Palladium in the structure of Crystal Structure of 25PD(Allyl)/Apo-Fr (pdb 3af7)

The binding sites of Palladium atom in the structure of Crystal Structure of 25PD(Allyl)/Apo-Fr (pdb code 3af7). This binding sites where shown with 5.0 Angstroms radius around Palladium atom. The 3af7 structure was solved by S.ABE, T.HIKAGE, Y.WATANABE, S.KITAGAWA, T.UENO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 25.2-1.6 Space group F432 a (A) 181.520 b (A) 181.520 c (A) 181.520 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 19.2 Rfree (%) 21.2 Palladium Binding Sites: Palladium binding site 1 out of 5 in 3af7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Palladium in the PDB 3af7. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Palladium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: Phe37, X: Asp38, X: Glu45, X: Cys48, X: His49, X: Pd178, X: Pll179, X: Hoh326, X: Hoh333, X: Hoh352, conact list: Atom Atom Distance (A) Pd O X:Phe37 4.73 Pd N X:Asp38 4.85 Pd CB X:Asp38 3.96 Pd OD2 X:Asp38 4.99 Pd OD1 X:Asp38 3.00 Pd CG X:Asp38 3.85 Pd CA X:Asp38 4.07 Pd O X:Glu45 4.63 Pd N X:Glu45 4.48 Pd CB X:Glu45 3.82 Pd CD X:Glu45 4.75 Pd C X:Glu45 4.70 Pd CG X:Glu45 3.69 Pd CA X:Glu45 3.70 Pd CB X:Cys48 3.80 Pd SG X:Cys48 3.76 Pd ND1 X:His49 4.85 Pd CE1 X:His49 4.55 Pd PD X:Pd178 4.89 Pd C20 X:Pll179 4.19 Pd PD X:Pll179 2.37 Pd C19 X:Pll179 4.65 Pd C21 X:Pll179 4.24 Pd O X:Hoh326 4.34 Pd O X:Hoh333 2.23 Pd O X:Hoh352 4.06 interactive model: Palladium binding site 2 out of 5 in 3af7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Palladium in the PDB 3af7. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Palladium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: Glu45, X: Cys48, X: His49, X: Arg52, X: Pd177, X: Pll179, X: Hoh352, conact list: Atom Atom Distance (A) Pd O X:Glu45 4.66 Pd O X:Cys48 4.03 Pd CB X:Cys48 4.11 Pd SG X:Cys48 3.18 Pd C X:Cys48 3.80 Pd CA X:Cys48 4.62 Pd NE2 X:His49 3.58 Pd N X:His49 3.49 Pd CB X:His49 3.77 Pd CB X:His49 3.72 Pd ND1 X:His49 1.90 Pd ND1 X:His49 4.08 Pd CD2 X:His49 3.89 Pd C X:His49 4.71 Pd CE1 X:His49 2.44 Pd CG X:His49 3.05 Pd CG X:His49 4.38 Pd CA X:His49 3.38 Pd CA X:His49 3.37 Pd CB X:Arg52 4.46 Pd CD X:Arg52 3.70 Pd CG X:Arg52 4.27 Pd NE X:Arg52 4.74 Pd NH1 X:Arg52 4.47 Pd PD X:Pd177 4.89 Pd C20 X:Pll179 4.93 Pd PD X:Pll179 3.23 Pd C19 X:Pll179 2.95 Pd C21 X:Pll179 3.97 Pd O X:Hoh352 4.14 interactive model: Palladium binding site 3 out of 5 in 3af7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Palladium in the PDB 3af7. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Palladium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: Asp38, X: Glu45, X: Cys48, X: His49, X: Arg52, X: Pd177, X: Pd178, X: Pll179, X: Hoh333, X: Hoh352, conact list: Atom Atom Distance (A) Pd CB X:Asp38 3.79 Pd OD2 X:Asp38 4.51 Pd OD1 X:Asp38 3.34 Pd CG X:Asp38 3.69 Pd CA X:Asp38 4.66 Pd CG X:Glu45 4.96 Pd CB X:Cys48 3.57 Pd SG X:Cys48 2.45 Pd CA X:Cys48 4.91 Pd ND1 X:His49 4.07 Pd CE1 X:His49 3.92 Pd CD X:Arg52 4.85 Pd PD X:Pd177 2.37 Pd PD X:Pd178 3.23 Pd C20 X:Pll179 2.55 Pd PD X:Pll179 0.00 Pd C19 X:Pll179 2.37 Pd C21 X:Pll179 2.29 Pd O X:Hoh333 4.35 Pd O X:Hoh352 3.84 interactive model: Palladium binding site 4 out of 5 in 3af7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Palladium in the PDB 3af7. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Palladium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: His114, X: Cys126, X: Asp127, X: Pll180, X: Pll181, X: Hoh304, conact list: Atom Atom Distance (A) Pd NE2 X:His114 2.20 Pd ND1 X:His114 4.30 Pd CD2 X:His114 3.16 Pd CE1 X:His114 3.20 Pd CG X:His114 4.32 Pd O X:Cys126 3.24 Pd CB X:Cys126 3.38 Pd CB X:Cys126 3.26 Pd SG X:Cys126 2.27 Pd SG X:Cys126 4.21 Pd C X:Cys126 3.55 Pd CA X:Cys126 3.71 Pd CA X:Cys126 3.73 Pd N X:Asp127 4.41 Pd C20 X:Pll180 2.29 Pd PD X:Pll180 0.00 Pd C19 X:Pll180 2.43 Pd C21 X:Pll180 2.29 Pd PD X:Pll181 3.77 Pd C19 X:Pll181 4.96 Pd C21 X:Pll181 4.89 Pd O X:Hoh304 3.80 interactive model: Palladium binding site 5 out of 5 in 3af7 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Palladium in the PDB 3af7. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Palladium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: His114, X: Ser118, X: Cys126, X: Pll180, X: Pll181, X: Hoh304, conact list: Atom Atom Distance (A) Pd NE2 X:His114 4.34 Pd CE1 X:His114 4.30 Pd OG X:Ser118 4.83 Pd CB X:Cys126 3.41 Pd CB X:Cys126 3.46 Pd SG X:Cys126 2.40 Pd SG X:Cys126 3.68 Pd CA X:Cys126 4.87 Pd CA X:Cys126 4.93 Pd PD X:Pll180 3.77 Pd C19 X:Pll180 4.95 Pd C20 X:Pll181 2.31 Pd PD X:Pll181 0.00 Pd C19 X:Pll181 2.29 Pd C21 X:Pll181 2.28 Pd O X:Hoh304 2.27 interactive model: