 17 1_555 hydrog WATSON-CRICK B C 109 B N4 C 8 1_555 B G 118 B O6 G 17 1_555 hydrog WATSON-CRICK B C 109 B O2 C 8 1_555 B G 118 B N2 G 17 1_555 hydrog WATSON-CRICK B U 110 B N3 U 9 1_555 B A 117 B N1 A 16 1_555 hydrog WATSON-CRICK B U 110 B O4 U 9 1_555 B A 117 B N6 A 16 1_555 hydrog WATSON-CRICK B C 111 B N3 C 10 1_555 B G 116 B N1 G 15 1_555 hydrog WATSON-CRICK B C 111 B N4 C 10 1_555 B G 116 B O6 G 15 1_555 hydrog WATSON-CRICK B C 111 B O2 C 10 1_555 B G 116 B N2 G 15 1_555 hydrog G-A MISPAIR B G 112 B N2 G 11 1_555 B A 115 B N7 A 14 1_555 RNA Hammerhead Ribozyme, RNA 1Q29 PDB 1 1Q29 1Q29 PDB 2 1Q29 10 26 1Q29 10 26 1Q29 A 1 1 17 102 125 1Q29 102 125 1Q29 B 2 1 24 BINDING SITE FOR RESIDUE CO A 1 A CO 1 Software 1 BINDING SITE FOR RESIDUE CO A 2 A CO 2 Software 1 BINDING SITE FOR RESIDUE CO B 3 B CO 3 Software 1 BINDING SITE FOR RESIDUE CO B 4 B CO 4 Software 1 BINDING SITE FOR RESIDUE CO A 5 A CO 5 Software 2 A G 14 A G 5 1 1_555 A G 18 A G 9 1 1_555 B G 116 B G 15 1 1_555 B G 118 B G 17 1 1_555 A A 22 A A 13 2 1_555 A G 23 A G 14 2 1_555 152 P 31 2 1