Barium in the structure of Sam-I Riboswitch Containing the Kt-23 Kink Turn of T. Solenopsae in Complex With S-Adenosylmethionine (pdb 4aeb)

The binding sites of Barium atom in the structure of Sam-I Riboswitch Containing the Kt-23 Kink Turn of T. Solenopsae in Complex With S-Adenosylmethionine (pdb code 4aeb). This binding sites where shown with 5.0 Angstroms radius around Barium atom. The 4aeb structure was solved by K.T.SCHROEDER, P.DALDROP, S.A.MCPHEE, D.M.J.LILLEY, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 57.1-2.9 Space group P43212 a (A) 61.300 b (A) 61.300 c (A) 157.538 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.373 Rfree (%) 24.853 Barium Binding Sites: Barium binding site 1 out of 15 in 4aeb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Barium in the PDB 4aeb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Barium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: A85, A: G86, A: A87, conact list: Atom Atom Distance (A) Ba C8 A:A85 4.35 Ba C6 A:A85 4.64 Ba C5 A:A85 4.29 Ba N6 A:A85 4.46 Ba N7 A:A85 3.74 Ba OP2 A:A85 4.59 Ba N9 A:G86 4.98 Ba C8 A:G86 3.79 Ba C6 A:G86 4.04 Ba C5 A:G86 3.74 Ba N7 A:G86 2.78 Ba C4 A:G86 4.97 Ba O6 A:G86 3.61 Ba N6 A:A87 4.49 Ba N7 A:A87 4.97 interactive model: Barium binding site 2 out of 15 in 4aeb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Barium in the PDB 4aeb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Barium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: U67, A: C69, A: A70, A: U81, A: G82, A: A83, A: Hoh2007, A: Hoh2008, conact list: Atom Atom Distance (A) Ba OP1 A:U67 4.27 Ba N4 A:C69 4.24 Ba N6 A:A70 4.65 Ba N3 A:U81 4.84 Ba C5 A:U81 4.31 Ba C4 A:U81 3.80 Ba O4 A:U81 2.95 Ba C6 A:G82 4.05 Ba C5 A:G82 4.60 Ba N7 A:G82 4.36 Ba O6 A:G82 2.96 Ba N6 A:A83 4.11 Ba O A:Hoh2007 4.70 Ba O A:Hoh2008 4.27 interactive model: Barium binding site 3 out of 15 in 4aeb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Barium in the PDB 4aeb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Barium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: A24, A: C25, A: U64, A: C66, A: U67, A: G68, conact list: Atom Atom Distance (A) Ba N6 A:A24 4.23 Ba N7 A:A24 4.82 Ba N4 A:C25 4.55 Ba N3 A:U64 4.72 Ba C2 A:U64 3.72 Ba N1 A:U64 4.38 Ba C1' A:U64 4.13 Ba O2 A:U64 2.65 Ba O3' A:U64 4.85 Ba C2' A:U64 4.22 Ba O2' A:U64 3.14 Ba OP2 A:C66 4.42 Ba C5 A:U67 4.41 Ba C4 A:U67 4.13 Ba O4 A:U67 3.20 Ba O6 A:G68 4.79 interactive model: Barium binding site 4 out of 15 in 4aeb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Barium in the PDB 4aeb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Barium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: G23, A: U26, A: G27, A: G28, A: Hoh2003, conact list: Atom Atom Distance (A) Ba O6 A:G23 4.98 Ba N3 A:U26 4.87 Ba C6 A:U26 4.49 Ba C5 A:U26 3.73 Ba C4 A:U26 3.95 Ba OP2 A:U26 4.72 Ba O4 A:U26 3.90 Ba C8 A:G27 4.34 Ba C6 A:G27 3.99 Ba C5 A:G27 3.95 Ba N7 A:G27 3.24 Ba O6 A:G27 3.36 Ba C6 A:G28 4.27 Ba C5 A:G28 4.45 Ba N7 A:G28 4.04 Ba O6 A:G28 3.60 Ba O A:Hoh2003 3.67 interactive model: Barium binding site 5 out of 15 in 4aeb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Barium in the PDB 4aeb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Barium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: G15, A: G16, A: G17, A: Hoh2002, conact list: Atom Atom Distance (A) Ba C8 A:G15 4.81 Ba C6 A:G15 3.98 Ba N1 A:G15 4.81 Ba C5 A:G15 4.06 Ba N7 A:G15 4.02 Ba C4 A:G15 4.93 Ba O6 A:G15 3.79 Ba C8 A:G16 4.23 Ba C6 A:G16 3.75 Ba C5 A:G16 3.75 Ba N7 A:G16 3.08 Ba O6 A:G16 3.07 Ba N7 A:G17 4.69 Ba O6 A:G17 4.59 Ba O A:Hoh2002 4.99 interactive model: Barium binding site 6 out of 15 in 4aeb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Barium in the PDB 4aeb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Barium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: G13, A: C60, A: A61, conact list: Atom Atom Distance (A) Ba C8 A:G13 4.21 Ba C6 A:G13 4.25 Ba C5 A:G13 4.06 Ba N7 A:G13 3.21 Ba OP2 A:G13 4.94 Ba O6 A:G13 3.72 Ba O2 A:C60 4.56 Ba C2' A:C60 4.56 Ba O2' A:C60 4.40 Ba OP2 A:A61 4.12 interactive model: Barium binding site 7 out of 15 in 4aeb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Barium in the PDB 4aeb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Barium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: G1, A: K1108, A: Ba1118, A: Hoh2010, conact list: Atom Atom Distance (A) Ba C8 A:G1 3.92 Ba C6 A:G1 4.24 Ba C5 A:G1 3.93 Ba N7 A:G1 2.98 Ba O6 A:G1 3.79 Ba K A:K1108 4.97 Ba BA A:Ba1118 4.49 Ba O A:Hoh2010 4.64 interactive model: Barium binding site 8 out of 15 in 4aeb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Barium in the PDB 4aeb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Barium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: A45, A: A46, A: U54, A: G55, conact list: Atom Atom Distance (A) Ba C6 A:A45 4.99 Ba N1 A:A45 4.54 Ba N6 A:A45 4.67 Ba N3 A:A46 4.77 Ba C2 A:A46 3.44 Ba C6 A:A46 4.13 Ba N1 A:A46 2.96 Ba N6 A:A46 4.40 Ba C5 A:U54 4.74 Ba C4 A:U54 4.57 Ba O4 A:U54 4.52 Ba C8 A:G55 3.94 Ba C6 A:G55 4.74 Ba C5 A:G55 4.28 Ba N7 A:G55 3.19 Ba OP2 A:G55 4.18 Ba O6 A:G55 4.41 interactive model: Barium binding site 9 out of 15 in 4aeb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Barium in the PDB 4aeb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Barium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: G74, A: Ba1104, conact list: Atom Atom Distance (A) Ba C6 A:G74 3.90 Ba N1 A:G74 4.36 Ba O6 A:G74 2.81 Ba BA A:Ba1104 4.62 interactive model: Barium binding site 10 out of 15 in 4aeb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Barium in the PDB 4aeb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Barium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: G73, A: G74, A: A76, A: Ba1103, conact list: Atom Atom Distance (A) Ba N7 A:G73 4.88 Ba OP2 A:G73 4.95 Ba C8 A:G74 4.02 Ba C6 A:G74 3.96 Ba C5 A:G74 3.77 Ba N7 A:G74 3.07 Ba C4 A:G74 4.90 Ba O6 A:G74 3.57 Ba OP2 A:A76 4.57 Ba BA A:Ba1103 4.62 interactive model: Barium binding site 11 out of 15 in 4aeb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Barium in the PDB 4aeb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Barium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: A49, A: A50, A: A52, A: Ba1106, conact list: Atom Atom Distance (A) Ba N6 A:A49 4.95 Ba N7 A:A49 4.43 Ba N9 A:A50 4.76 Ba C8 A:A50 3.51 Ba C6 A:A50 4.37 Ba C5 A:A50 3.80 Ba N6 A:A50 4.05 Ba N7 A:A50 2.70 Ba C4 A:A50 4.91 Ba OP1 A:A52 3.57 Ba P A:A52 4.83 Ba BA A:Ba1106 4.86 interactive model: Barium binding site 12 out of 15 in 4aeb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Barium in the PDB 4aeb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Barium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: A50, A: A52, A: Ba1105, conact list: Atom Atom Distance (A) Ba C6 A:A50 3.72 Ba N1 A:A50 4.35 Ba C5 A:A50 4.75 Ba N6 A:A50 2.50 Ba OP1 A:A52 4.02 Ba C5' A:A52 4.75 Ba BA A:Ba1105 4.86 interactive model: Barium binding site 13 out of 15 in 4aeb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Barium in the PDB 4aeb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Barium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: C8, A: A10, A: G11, A: A12, A: U64, A: K1112, A: Sam1116, conact list: Atom Atom Distance (A) Ba O2' A:C8 4.51 Ba N6 A:A10 4.22 Ba N7 A:A10 4.30 Ba C6 A:G11 3.94 Ba N1 A:G11 4.81 Ba C5 A:G11 4.90 Ba O6 A:G11 2.73 Ba N6 A:A12 4.99 Ba OP1 A:U64 3.10 Ba P A:U64 3.86 Ba OP2 A:U64 3.99 Ba C5' A:U64 4.68 Ba O5' A:U64 4.21 Ba K A:K1112 3.72 Ba OXT A:Sam1116 4.54 interactive model: Barium binding site 14 out of 15 in 4aeb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 14 of Barium in the PDB 4aeb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Barium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: A33, A: Hoh2009, conact list: Atom Atom Distance (A) Ba OP2 A:A33 4.23 Ba O A:Hoh2009 3.13 interactive model: Barium binding site 15 out of 15 in 4aeb Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 15 of Barium in the PDB 4aeb. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Barium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: G1, A: Ba1101, A: Hoh2010, conact list: Atom Atom Distance (A) Ba P A:G1 4.26 Ba N7 A:G1 4.99 Ba OP2 A:G1 2.84 Ba O5' A:G1 4.72 Ba BA A:Ba1101 4.49 Ba O A:Hoh2010 3.18 interactive model: