1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Thiviyanathan, V. Guliaev, A.B. Leontis, N.B. Gorenstein, D.G. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 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 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 UK J.Mol.Biol. JMOBAK 0070 0022-2836 300 1143 1154 10.1006/jmbi.2000.3931 10903860 Solution conformation of a bulged adenosine base in an RNA duplex by relaxation matrix refinement. 2000 10.2210/pdb1k8s/pdb pdb_00001k8s 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M 1 1.0 Bulged base RNA duplex E Coli 5S rRNA 4211.582 5'-R(*GP*GP*CP*AP*GP*AP*GP*UP*GP*CP*CP*GP*C)-3' 1 syn polymer 3802.328 5'-R(*GP*CP*GP*GP*CP*AP*CP*CP*UP*GP*CP*C)-3' 1 syn polymer no no GGCAGAGUGCCGC GGCAGAGUGCCGC A polyribonucleotide no no GCGGCACCUGCC GCGGCACCUGCC 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 -7.155 1 19 A 1 B 25 -0.662 A_G1:C25_B 1 3.286 -0.439 -0.222 -0.234 2.275 1 19 A 2 B 24 0.373 A_G2:C24_B 2 -6.351 -0.267 0.126 -0.155 2.881 1 19 A 3 B 23 0.310 A_C3:G23_B 3 -15.578 0.548 -0.103 -0.272 -15.588 1 20 A 4 B 22 0.583 A_A4:U22_B 4 -13.630 -0.112 -0.108 -0.089 -10.459 1 19 A 5 B 21 -1.259 A_G5:C21_B 5 -19.144 -0.318 -0.157 -0.189 -17.716 1 19 A 7 B 20 0.348 A_G7:C20_B 6 -19.435 -0.321 0.098 -0.162 -11.636 1 20 A 8 B 19 4.834 A_U8:A19_B 7 -0.894 0.004 0.873 -0.143 5.892 1 19 A 9 B 18 -0.340 A_G9:C18_B 8 -19.264 -0.475 0.250 -0.261 -3.253 1 19 A 10 B 17 -0.539 A_C10:G17_B 9 -15.494 0.370 0.353 -0.213 -0.738 1 19 A 11 B 16 -0.446 A_C11:G16_B 10 -24.110 0.316 0.070 -0.231 -24.806 1 19 A 12 B 15 7.363 A_G12:C15_B 11 -29.070 -0.632 -0.937 -0.239 -24.615 1 19 A 13 B 14 2.101 A_C13:G14_B 12 12.521 0.489 0.469 -0.125 2.662 30.279 A A 1 2 11.188 B B 25 24 3.034 5.808 0.730 -1.574 AA_G1G2:C24C25_BB 1 -0.897 1.729 29.716 -4.045 -1.558 3.183 38.911 A A 2 3 1.850 B B 24 23 3.254 1.231 -0.261 -1.468 AA_G2C3:G23C24_BB 2 2.771 -4.164 38.797 -2.350 0.723 2.732 36.608 A A 3 4 23.667 B B 23 22 3.484 14.476 0.584 -1.335 AA_C3A4:U22G23_BB 3 2.208 -3.610 33.644 -4.103 -0.628 2.619 31.933 A A 4 5 17.684 B B 22 21 3.127 9.586 -0.498 -1.299 AA_A4G5:C21U22_BB 4 -0.707 1.304 30.488 -3.927 0.790 3.908 58.187 A A 5 7 17.260 B B 21 20 5.388 16.254 -1.867 -1.279 AA_G5G7:C20C21_BB 5 21.207 -22.519 52.172 -2.618 3.621 2.996 34.430 A A 7 8 0.529 B B 20 19 3.142 0.310 0.183 -0.989 AA_G7U8:A19C20_BB 6 -8.535 14.562 33.385 -1.716 -1.576 2.261 28.785 A A 8 9 8.420 B B 19 18 2.566 4.167 -0.756 -1.497 AA_U8G9:C18A19_BB 7 2.285 -4.617 28.398 -3.705 1.901 3.265 37.675 A A 9 10 5.347 B B 18 17 3.414 3.440 -0.231 -1.566 AA_G9C10:G17C18_BB 8 -4.766 7.408 37.230 -2.883 -0.277 2.932 29.826 A A 10 11 8.387 B B 17 16 3.134 4.286 0.762 -1.779 AA_C10C11:G16G17_BB 9 4.623 -9.048 29.166 -4.294 -0.576 1.289 41.499 A A 11 12 55.647 B B 16 15 3.794 33.575 0.315 -1.124 AA_C11G12:C15G16_BB 10 9.608 -15.924 22.778 -5.264 0.607 3.047 32.789 A A 12 13 5.296 B B 15 14 3.470 2.907 0.182 -0.758 AA_G12C13:G14C15_BB 11 -13.045 23.766 30.010 -1.864 -2.663 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2001-11-14 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name RCSB Y RCSB 2001-10-25 REL Enzymatically synthesized using T7 RNA Polymerase. sample Enzymatically synthesized using T7 RNA Polymerase. sample 1 2D NOESY 110 mM 6.8 ambient 298 K matrix relaxation, molecular dynamics, torsion angle dynamics 100 mM NaCl, 10 mM sodium phosphate, 0.02 mM EDTA D2O/H2O MSI data analysis Felix 95 Meadows, Gorenstein et al. iterative matrix relaxation MORASS 2.1 UCSF refinement Amber 5.0 500 Varian VXRS RG5 1 n 1 G 1 A RG 2 n 2 G 2 A RC 3 n 3 C 3 A RA 4 n 4 A 4 A RG 5 n 5 G 5 A RA 6 n 6 A 6 A RG 7 n 7 G 7 A RU 8 n 8 U 8 A RG 9 n 9 G 9 A RC 10 n 10 C 10 A RC 11 n 11 C 11 A RG 12 n 12 G 12 A RC3 13 n 13 C 13 A RG5 14 n 1 G 14 B RC 15 n 2 C 15 B RG 16 n 3 G 16 B RG 17 n 4 G 17 B RC 18 n 5 C 18 B RA 19 n 6 A 19 B RC 20 n 7 C 20 B RC 21 n 8 C 21 B RU 22 n 9 U 22 B RG 23 n 10 G 23 B RC 24 n 11 C 24 B RC3 25 n 12 C 25 B author_defined_assembly 2 dimeric 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 A 4 0.071 SIDE CHAIN 1 A G 7 0.051 SIDE CHAIN 1 A G 9 0.092 SIDE CHAIN 1 A C 11 0.089 SIDE CHAIN 1 A G 12 0.079 SIDE CHAIN 1 A C 13 0.087 SIDE CHAIN 1 B C 20 0.061 SIDE CHAIN 1 B C 21 0.096 SIDE CHAIN 1 4.97 0.70 108.50 113.47 A A A O4' C1' N9 G G G 1 1 1 N 1 4.74 0.70 108.50 113.24 A A A O4' C1' N1 C C C 3 3 3 N 1 4.41 0.70 108.50 112.91 A A A O4' C1' N9 A A A 4 4 4 N 1 3.29 0.50 117.70 120.99 A A A C5 C6 N1 A A A 6 6 6 N 1 -4.11 0.60 118.60 114.49 A A A N1 C6 N6 A A A 6 6 6 N 1 6.59 0.70 108.50 115.09 A A A O4' C1' N1 U U U 8 8 8 N 1 6.37 0.70 108.50 114.87 A A A O4' C1' N1 C C C 11 11 11 N 1 -4.31 0.70 121.90 117.59 A A A N3 C2 O2 C C C 11 11 11 N 1 4.47 0.70 108.50 112.97 A A A O4' C1' N9 G G G 12 12 12 N 1 4.80 0.70 108.50 113.30 A A A O4' C1' N1 C C C 13 13 13 N 1 5.92 0.80 101.50 107.42 B B B C3' C2' C1' C C C 15 15 15 N 1 4.84 0.70 108.50 113.34 B B B O4' C1' N1 C C C 15 15 15 N 1 4.62 0.70 108.50 113.12 B B B O4' C1' N9 G G G 16 16 16 N 1 4.81 0.70 108.50 113.31 B B B O4' C1' N1 C C C 18 18 18 N 1 4.22 0.70 108.50 112.72 B B B O4' C1' N9 A A A 19 19 19 N 1 -4.15 0.60 118.60 114.45 B B B N1 C6 N6 A A A 19 19 19 N 1 4.46 0.70 108.50 112.96 B B B O4' C1' N1 C C C 20 20 20 N 1 5.15 0.80 101.50 106.65 B B B C3' C2' C1' C C C 21 21 21 N 1 5.26 0.80 101.50 106.76 B B B C3' C2' C1' U U U 22 22 22 N 1 5.15 0.70 108.50 113.65 B B B O4' C1' N1 U U U 22 22 22 N BULGED ADENOSINE IN AN RNA DUPLEX 1 N N 2 N N hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 B C 25 B N3 C 12 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 B C 25 B O2 C 12 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 B C 25 B N4 C 12 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 B C 24 B N3 C 11 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 B C 24 B O2 C 11 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 B C 24 B N4 C 11 1_555 hydrog WATSON-CRICK A C 3 A N3 C 3 1_555 B G 23 B N1 G 10 1_555 hydrog WATSON-CRICK A C 3 A N4 C 3 1_555 B G 23 B O6 G 10 1_555 hydrog WATSON-CRICK A C 3 A O2 C 3 1_555 B G 23 B N2 G 10 1_555 hydrog WATSON-CRICK A A 4 A N1 A 4 1_555 B U 22 B N3 U 9 1_555 hydrog WATSON-CRICK A A 4 A N6 A 4 1_555 B U 22 B O4 U 9 1_555 hydrog WATSON-CRICK A G 5 A N1 G 5 1_555 B C 21 B N3 C 8 1_555 hydrog WATSON-CRICK A G 5 A N2 G 5 1_555 B C 21 B O2 C 8 1_555 hydrog WATSON-CRICK A G 5 A O6 G 5 1_555 B C 21 B N4 C 8 1_555 hydrog WATSON-CRICK A G 7 A N1 G 7 1_555 B C 20 B N3 C 7 1_555 hydrog WATSON-CRICK A G 7 A N2 G 7 1_555 B C 20 B O2 C 7 1_555 hydrog WATSON-CRICK A G 7 A O6 G 7 1_555 B C 20 B N4 C 7 1_555 hydrog WATSON-CRICK A U 8 A N3 U 8 1_555 B A 19 B N1 A 6 1_555 hydrog WATSON-CRICK A U 8 A O4 U 8 1_555 B A 19 B N6 A 6 1_555 hydrog WATSON-CRICK A G 9 A N1 G 9 1_555 B C 18 B N3 C 5 1_555 hydrog WATSON-CRICK A G 9 A N2 G 9 1_555 B C 18 B O2 C 5 1_555 hydrog WATSON-CRICK A G 9 A O6 G 9 1_555 B C 18 B N4 C 5 1_555 hydrog WATSON-CRICK A C 10 A N3 C 10 1_555 B G 17 B N1 G 4 1_555 hydrog WATSON-CRICK A C 10 A N4 C 10 1_555 B G 17 B O6 G 4 1_555 hydrog WATSON-CRICK A C 10 A O2 C 10 1_555 B G 17 B N2 G 4 1_555 hydrog WATSON-CRICK A C 11 A N3 C 11 1_555 B G 16 B N1 G 3 1_555 hydrog WATSON-CRICK A C 11 A N4 C 11 1_555 B G 16 B O6 G 3 1_555 hydrog WATSON-CRICK A C 11 A O2 C 11 1_555 B G 16 B N2 G 3 1_555 hydrog WATSON-CRICK A G 12 A N1 G 12 1_555 B C 15 B N3 C 2 1_555 hydrog WATSON-CRICK A G 12 A N2 G 12 1_555 B C 15 B O2 C 2 1_555 hydrog WATSON-CRICK A G 12 A O6 G 12 1_555 B C 15 B N4 C 2 1_555 hydrog WATSON-CRICK A C 13 A N3 C 13 1_555 B G 14 B N1 G 1 1_555 hydrog WATSON-CRICK A C 13 A N4 C 13 1_555 B G 14 B O6 G 1 1_555 hydrog WATSON-CRICK A C 13 A O2 C 13 1_555 B G 14 B N2 G 1 1_555 RNA Bulged base, bulged adenosine, bulged RNA, RNA bulges, RNA 1K8S PDB 1 1K8S 1K8S PDB 2 1K8S 1 13 1K8S 1 13 1K8S A 1 1 13 14 25 1K8S 14 25 1K8S B 2 1 12