Barium in the structure of Crystal Structure of An Rna Tetraplex (Ugaggu)4 With A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads (pdb 1j6s)

The binding sites of Barium atom in the structure of Crystal Structure of An Rna Tetraplex (Ugaggu)4 With A- Tetrads, G-Tetrads, U-Tetrads and G-U Octads (pdb code 1j6s). This binding sites where shown with 5.0 Angstroms radius around Barium atom. The 1j6s structure was solved by B.PAN, Y.XIONG, K.SHI, J.DENG, M.SUNDARALINGAM, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-1.4 Space group P4212 a (A) 37.984 b (A) 37.984 c (A) 82.195 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.6 Rfree (%) 18.4 Barium Binding Sites: Barium binding site 1 out of 8 in 1j6s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Barium in the PDB 1j6s. 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: G4, A: G5, A: Ba108, conact list: Atom Atom Distance (A) Ba C6 A:G4 3.62 Ba N1 A:G4 3.88 Ba C5 A:G4 4.88 Ba O6 A:G4 2.79 Ba C6 A:G5 3.70 Ba N1 A:G5 4.00 Ba C5 A:G5 4.98 Ba O6 A:G5 2.73 Ba BA A:Ba108 4.39 interactive model: Barium binding site 2 out of 8 in 1j6s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Barium in the PDB 1j6s. 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: G5, A: U6, A: Ba105, A: Hoh387, conact list: Atom Atom Distance (A) Ba C6 A:G5 4.19 Ba N1 A:G5 4.47 Ba O6 A:G5 3.66 Ba N3 A:U6 3.55 Ba C2 A:U6 4.84 Ba C5 A:U6 4.64 Ba C4 A:U6 3.32 Ba O4 A:U6 2.37 Ba BA A:Ba105 4.39 Ba O A:Hoh387 2.35 interactive model: Barium binding site 3 out of 8 in 1j6s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Barium in the PDB 1j6s. 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: B: G10, B: G11, B: U12, B: Na207, conact list: Atom Atom Distance (A) Ba C6 B:G10 3.60 Ba N1 B:G10 3.94 Ba C5 B:G10 4.84 Ba O6 B:G10 2.70 Ba C6 B:G11 3.68 Ba N1 B:G11 3.99 Ba C5 B:G11 4.96 Ba O6 B:G11 2.70 Ba O4 B:U12 4.94 Ba NA B:Na207 3.32 interactive model: Barium binding site 4 out of 8 in 1j6s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Barium in the PDB 1j6s. 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: B: Bru7, B: G8, B: Na202, C: Na209, conact list: Atom Atom Distance (A) Ba N3 B:Bru7 4.29 Ba C4 B:Bru7 3.75 Ba O4 B:Bru7 2.56 Ba C6 B:G8 3.86 Ba N1 B:G8 4.19 Ba O6 B:G8 3.02 Ba NA B:Na202 4.05 Ba NA C:Na209 2.61 interactive model: Barium binding site 5 out of 8 in 1j6s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Barium in the PDB 1j6s. 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: C: G16, C: G17, C: Na201, conact list: Atom Atom Distance (A) Ba C6 C:G16 3.64 Ba N1 C:G16 3.93 Ba C5 C:G16 4.88 Ba O6 C:G16 2.73 Ba C6 C:G17 3.69 Ba N1 C:G17 3.98 Ba O6 C:G17 2.74 Ba NA C:Na201 3.11 interactive model: Barium binding site 6 out of 8 in 1j6s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Barium in the PDB 1j6s. 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: C: G17, C: U18, C: Hoh313, C: Hoh369, C: Hoh371, conact list: Atom Atom Distance (A) Ba OP2 C:G17 3.89 Ba C3' C:U18 3.67 Ba C1' C:U18 4.41 Ba O2 C:U18 4.92 Ba O3' C:U18 2.79 Ba C2' C:U18 3.62 Ba C4' C:U18 4.98 Ba O2' C:U18 2.89 Ba O C:Hoh313 2.91 Ba O C:Hoh369 3.14 Ba O C:Hoh371 2.83 interactive model: Barium binding site 7 out of 8 in 1j6s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Barium in the PDB 1j6s. 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: D: G22, D: G23, conact list: Atom Atom Distance (A) Ba C6 D:G22 3.60 Ba N1 D:G22 3.87 Ba C5 D:G22 4.82 Ba O6 D:G22 2.80 Ba C6 D:G23 3.73 Ba N1 D:G23 4.04 Ba O6 D:G23 2.80 interactive model: Barium binding site 8 out of 8 in 1j6s Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Barium in the PDB 1j6s. 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: D: Bru19, D: G20, D: Na208, conact list: Atom Atom Distance (A) Ba N3 D:Bru19 4.34 Ba C4 D:Bru19 3.89 Ba O4 D:Bru19 2.78 Ba C6 D:G20 3.72 Ba N1 D:G20 4.09 Ba C5 D:G20 4.92 Ba O6 D:G20 2.77 Ba NA D:Na208 3.84 interactive model: