Potassium in the structure of The Structure Of The Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb 1vqp)

The binding sites of Potassium atom in the structure of The Structure Of The Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 1vqp). This binding sites where shown with 5.0 Angstroms radius around Potassium atom. The 1vqp structure was solved by T.M.SCHMEING, T.A.STEITZ, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-2.2 Space group C2221 a (A) 211.610 b (A) 298.189 c (A) 574.980 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.8 Rfree (%) 24.7 Potassium Binding Sites: Potassium binding site 1 out of 3 in 1vqp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Potassium in the PDB 1vqp. 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: 0: G2102, 0: G2482, 0: A2486, 0: U2535, 0: C2536, 0: U2539, conact list: Atom Atom Distance (A) K C8 0:G2102 4.54 K C6 0:G2102 3.54 K N1 0:G2102 4.83 K C5 0:G2102 3.76 K N7 0:G2102 3.36 K O6 0:G2102 2.80 K C8 0:G2482 4.06 K C6 0:G2482 3.41 K N1 0:G2482 4.76 K C5 0:G2482 3.44 K N7 0:G2482 2.88 K C4 0:G2482 4.75 K O6 0:G2482 2.81 K N6 0:A2486 4.00 K C2 0:U2535 4.73 K O2 0:U2535 4.47 K C2' 0:U2535 4.80 K N3 0:C2536 4.35 K C2 0:C2536 3.46 K C6 0:C2536 4.67 K N1 0:C2536 3.65 K C1' 0:C2536 3.40 K O2 0:C2536 3.06 K O4' 0:C2536 2.98 K C5' 0:C2536 4.43 K C2' 0:C2536 4.85 K C4' 0:C2536 3.82 K O5' 0:C2536 4.99 K OP1 0:U2539 4.74 interactive model: Potassium binding site 2 out of 3 in 1vqp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Potassium in the PDB 1vqp. 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: 0: C162, 0: U163, 0: G164, 0: A169, 0: C171, 0: U172, 0: C173, M: Arg82, 0: Mg8054, 0: Hoh5510, 0: Hoh8368, 0: Hoh8369, 0: Hoh9642, 0: Hoh9737, 0: Hoh9773, 0: Hoh9950, conact list: Atom Atom Distance (A) K OP1 0:C162 4.84 K P 0:C162 4.51 K OP2 0:C162 3.24 K C5 0:U163 4.58 K C4 0:U163 4.02 K O4 0:U163 2.94 K O6 0:G164 4.59 K OP1 0:A169 4.86 K OP2 0:A169 4.41 K N4 0:C171 4.36 K N3 0:U172 3.92 K C4 0:U172 3.74 K O4 0:U172 2.80 K N3 0:C173 4.98 K CB M:Arg82 4.64 K CD M:Arg82 3.23 K CZ M:Arg82 4.98 K CG M:Arg82 4.46 K NE M:Arg82 3.99 K MG 0:Mg8054 4.79 K O 0:Hoh5510 3.35 K O 0:Hoh8368 3.94 K O 0:Hoh8369 3.34 K O 0:Hoh9642 2.77 K O 0:Hoh9737 3.03 K O 0:Hoh9773 3.06 K O 0:Hoh9950 3.94 interactive model: Potassium binding site 3 out of 3 in 1vqp Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Potassium in the PDB 1vqp. 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: 0: C2104, 0: C2105, 0: A2474, 4: A176, 4: C175, 0: Hoh8310, 4: Hoh7915, conact list: Atom Atom Distance (A) K C3' 0:C2104 3.85 K O3' 0:C2104 2.87 K C2' 0:C2104 4.10 K C4' 0:C2104 4.10 K O2' 0:C2104 3.22 K OP1 0:C2105 3.46 K P 0:C2105 3.82 K OP2 0:C2105 5.00 K C5' 0:C2105 4.45 K O5' 0:C2105 4.63 K N6 0:A2474 4.60 K P 4:A176 4.00 K O4' 4:A176 4.92 K OP2 4:A176 3.61 K C4' 4:A176 4.80 K C3' 4:C175 3.81 K C1' 4:C175 4.72 K O3' 4:C175 2.99 K O4' 4:C175 4.87 K C2' 4:C175 3.78 K C4' 4:C175 4.08 K O2' 4:C175 2.73 K O 0:Hoh8310 4.26 K O 4:Hoh7915 4.75 interactive model: