Potassium in the structure of Crystal Structure of Manganese Bound M-Box Rna (pdb 3pdr)

The binding sites of Potassium atom in the structure of Crystal Structure of Manganese Bound M-Box Rna (pdb code 3pdr). This binding sites where shown with 5.0 Angstroms radius around Potassium atom. The 3pdr structure was solved by A RAMESH, W.C.WINKLER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 47.5-1.9 Space group P212121 a (A) 68.780 b (A) 102.487 c (A) 126.375 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.2 Rfree (%) 22.8 Potassium Binding Sites: Potassium binding site 1 out of 6 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Potassium in the PDB 3pdr. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Potassium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: G27, X: U28, X: G29, X: A155, X: A156, X: G157, X: C158, X: Hoh212, X: Hoh213, X: Hoh236, X: Hoh266, X: Hoh342, conact list: Atom Atom Distance (A) K C6 X:G27 4.43 K O6 X:G27 3.39 K N3 X:U28 3.94 K C4 X:U28 3.86 K O4 X:U28 2.97 K N3 X:G29 4.95 K N2 X:G29 3.81 K C2 X:G29 4.05 K C6 X:G29 4.72 K N1 X:G29 3.87 K OP1 X:A155 4.65 K P X:A155 3.97 K OP2 X:A155 2.93 K C5' X:A155 3.70 K O5' X:A155 4.18 K OP1 X:A156 4.71 K C6 X:G157 4.02 K C5 X:G157 4.57 K N7 X:G157 4.39 K O6 X:G157 3.00 K N3 X:C158 4.88 K C4 X:C158 4.34 K N4 X:C158 3.31 K O X:Hoh212 3.02 K O X:Hoh213 4.67 K O X:Hoh236 4.40 K O X:Hoh266 3.60 K O X:Hoh342 3.07 interactive model: Potassium binding site 2 out of 6 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Potassium in the PDB 3pdr. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Potassium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: G66, X: U67, X: C68, X: A74, X: C75, X: A106, X: G107, X: Hoh186, conact list: Atom Atom Distance (A) K N2 X:G66 4.01 K C2 X:G66 4.93 K C2 X:U67 4.10 K N1 X:U67 4.76 K C1' X:U67 4.31 K O2 X:U67 2.95 K C2' X:U67 4.45 K O2' X:U67 4.06 K O4' X:C68 4.67 K N3 X:A74 4.91 K C2 X:A74 4.29 K C2 X:C75 4.20 K N1 X:C75 4.88 K C1' X:C75 4.63 K O2 X:C75 3.21 K C3' X:A106 4.01 K O3' X:A106 3.18 K C2' X:A106 4.27 K C4' X:A106 4.10 K O2' X:A106 3.35 K OP1 X:G107 3.97 K P X:G107 4.25 K O5' X:G107 4.90 K O X:Hoh186 3.27 interactive model: Potassium binding site 3 out of 6 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Potassium in the PDB 3pdr. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Potassium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: A25, X: A72, X: G73, X: A162, X: Hoh538, conact list: Atom Atom Distance (A) K N9 X:A25 4.81 K C1' X:A25 4.07 K O4' X:A25 4.10 K O3' X:A72 4.32 K OP1 X:G73 3.48 K P X:G73 4.61 K C1' X:A162 4.86 K O2' X:A162 4.78 K O X:Hoh538 3.62 interactive model: Potassium binding site 4 out of 6 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Potassium in the PDB 3pdr. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Potassium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: G27, A: U28, A: G29, A: A155, A: A156, A: G157, A: C158, A: Hoh181, A: Hoh225, A: Hoh235, A: Hoh260, A: Hoh276, conact list: Atom Atom Distance (A) K C6 A:G27 4.52 K O6 A:G27 3.52 K N3 A:U28 3.84 K C4 A:U28 3.81 K O4 A:U28 2.95 K N3 A:G29 4.77 K N2 A:G29 3.63 K C2 A:G29 3.87 K C6 A:G29 4.59 K N1 A:G29 3.73 K O6 A:G29 4.98 K OP1 A:A155 4.54 K P A:A155 3.94 K OP2 A:A155 2.89 K C5' A:A155 3.85 K O5' A:A155 4.30 K OP1 A:A156 4.90 K C6 A:G157 3.88 K C5 A:G157 4.44 K N7 A:G157 4.28 K O6 A:G157 2.87 K N3 A:C158 4.82 K C4 A:C158 4.19 K N4 A:C158 3.18 K O A:Hoh181 2.97 K O A:Hoh225 3.08 K O A:Hoh235 4.66 K O A:Hoh260 3.52 K O A:Hoh276 4.43 interactive model: Potassium binding site 5 out of 6 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Potassium in the PDB 3pdr. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Potassium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: G66, A: U67, A: C68, A: A74, A: C75, A: A106, A: G107, A: Hoh228, A: Hoh270, A: Hoh349, conact list: Atom Atom Distance (A) K N2 A:G66 3.82 K C2 A:G66 4.85 K N3 A:U67 4.92 K C2 A:U67 4.03 K N1 A:U67 4.82 K C1' A:U67 4.53 K O2 A:U67 2.90 K C2' A:U67 4.72 K O2' A:U67 4.44 K O4' A:C68 4.76 K N3 A:A74 4.59 K C2 A:A74 4.11 K N1 A:A74 4.95 K N3 A:C75 4.93 K C2 A:C75 4.07 K N1 A:C75 4.71 K C1' A:C75 4.40 K O2 A:C75 3.07 K O2' A:C75 4.75 K C3' A:A106 4.00 K O3' A:A106 3.16 K C2' A:A106 4.15 K C4' A:A106 4.16 K O2' A:A106 3.14 K OP1 A:G107 3.93 K P A:G107 4.20 K O5' A:G107 4.72 K O A:Hoh228 4.35 K O A:Hoh270 3.21 K O A:Hoh349 3.40 interactive model: Potassium binding site 6 out of 6 in 3pdr Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Potassium in the PDB 3pdr. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Potassium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: A25, A: A72, A: G73, A: A162, A: Hoh353, A: Hoh530, conact list: Atom Atom Distance (A) K C1' A:A25 4.64 K O4' A:A25 4.86 K O3' A:A72 4.73 K OP1 A:G73 3.99 K C1' A:A162 4.80 K O2' A:A162 4.58 K O A:Hoh353 3.76 K O A:Hoh530 3.64 interactive model: