HEADER RIBOSOME 31-DEC-69 5NDV TITLE Crystal structure of Paromomycin bound to the yeast 80S ribosome COMPND MOL_ID: 1; COMPND 2 MOLECULE: 25S ribosomal RNA; COMPND 3 CHAIN: 1, 5; COMPND 4 MOL_ID: 13; COMPND 5 60S ribosomal protein L11-B; COMPND 6 CHAIN: M1, m1; COMPND 7 MOL_ID: 22; COMPND 8 60S ribosomal protein L21-A; COMPND 9 CHAIN: N1, n1; COMPND 10 MOL_ID: 32; COMPND 11 60S ribosomal protein L31-A; COMPND 12 CHAIN: O1, o1; COMPND 13 MOL_ID: 42; COMPND 14 60S ribosomal protein L41-B; COMPND 15 CHAIN: Q1, q1; COMPND 16 MOL_ID: 47; COMPND 17 40S ribosomal protein S1-A; COMPND 18 CHAIN: S1, s1; COMPND 19 MOL_ID: 57; COMPND 20 40S ribosomal protein S11-A; COMPND 21 CHAIN: C1, c1; COMPND 22 MOL_ID: 67; COMPND 23 40S ribosomal protein S21-A; COMPND 24 CHAIN: D1, d1; COMPND 25 MOL_ID: 42; COMPND 26 60S ribosomal protein L41-B; COMPND 27 CHAIN: Q1, q1; EXPDTA X-RAY DIFFRACTION REMARK 2 RESOLUTION. 3.30 ANGSTORMS DBREF 5NDV 1 1 3396 GB 83477482 CP011821.1 4551 45176 DBREF 5NDV Q 1 25 UNP P0CX87 RL41B_YEAST 1 25 SEQRES 1 Q1 25 MET ARG ALA LYS TRP ARG LYS LYS ARG THR ARG ARG LEU SEQRES 2 Q1 25 LYS ARG LYS ARG ARG LYS VAL ARG ALA ARG SER LYS ATOM 1 N MET Q 1 -45.952 -3.902 78.336 1.00 68.70 ATOM 2 CA MET Q 1 -45.184 -4.354 79.496 1.00 68.23 ATOM 3 C MET Q 1 -45.724 -3.785 80.807 1.00 68.13 ATOM 4 O MET Q 1 -46.313 -2.706 80.826 1.00 68.32 ATOM 5 CB MET Q 1 -43.718 -3.970 79.342 1.00 67.85 ATOM 6 CG MET Q 1 -43.511 -2.492 79.135 1.00 67.87 ATOM 7 SD MET Q 1 -41.819 -2.011 79.462 1.00 67.35 ATOM 8 CE MET Q 1 -41.009 -3.534 79.051 1.00 67.17 ATOM 9 N ARG Q 2 -45.493 -4.510 81.900 1.00 73.37 ATOM 10 CA ARG Q 2 -45.997 -4.106 83.207 1.00 73.27 ATOM 11 C ARG Q 2 -45.554 -2.687 83.553 1.00 73.12 ATOM 12 O ARG Q 2 -44.464 -2.246 83.178 1.00 72.89 ATOM 13 CB ARG Q 2 -45.508 -5.082 84.277 1.00 72.92 ATOM 14 CG ARG Q 2 -45.412 -4.505 85.681 1.00 72.66 ATOM 15 CD ARG Q 2 -45.934 -5.500 86.693 1.00 72.61 ATOM 16 NE ARG Q 2 -44.887 -6.266 87.359 1.00 72.21 ATOM 17 CZ ARG Q 2 -44.728 -6.304 88.677 1.00 71.96 ATOM 18 NH1 ARG Q 2 -45.546 -5.622 89.466 1.00 72.06 ATOM 19 NH2 ARG Q 2 -43.758 -7.032 89.208 1.00 71.63 ATOM 20 N ALA Q 3 -46.421 -1.971 84.279 1.00 57.85 ATOM 21 CA ALA Q 3 -46.216 -0.545 84.523 1.00 57.80 ATOM 22 C ALA Q 3 -44.880 -0.264 85.203 1.00 57.32 ATOM 23 O ALA Q 3 -44.117 0.604 84.763 1.00 57.23 ATOM 24 CB ALA Q 3 -47.364 0.007 85.360 1.00 58.00 ATOM 25 N LYS Q 4 -44.580 -0.981 86.286 1.00 67.25 ATOM 26 CA LYS Q 4 -43.375 -0.657 87.037 1.00 66.81 ATOM 27 C LYS Q 4 -42.108 -1.020 86.271 1.00 66.59 ATOM 28 O LYS Q 4 -41.069 -0.383 86.468 1.00 66.31 ATOM 29 CB LYS Q 4 -43.396 -1.344 88.402 1.00 66.58 ATOM 30 CG LYS Q 4 -42.766 -2.725 88.437 1.00 66.37 ATOM 31 CD LYS Q 4 -42.108 -3.014 89.792 1.00 65.99 ATOM 32 CE LYS Q 4 -43.100 -2.966 90.946 1.00 66.08 ATOM 33 NZ LYS Q 4 -42.448 -3.335 92.232 1.00 65.74 ATOM 34 N TRP Q 5 -42.160 -2.023 85.391 1.00 66.36 ATOM 35 CA TRP Q 5 -40.956 -2.358 84.637 1.00 66.16 ATOM 36 C TRP Q 5 -40.670 -1.323 83.562 1.00 66.31 ATOM 37 O TRP Q 5 -39.506 -1.107 83.206 1.00 66.07 ATOM 38 CB TRP Q 5 -41.066 -3.752 84.022 1.00 66.26 ATOM 39 CG TRP Q 5 -41.210 -4.879 85.017 1.00 66.11 ATOM 40 CD1 TRP Q 5 -41.900 -6.046 84.831 1.00 66.32 ATOM 41 CD2 TRP Q 5 -40.650 -4.957 86.335 1.00 65.76 ATOM 42 NE1 TRP Q 5 -41.807 -6.839 85.947 1.00 66.10 ATOM 43 CE2 TRP Q 5 -41.045 -6.190 86.883 1.00 65.76 ATOM 44 CE3 TRP Q 5 -39.861 -4.106 87.107 1.00 65.46 ATOM 45 CZ2 TRP Q 5 -40.678 -6.580 88.157 1.00 65.48 ATOM 46 CZ3 TRP Q 5 -39.504 -4.499 88.359 1.00 65.17 ATOM 47 CH2 TRP Q 5 -39.916 -5.718 88.879 1.00 65.19 ATOM 48 N ARG Q 6 -41.710 -0.678 83.038 1.00 92.92 ATOM 49 CA ARG Q 6 -41.487 0.435 82.124 1.00 93.08 ATOM 50 C ARG Q 6 -40.918 1.640 82.865 1.00 92.86 ATOM 51 O ARG Q 6 -40.065 2.357 82.329 1.00 92.76 ATOM 52 CB ARG Q 6 -42.788 0.792 81.402 1.00 93.58 ATOM 53 CG ARG Q 6 -42.710 2.066 80.575 1.00 93.78 ATOM 54 CD ARG Q 6 -43.687 2.072 79.393 1.00 94.29 ATOM 55 NE ARG Q 6 -44.300 3.393 79.194 1.00 94.59 ATOM 56 CZ ARG Q 6 -43.687 4.463 78.672 1.00 94.59 ATOM 57 NH1 ARG Q 6 -42.412 4.402 78.279 1.00 94.31 ATOM 58 NH2 ARG Q 6 -44.354 5.609 78.549 1.00 94.90 ATOM 59 N LYS Q 7 -41.368 1.870 84.101 1.00 54.98 ATOM 60 CA LYS Q 7 -40.782 2.931 84.913 1.00 54.75 ATOM 61 C LYS Q 7 -39.290 2.703 85.115 1.00 54.32 ATOM 62 O LYS Q 7 -38.491 3.640 85.008 1.00 54.19 ATOM 63 CB LYS Q 7 -41.500 3.016 86.257 1.00 54.73 ATOM 64 CG LYS Q 7 -40.991 4.117 87.173 1.00 54.53 ATOM 65 CD LYS Q 7 -41.790 4.152 88.465 1.00 54.54 ATOM 66 CE LYS Q 7 -41.511 5.404 89.271 1.00 54.45 ATOM 67 NZ LYS Q 7 -42.417 5.488 90.455 1.00 54.52 ATOM 68 N LYS Q 8 -38.896 1.458 85.393 1.00 62.01 ATOM 69 CA LYS Q 8 -37.478 1.136 85.521 1.00 61.63 ATOM 70 C LYS Q 8 -36.745 1.319 84.197 1.00 61.67 ATOM 71 O LYS Q 8 -35.583 1.737 84.173 1.00 61.41 ATOM 72 CB LYS Q 8 -37.318 -0.298 86.026 1.00 61.44 ATOM 73 CG LYS Q 8 -35.882 -0.703 86.313 1.00 61.05 ATOM 74 CD LYS Q 8 -35.692 -2.208 86.217 1.00 60.97 ATOM 75 CE LYS Q 8 -36.496 -2.955 87.257 1.00 60.99 ATOM 76 NZ LYS Q 8 -35.903 -2.871 88.621 1.00 60.67 ATOM 77 N ARG Q 9 -37.405 1.012 83.081 1.00 72.73 ATOM 78 CA ARG Q 9 -36.736 1.125 81.790 1.00 72.79 ATOM 79 C ARG Q 9 -36.413 2.574 81.462 1.00 72.84 ATOM 80 O ARG Q 9 -35.354 2.868 80.898 1.00 72.69 ATOM 81 CB ARG Q 9 -37.599 0.503 80.695 1.00 73.17 ATOM 82 CG ARG Q 9 -36.798 -0.157 79.586 1.00 73.14 ATOM 83 CD ARG Q 9 -37.168 0.386 78.211 1.00 73.52 ATOM 84 NE ARG Q 9 -38.408 -0.178 77.679 1.00 73.92 ATOM 85 CZ ARG Q 9 -38.504 -1.390 77.141 1.00 74.01 ATOM 86 NH1 ARG Q 9 -37.437 -2.178 77.083 1.00 73.72 ATOM 87 NH2 ARG Q 9 -39.664 -1.820 76.668 1.00 74.40 ATOM 88 N THR Q 10 -37.311 3.494 81.799 1.00 67.13 ATOM 89 CA THR Q 10 -36.997 4.900 81.613 1.00 67.18 ATOM 90 C THR Q 10 -36.104 5.436 82.719 1.00 66.80 ATOM 91 O THR Q 10 -35.503 6.501 82.549 1.00 66.77 ATOM 92 CB THR Q 10 -38.267 5.743 81.534 1.00 67.58 ATOM 93 OG1 THR Q 10 -38.691 6.089 82.857 1.00 67.49 ATOM 94 CG2 THR Q 10 -39.374 4.975 80.804 1.00 67.94 ATOM 95 N ARG Q 11 -36.011 4.737 83.851 1.00 70.37 ATOM 96 CA ARG Q 11 -34.948 5.050 84.798 1.00 69.99 ATOM 97 C ARG Q 11 -33.594 4.808 84.152 1.00 69.75 ATOM 98 O ARG Q 11 -32.737 5.700 84.116 1.00 69.63 ATOM 99 CB ARG Q 11 -35.091 4.217 86.075 1.00 69.78 ATOM 100 CG ARG Q 11 -35.550 4.991 87.295 1.00 69.77 ATOM 101 CD ARG Q 11 -37.019 5.326 87.184 1.00 70.15 ATOM 102 NE ARG Q 11 -37.506 6.111 88.314 1.00 70.17 ATOM 103 CZ ARG Q 11 -37.836 5.606 89.503 1.00 70.05 ATOM 104 NH1 ARG Q 11 -37.726 4.301 89.744 1.00 69.89 ATOM 105 NH2 ARG Q 11 -38.273 6.416 90.461 1.00 70.10 ATOM 106 N ARG Q 12 -33.396 3.603 83.612 1.00 67.72 ATOM 107 CA ARG Q 12 -32.171 3.312 82.881 1.00 67.54 ATOM 108 C ARG Q 12 -31.945 4.332 81.775 1.00 67.72 ATOM 109 O ARG Q 12 -30.816 4.786 81.555 1.00 67.53 ATOM 110 CB ARG Q 12 -32.227 1.897 82.300 1.00 67.57 ATOM 111 CG ARG Q 12 -32.617 0.814 83.299 1.00 67.44 ATOM 112 CD ARG Q 12 -31.989 -0.531 82.942 1.00 67.31 ATOM 113 NE ARG Q 12 -32.442 -1.599 83.832 1.00 67.24 ATOM 114 CZ ARG Q 12 -33.171 -2.644 83.446 1.00 67.44 ATOM 115 NH1 ARG Q 12 -33.526 -2.788 82.172 1.00 67.72 ATOM 116 NH2 ARG Q 12 -33.531 -3.562 84.336 1.00 67.37 ATOM 117 N LEU Q 13 -33.011 4.703 81.069 1.00 69.63 ATOM 118 CA LEU Q 13 -32.898 5.686 80.000 1.00 69.85 ATOM 119 C LEU Q 13 -32.351 7.008 80.523 1.00 69.74 ATOM 120 O LEU Q 13 -31.278 7.457 80.108 1.00 69.59 ATOM 121 CB LEU Q 13 -34.257 5.873 79.338 1.00 70.31 ATOM 122 CG LEU Q 13 -34.249 6.129 77.834 1.00 70.61 ATOM 123 CD1 LEU Q 13 -33.787 7.514 77.556 1.00 70.66 ATOM 124 CD2 LEU Q 13 -33.321 5.172 77.136 1.00 70.43 ATOM 125 N LYS Q 14 -33.091 7.654 81.427 1.00 66.62 ATOM 126 CA LYS Q 14 -32.711 8.988 81.875 1.00 66.57 ATOM 127 C LYS Q 14 -31.312 9.006 82.466 1.00 66.15 ATOM 128 O LYS Q 14 -30.640 10.041 82.441 1.00 66.10 ATOM 129 CB LYS Q 14 -33.717 9.505 82.901 1.00 66.69 ATOM 130 CG LYS Q 14 -35.144 9.582 82.400 1.00 67.13 ATOM 131 CD LYS Q 14 -35.968 10.554 83.231 1.00 67.30 ATOM 132 CE LYS Q 14 -36.166 10.083 84.660 1.00 67.08 ATOM 133 NZ LYS Q 14 -37.040 11.035 85.401 1.00 67.28 ATOM 134 N ARG Q 15 -30.857 7.880 83.000 1.00 85.26 ATOM 135 CA ARG Q 15 -29.519 7.835 83.567 1.00 84.88 ATOM 136 C ARG Q 15 -28.455 7.776 82.475 1.00 84.80 ATOM 137 O ARG Q 15 -27.459 8.505 82.534 1.00 84.64 ATOM 138 CB ARG Q 15 -29.402 6.641 84.506 1.00 84.63 ATOM 139 CG ARG Q 15 -28.124 6.597 85.286 1.00 84.24 ATOM 140 CD ARG Q 15 -28.044 5.295 86.045 1.00 84.03 ATOM 141 NE ARG Q 15 -29.318 4.922 86.660 1.00 84.18 ATOM 142 CZ ARG Q 15 -29.428 3.996 87.608 1.00 84.03 ATOM 143 NH1 ARG Q 15 -28.335 3.370 88.045 1.00 83.72 ATOM 144 NH2 ARG Q 15 -30.617 3.702 88.129 1.00 84.19 ATOM 145 N LYS Q 16 -28.652 6.911 81.470 1.00 58.93 ATOM 146 CA LYS Q 16 -27.723 6.834 80.345 1.00 58.90 ATOM 147 C LYS Q 16 -27.613 8.177 79.639 1.00 59.09 ATOM 148 O LYS Q 16 -26.528 8.580 79.211 1.00 58.96 ATOM 149 CB LYS Q 16 -28.183 5.746 79.375 1.00 59.07 ATOM 150 CG LYS Q 16 -27.059 4.985 78.680 1.00 58.89 ATOM 151 CD LYS Q 16 -26.787 5.499 77.261 1.00 59.11 ATOM 152 CE LYS Q 16 -25.425 5.013 76.739 1.00 58.87 ATOM 153 NZ LYS Q 16 -24.256 5.459 77.598 1.00 58.50 ATOM 154 N ARG Q 17 -28.733 8.889 79.523 1.00 77.44 ATOM 155 CA ARG Q 17 -28.707 10.250 79.000 1.00 77.64 ATOM 156 C ARG Q 17 -27.826 11.148 79.856 1.00 77.40 ATOM 157 O ARG Q 17 -26.961 11.862 79.338 1.00 77.37 ATOM 158 CB ARG Q 17 -30.129 10.811 78.937 1.00 78.04 ATOM 159 CG ARG Q 17 -31.102 9.998 78.095 1.00 78.34 ATOM 160 CD ARG Q 17 -32.135 10.905 77.405 1.00 78.81 ATOM 161 NE ARG Q 17 -33.514 10.606 77.798 1.00 79.04 ATOM 162 CZ ARG Q 17 -34.559 10.643 76.971 1.00 79.47 ATOM 163 NH1 ARG Q 17 -34.388 10.947 75.686 1.00 79.71 ATOM 164 NH2 ARG Q 17 -35.772 10.350 77.426 1.00 79.67 ATOM 165 N ARG Q 18 -28.053 11.142 81.172 1.00 75.96 ATOM 166 CA ARG Q 18 -27.242 11.951 82.073 1.00 75.74 ATOM 167 C ARG Q 18 -25.767 11.721 81.811 1.00 75.44 ATOM 168 O ARG Q 18 -25.013 12.664 81.556 1.00 75.43 ATOM 169 CB ARG Q 18 -27.579 11.622 83.529 1.00 75.56 ATOM 170 CG ARG Q 18 -28.605 12.542 84.163 1.00 75.80 ATOM 171 CD ARG Q 18 -28.747 12.288 85.671 1.00 75.60 ATOM 172 NE ARG Q 18 -29.894 11.433 85.997 1.00 75.71 ATOM 173 CZ ARG Q 18 -29.815 10.253 86.615 1.00 75.48 ATOM 174 NH1 ARG Q 18 -28.637 9.774 86.997 1.00 75.13 ATOM 175 NH2 ARG Q 18 -30.919 9.545 86.856 1.00 75.62 ATOM 176 N LYS Q 19 -25.348 10.458 81.846 1.00 63.20 ATOM 177 CA LYS Q 19 -23.984 10.093 81.490 1.00 62.95 ATOM 178 C LYS Q 19 -23.595 10.683 80.139 1.00 63.12 ATOM 179 O LYS Q 19 -22.676 11.503 80.046 1.00 63.03 ATOM 180 CB LYS Q 19 -23.853 8.569 81.480 1.00 62.78 ATOM 181 CG LYS Q 19 -22.429 8.032 81.445 1.00 62.47 ATOM 182 CD LYS Q 19 -22.429 6.504 81.554 1.00 62.33 ATOM 183 CE LYS Q 19 -21.018 5.941 81.707 1.00 62.01 ATOM 184 NZ LYS Q 19 -20.301 6.489 82.893 1.00 61.76 ATOM 185 N VAL Q 20 -24.299 10.269 79.079 1.00 52.33 ATOM 186 CA VAL Q 20 -23.987 10.726 77.724 1.00 52.53 ATOM 187 C VAL Q 20 -23.855 12.240 77.680 1.00 52.67 ATOM 188 O VAL Q 20 -22.901 12.785 77.114 1.00 52.62 ATOM 189 CB VAL Q 20 -25.062 10.243 76.736 1.00 52.88 ATOM 190 CG1 VAL Q 20 -24.955 11.016 75.441 1.00 53.15 ATOM 191 CG2 VAL Q 20 -24.922 8.760 76.485 1.00 52.75 ATOM 192 N ARG Q 21 -24.814 12.940 78.284 1.00 55.72 ATOM 193 CA ARG Q 21 -24.839 14.391 78.180 1.00 55.91 ATOM 194 C ARG Q 21 -23.735 15.046 78.990 1.00 55.64 ATOM 195 O ARG Q 21 -23.350 16.181 78.685 1.00 55.76 ATOM 196 CB ARG Q 21 -26.197 14.932 78.623 1.00 56.21 ATOM 197 CG ARG Q 21 -26.468 16.329 78.116 1.00 56.54 ATOM 198 CD ARG Q 21 -27.702 16.900 78.736 1.00 56.80 ATOM 199 NE ARG Q 21 -27.757 18.339 78.530 1.00 57.05 ATOM 200 CZ ARG Q 21 -28.582 19.156 79.176 1.00 57.26 ATOM 201 NH1 ARG Q 21 -28.565 20.455 78.920 1.00 57.51 ATOM 202 NH2 ARG Q 21 -29.427 18.678 80.079 1.00 57.24 ATOM 203 N ALA Q 22 -23.217 14.360 80.010 1.00 57.14 ATOM 204 CA ALA Q 22 -22.151 14.939 80.816 1.00 56.88 ATOM 205 C ALA Q 22 -20.861 15.084 80.022 1.00 56.76 ATOM 206 O ALA Q 22 -20.059 15.975 80.314 1.00 56.68 ATOM 207 CB ALA Q 22 -21.918 14.088 82.061 1.00 56.57 ATOM 208 N ARG Q 23 -20.657 14.240 79.006 1.00 52.66 ATOM 209 CA ARG Q 23 -19.420 14.272 78.227 1.00 52.54 ATOM 210 C ARG Q 23 -19.114 15.659 77.691 1.00 52.74 ATOM 211 O ARG Q 23 -17.948 16.003 77.487 1.00 52.59 ATOM 212 CB ARG Q 23 -19.500 13.279 77.066 1.00 52.62 ATOM 213 CG ARG Q 23 -19.503 11.836 77.493 1.00 52.41 ATOM 214 CD ARG Q 23 -19.681 10.924 76.313 1.00 52.53 ATOM 215 NE ARG Q 23 -18.633 9.917 76.282 1.00 52.24 ATOM 216 CZ ARG Q 23 -17.605 9.941 75.441 1.00 52.18 ATOM 217 NH1 ARG Q 23 -16.686 8.986 75.484 1.00 51.93 ATOM 218 NH2 ARG Q 23 -17.497 10.912 74.551 1.00 52.40 ATOM 219 N SER Q 24 -20.130 16.460 77.445 1.00 66.04 ATOM 220 CA SER Q 24 -19.939 17.849 77.065 1.00 66.26 ATOM 221 C SER Q 24 -20.055 18.693 78.328 1.00 66.21 ATOM 222 O SER Q 24 -21.136 18.790 78.919 1.00 66.35 ATOM 223 CB SER Q 24 -20.969 18.263 76.020 1.00 66.69 ATOM 224 OG SER Q 24 -22.282 17.976 76.480 1.00 66.85 ATOM 225 N LYS Q 25 -18.946 19.287 78.748 1.00 82.13 ATOM 226 CA LYS Q 25 -18.959 20.144 79.926 1.00 82.10 ATOM 227 C LYS Q 25 -17.842 21.187 79.849 1.00 82.06 ATOM 228 O LYS Q 25 -18.075 22.382 80.071 1.00 82.28 ATOM 229 CB LYS Q 25 -18.832 19.310 81.213 1.00 81.77 ATOM 230 CG LYS Q 25 -20.177 18.862 81.808 1.00 81.87 ATOM 231 CD LYS Q 25 -20.168 18.821 83.341 1.00 81.67 ATOM 232 CE LYS Q 25 -19.270 17.717 83.896 1.00 81.28 ATOM 233 NZ LYS Q 25 -19.251 17.712 85.393 1.00 81.10 ATOM 234 MG MG Q1301 -31.498 -1.657 87.322 1.00 58.86 TER