Barium in the structure of Sam-I Riboswitch From T. Tencongensis Variant A94G Bound With Sam (pdb 3iqr)

The binding sites of Barium atom in the structure of Sam-I Riboswitch From T. Tencongensis Variant A94G Bound With Sam (pdb code 3iqr). This binding sites where shown with 5.0 Angstroms radius around Barium atom. The 3iqr structure was solved by R.K.MONTANGE, R.T.BATEY, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.9-2.5 Space group P43212 a (A) 61.804 b (A) 61.804 c (A) 157.568 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 24.9 Rfree (%) 29.3 Barium Binding Sites: Barium binding site 1 out of 9 in 3iqr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Barium in the PDB 3iqr. 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: G50, A: A52, A: Hoh440, conact list: Atom Atom Distance (A) Ba N7 A:A49 4.62 Ba N9 A:G50 4.99 Ba C8 A:G50 3.97 Ba C6 A:G50 3.58 Ba N1 A:G50 4.91 Ba C5 A:G50 3.50 Ba N7 A:G50 2.87 Ba C4 A:G50 4.77 Ba O6 A:G50 3.07 Ba OP1 A:A52 4.13 Ba P A:A52 4.65 Ba OP2 A:A52 4.22 Ba O A:Hoh440 3.50 interactive model: Barium binding site 2 out of 9 in 3iqr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Barium in the PDB 3iqr. 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: G16, A: U17, A: G18, A: G19, conact list: Atom Atom Distance (A) Ba OP2 A:G16 4.99 Ba C5 A:U17 4.92 Ba OP2 A:U17 4.75 Ba O4 A:U17 4.77 Ba C6 A:G18 3.75 Ba N1 A:G18 4.78 Ba C5 A:G18 4.51 Ba N7 A:G18 4.54 Ba O6 A:G18 2.66 Ba O6 A:G19 4.81 interactive model: Barium binding site 3 out of 9 in 3iqr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Barium in the PDB 3iqr. 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: Hoh405, conact list: Atom Atom Distance (A) Ba N7 A:G73 4.88 Ba C8 A:G74 4.25 Ba C6 A:G74 3.37 Ba N1 A:G74 4.64 Ba C5 A:G74 3.54 Ba N7 A:G74 3.11 Ba C4 A:G74 4.80 Ba O6 A:G74 2.72 Ba OP1 A:A76 4.35 Ba OP2 A:A76 4.84 Ba O A:Hoh405 4.23 interactive model: Barium binding site 4 out of 9 in 3iqr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Barium in the PDB 3iqr. 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: C25, A: U64, A: C66, A: U67, A: G68, A: Hoh419, conact list: Atom Atom Distance (A) Ba N4 A:C25 4.57 Ba C2 A:U64 4.11 Ba N1 A:U64 4.73 Ba C1' A:U64 4.32 Ba O2 A:U64 3.06 Ba C2' A:U64 3.66 Ba O2' A:U64 2.87 Ba OP2 A:C66 4.32 Ba C5 A:U67 4.29 Ba C4 A:U67 3.98 Ba O4 A:U67 3.04 Ba O6 A:G68 4.71 Ba O A:Hoh419 4.74 interactive model: Barium binding site 5 out of 9 in 3iqr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Barium in the PDB 3iqr. 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: C31, A: G32, conact list: Atom Atom Distance (A) Ba OP2 A:C31 4.74 Ba C8 A:G32 4.57 Ba C5 A:G32 4.68 Ba N7 A:G32 3.87 Ba OP2 A:G32 4.62 Ba O6 A:G32 4.71 interactive model: Barium binding site 6 out of 9 in 3iqr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Barium in the PDB 3iqr. 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: A9, A: A10, A: G11, A: A62, A: U63, A: U64, conact list: Atom Atom Distance (A) Ba C3' A:A9 4.91 Ba O3' A:A9 3.64 Ba C8 A:A10 4.77 Ba P A:A10 3.78 Ba N7 A:A10 4.65 Ba OP2 A:A10 2.90 Ba O5' A:A10 4.17 Ba C8 A:G11 5.00 Ba C6 A:G11 4.97 Ba C5 A:G11 4.86 Ba N7 A:G11 4.00 Ba OP2 A:G11 4.70 Ba O6 A:G11 4.30 Ba OP1 A:A62 3.93 Ba C3' A:U63 4.27 Ba O3' A:U63 3.43 Ba C5' A:U63 4.69 Ba C4' A:U63 4.11 Ba OP1 A:U64 4.39 Ba P A:U64 3.84 Ba OP2 A:U64 3.20 interactive model: Barium binding site 7 out of 9 in 3iqr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Barium in the PDB 3iqr. 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 4.69 Ba C6 A:A85 4.70 Ba C5 A:A85 4.47 Ba N6 A:A85 4.39 Ba N7 A:A85 3.95 Ba OP2 A:A85 4.92 Ba C8 A:G86 4.22 Ba C6 A:G86 3.90 Ba C5 A:G86 3.83 Ba N7 A:G86 3.11 Ba O6 A:G86 3.29 Ba N6 A:A87 4.72 interactive model: Barium binding site 8 out of 9 in 3iqr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Barium in the PDB 3iqr. 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: G55, A: G56, conact list: Atom Atom Distance (A) Ba C6 A:A45 4.88 Ba N1 A:A45 4.30 Ba N6 A:A45 4.62 Ba N3 A:A46 4.65 Ba C2 A:A46 3.37 Ba C6 A:A46 4.36 Ba N1 A:A46 3.12 Ba N6 A:A46 4.75 Ba C8 A:G55 4.25 Ba C6 A:G55 4.23 Ba C5 A:G55 4.03 Ba N7 A:G55 3.31 Ba OP2 A:G55 4.79 Ba O6 A:G55 3.80 Ba O6 A:G56 4.99 interactive model: Barium binding site 9 out of 9 in 3iqr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Barium in the PDB 3iqr. 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: G2, A: Hoh402, A: Hoh403, conact list: Atom Atom Distance (A) Ba C8 A:G1 3.95 Ba C6 A:G1 4.00 Ba C5 A:G1 3.79 Ba N7 A:G1 2.91 Ba OP3 A:G1 4.54 Ba O6 A:G1 3.48 Ba O6 A:G2 5.00 Ba O A:Hoh402 4.89 Ba O A:Hoh403 4.22 interactive model: