The following lists all nucleosides found in tRNAPhe (the models shown here have different conformations from their occurences in tRNA): Adenosine(A, 5,9,13,14,21,23,29,31,35,36,38,39,44,62,64,66,67,73,76) in tRNA: show - hide reset 1-methyladenosine (1MA, 58) in tRNA: show - hide reset Guanosine(G, 1,3,4,15,18-20,22,24,30,42,43,45,51,53,57,65,71) in tRNA: show - hide reset N2-methylguanosine (2MG, 10) in tRNA: show - hide reset N2-dimethylguanosine (M2G, 26) in tRNA: show - hide reset 7-methylguanosine (7MG, 46) in tRNA: show - hide reset O2'-methylguanosine (OMG, 34) in tRNA: show - hide reset Cytidine(C, 2,11,13,25,27,28,48,56,60,61,63,70,72,74,75) in tRNA: show - hide reset 5-methylcytidine (5MC, 40,49) in tRNA: show - hide reset O2'-methylcytidine (OMC, 32) in tRNA: show - hide reset Uridine(U, 6-8,12,33,41,49,50,52,59,68,69) in tRNA: show - hide reset 5-methyluridine (5MU, 54) in tRNA: show - hide reset 5,6-dihydrouridine (H2U, 16,17) in tRNA: show - hide reset Pseudouridine (PSU, 39,55) in tRNA: show - hide reset Wybutosine (YG, 37) in tRNA: show - hide reset Basepairings in tRNAPhe are: G 1 - C 72 C 2 - G 71 G 3 - C 70 G 4 - U 69 : non-Watson-Crick A 5 - U 68 U 6 - A 67 U 7 - A 66 U 8 - A 14 - A 21 : non-W-C/triple pair A 9 - U 12 - A 23 : triple pair 2MG 10 - C 25 - G 45 : triple pair C 11 - G 24 - G 45 : triple pair C 13 - G 22 - 7MG 46 : triple pair G 15 - C 48 : non-Watson-Crick H2U 16 - U 59 : non-Watson-Crick G 18 - PSU 55 : non-Watson-Crick G 19 - C 56 M2G 26 - A 44 : non-Watson-Crick C 27 - G 43 C 28 - G 42 A 29 - U 41 G 30 - 5MC 40 A 31 - PSU 39 : non-Watson-Crick OMC 32 - A 38 : non-Watson-Crick 5MC 49 - G 65 U 50 - A 64 G 51 - C 63 U 52 - A 62 G 53 - C 61 5MU 54 - 1MA 58 : non-Watson-Crick nucleotides from acceptor to anticodon Unpaired bases in acceptor arm (A73, C74, C75, A76) in D arm (H2U17,G20) in anticodon arm (U33, YG37) in anticodon (OMG34, A35, A36) in variable loop (U47) in T psi C arm (G57, C60) The 'arm' designation originates from the time when only the secondary structure was known ('cloverleaf') and is somewhat misleading in the tertiary structure . The structures marked red and dark green in the left frame are magnesium ions partly coordinated with water molecules. They stabilize the tRNA once it is folded to its final form. One magnesium in the variable loop is completely (tetrahedrally) coordinated with water (shown as red spheres here) . The waters are hydrogen bridged to the phosphate backbone of U8 to U12 . Another magnesium surrounded by six waters is situated in the anticodon arm and held by G24, C25 and 5MC40 - G42 . Some more tightly bound water molecules are involved in hydrogen bridges . Other magnesiums are partly coordinated to the backbone phosphate groups by G19 by G20, A21 The backbone of the tRNA is partly stabilized by water molecules as shown here for the T psi C arm (G51 - U59) . The water molecules bind to posphate oxygens to bridge two nucleotides each . Some twin water molecules bridge the ribose 2' hydroxyl group to a phosphate oxygen of the next nucleotide . The most rigid part of the tRNA is the central domain formed by the D arm and the T psi C arm (which are folded tightly together) as judged from the temperature factor of the X-ray data (blue = rigid, red = movable). Literature: H Shi & PB Moore, The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: A classic structure revisited, RNA 6 (2000) 1091-1105 L Jovine et al, The crystal structure of yeast phenylalanine tRNA at 2.0 Å resolution: Cleavage by Mg2+ in 15-year old crystals, J. Mol. Biol. 301 (2000) 401-414 10-01 - Rolf Bergmann
Basepairings in tRNAPhe are:
nucleotides from acceptor to anticodon Unpaired bases in acceptor arm (A73, C74, C75, A76) in D arm (H2U17,G20) in anticodon arm (U33, YG37) in anticodon (OMG34, A35, A36) in variable loop (U47) in T psi C arm (G57, C60) The 'arm' designation originates from the time when only the secondary structure was known ('cloverleaf') and is somewhat misleading in the tertiary structure . The structures marked red and dark green in the left frame are magnesium ions partly coordinated with water molecules. They stabilize the tRNA once it is folded to its final form. One magnesium in the variable loop is completely (tetrahedrally) coordinated with water (shown as red spheres here) . The waters are hydrogen bridged to the phosphate backbone of U8 to U12 . Another magnesium surrounded by six waters is situated in the anticodon arm and held by G24, C25 and 5MC40 - G42 . Some more tightly bound water molecules are involved in hydrogen bridges . Other magnesiums are partly coordinated to the backbone phosphate groups by G19 by G20, A21 The backbone of the tRNA is partly stabilized by water molecules as shown here for the T psi C arm (G51 - U59) . The water molecules bind to posphate oxygens to bridge two nucleotides each . Some twin water molecules bridge the ribose 2' hydroxyl group to a phosphate oxygen of the next nucleotide . The most rigid part of the tRNA is the central domain formed by the D arm and the T psi C arm (which are folded tightly together) as judged from the temperature factor of the X-ray data (blue = rigid, red = movable). Literature: H Shi & PB Moore, The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: A classic structure revisited, RNA 6 (2000) 1091-1105 L Jovine et al, The crystal structure of yeast phenylalanine tRNA at 2.0 Å resolution: Cleavage by Mg2+ in 15-year old crystals, J. Mol. Biol. 301 (2000) 401-414 10-01 - Rolf Bergmann
Unpaired bases
The 'arm' designation originates from the time when only the secondary structure was known ('cloverleaf') and is somewhat misleading in the tertiary structure . The structures marked red and dark green in the left frame are magnesium ions partly coordinated with water molecules. They stabilize the tRNA once it is folded to its final form. One magnesium in the variable loop is completely (tetrahedrally) coordinated with water (shown as red spheres here) . The waters are hydrogen bridged to the phosphate backbone of U8 to U12 . Another magnesium surrounded by six waters is situated in the anticodon arm and held by G24, C25 and 5MC40 - G42 . Some more tightly bound water molecules are involved in hydrogen bridges . Other magnesiums are partly coordinated to the backbone phosphate groups by G19 by G20, A21 The backbone of the tRNA is partly stabilized by water molecules as shown here for the T psi C arm (G51 - U59) . The water molecules bind to posphate oxygens to bridge two nucleotides each . Some twin water molecules bridge the ribose 2' hydroxyl group to a phosphate oxygen of the next nucleotide . The most rigid part of the tRNA is the central domain formed by the D arm and the T psi C arm (which are folded tightly together) as judged from the temperature factor of the X-ray data (blue = rigid, red = movable). Literature: H Shi & PB Moore, The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: A classic structure revisited, RNA 6 (2000) 1091-1105 L Jovine et al, The crystal structure of yeast phenylalanine tRNA at 2.0 Å resolution: Cleavage by Mg2+ in 15-year old crystals, J. Mol. Biol. 301 (2000) 401-414 10-01 - Rolf Bergmann
The structures marked red and dark green in the left frame are magnesium ions partly coordinated with water molecules. They stabilize the tRNA once it is folded to its final form. One magnesium in the variable loop is completely (tetrahedrally) coordinated with water (shown as red spheres here) . The waters are hydrogen bridged to the phosphate backbone of U8 to U12 . Another magnesium surrounded by six waters is situated in the anticodon arm and held by G24, C25 and 5MC40 - G42 . Some more tightly bound water molecules are involved in hydrogen bridges . Other magnesiums are partly coordinated to the backbone phosphate groups by G19 by G20, A21 The backbone of the tRNA is partly stabilized by water molecules as shown here for the T psi C arm (G51 - U59) . The water molecules bind to posphate oxygens to bridge two nucleotides each . Some twin water molecules bridge the ribose 2' hydroxyl group to a phosphate oxygen of the next nucleotide . The most rigid part of the tRNA is the central domain formed by the D arm and the T psi C arm (which are folded tightly together) as judged from the temperature factor of the X-ray data (blue = rigid, red = movable). Literature: H Shi & PB Moore, The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: A classic structure revisited, RNA 6 (2000) 1091-1105 L Jovine et al, The crystal structure of yeast phenylalanine tRNA at 2.0 Å resolution: Cleavage by Mg2+ in 15-year old crystals, J. Mol. Biol. 301 (2000) 401-414 10-01 - Rolf Bergmann
The backbone of the tRNA is partly stabilized by water molecules as shown here for the T psi C arm (G51 - U59) . The water molecules bind to posphate oxygens to bridge two nucleotides each . Some twin water molecules bridge the ribose 2' hydroxyl group to a phosphate oxygen of the next nucleotide . The most rigid part of the tRNA is the central domain formed by the D arm and the T psi C arm (which are folded tightly together) as judged from the temperature factor of the X-ray data (blue = rigid, red = movable). Literature: H Shi & PB Moore, The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: A classic structure revisited, RNA 6 (2000) 1091-1105 L Jovine et al, The crystal structure of yeast phenylalanine tRNA at 2.0 Å resolution: Cleavage by Mg2+ in 15-year old crystals, J. Mol. Biol. 301 (2000) 401-414 10-01 - Rolf Bergmann
The most rigid part of the tRNA is the central domain formed by the D arm and the T psi C arm (which are folded tightly together) as judged from the temperature factor of the X-ray data (blue = rigid, red = movable). Literature: H Shi & PB Moore, The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: A classic structure revisited, RNA 6 (2000) 1091-1105 L Jovine et al, The crystal structure of yeast phenylalanine tRNA at 2.0 Å resolution: Cleavage by Mg2+ in 15-year old crystals, J. Mol. Biol. 301 (2000) 401-414 10-01 - Rolf Bergmann
