Mercury in the structure of Proteinase K By Lb Nanotemplate Method After High X-Ray Dose on ID14-2 Beamline At Esrf (pdb 3i34)

The binding sites of Mercury atom in the structure of Proteinase K By Lb Nanotemplate Method After High X-Ray Dose on ID14-2 Beamline At Esrf (pdb code 3i34). This binding sites where shown with 5.0 Angstroms radius around Mercury atom. The 3i34 structure was solved by E.PECHKOVA, S.K.TRIPATHI, R.RAVELLI, S.MCSWEENEY, C.NICOLINI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 24.0-1.0 Space group P43212 a (A) 67.865 b (A) 67.865 c (A) 102.335 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.6 Rfree (%) 22 Mercury Binding Sites: Mercury binding site 1 out of 3 in 3i34 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Mercury in the PDB 3i34. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Mercury atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: Gly68, X: His69, X: Gly70, X: His72, X: Cys73, X: Trp212, X: Ile220, X: Ser224, X: Met225, X: Hg282, X: Hoh562, X: Hoh610, conact list: Atom Atom Distance (A) Hg O X:Gly68 4.51 Hg C X:Gly68 4.82 Hg O X:His69 2.65 Hg NE2 X:His69 4.52 Hg N X:His69 4.29 Hg CB X:His69 3.46 Hg ND1 X:His69 2.43 Hg CD2 X:His69 4.47 Hg C X:His69 3.18 Hg CE1 X:His69 3.45 Hg CG X:His69 3.29 Hg CA X:His69 3.01 Hg N X:Gly70 4.48 Hg N X:His72 4.73 Hg CB X:His72 3.34 Hg ND1 X:His72 3.98 Hg CD2 X:His72 4.98 Hg C X:His72 4.62 Hg CG X:His72 3.91 Hg CA X:His72 4.43 Hg N X:Cys73 4.10 Hg CB X:Cys73 4.77 Hg SG X:Cys73 3.60 Hg CA X:Cys73 4.89 Hg CZ3 X:Trp212 4.46 Hg CD1 X:Ile220 3.21 Hg CG1 X:Ile220 4.41 Hg OG X:Ser224 4.15 Hg CE X:Met225 2.93 Hg SD X:Met225 4.41 Hg HG X:Hg282 4.97 Hg O X:Hoh562 4.85 Hg O X:Hoh610 3.86 interactive model: Mercury binding site 2 out of 3 in 3i34 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Mercury in the PDB 3i34. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Mercury atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: His72, X: Cys73, X: Thr76, X: Ile208, X: Ser210, X: Ser224, X: Met225, X: Pro228, X: His229, X: Hg282, X: Hoh329, conact list: Atom Atom Distance (A) Hg O X:His72 3.93 Hg NE2 X:His72 4.49 Hg ND1 X:His72 3.09 Hg C X:His72 4.40 Hg CE1 X:His72 3.23 Hg CG X:His72 4.37 Hg N X:Cys73 4.65 Hg CA X:Cys73 4.46 Hg N X:Thr76 4.89 Hg CB X:Thr76 3.32 Hg CG2 X:Thr76 3.86 Hg OG1 X:Thr76 2.43 Hg CA X:Thr76 4.65 Hg CB X:Ile208 4.16 Hg CG2 X:Ile208 3.42 Hg CG1 X:Ile208 4.88 Hg CB X:Ser210 4.42 Hg OG X:Ser210 4.82 Hg O X:Ser224 4.84 Hg O X:Met225 3.82 Hg N X:Met225 4.76 Hg CB X:Met225 3.52 Hg CE X:Met225 4.21 Hg C X:Met225 4.17 Hg CG X:Met225 3.33 Hg SD X:Met225 4.65 Hg CA X:Met225 3.55 Hg CG X:Pro228 4.15 Hg NE2 X:His229 4.98 Hg HG X:Hg282 0.00 Hg HG X:Hg282 1.08 Hg O X:Hoh329 4.63 interactive model: Mercury binding site 3 out of 3 in 3i34 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Mercury in the PDB 3i34. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Mercury atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: X: His72, X: Cys73, X: Thr76, X: Ile208, X: Ser210, X: Ser224, X: Met225, X: Pro228, X: Hg280, X: Hg282, conact list: Atom Atom Distance (A) Hg O X:His72 3.46 Hg NE2 X:His72 4.74 Hg CB X:His72 4.59 Hg ND1 X:His72 2.93 Hg C X:His72 3.72 Hg CE1 X:His72 3.50 Hg CG X:His72 4.11 Hg CA X:His72 4.76 Hg O X:Cys73 4.46 Hg N X:Cys73 3.74 Hg CB X:Cys73 4.39 Hg SG X:Cys73 4.22 Hg C X:Cys73 4.45 Hg CA X:Cys73 3.50 Hg N X:Thr76 4.85 Hg CB X:Thr76 3.56 Hg CG2 X:Thr76 4.30 Hg OG1 X:Thr76 2.92 Hg CA X:Thr76 4.83 Hg CG2 X:Ile208 4.48 Hg CB X:Ser210 4.76 Hg OG X:Ser210 4.96 Hg O X:Ser224 4.16 Hg C X:Ser224 4.72 Hg O X:Met225 4.09 Hg N X:Met225 4.49 Hg CB X:Met225 3.80 Hg CE X:Met225 3.64 Hg C X:Met225 4.31 Hg CG X:Met225 3.52 Hg SD X:Met225 4.46 Hg CA X:Met225 3.51 Hg CB X:Pro228 4.75 Hg CD X:Pro228 4.74 Hg CG X:Pro228 3.69 Hg HG X:Hg280 4.97 Hg HG X:Hg282 1.08 Hg HG X:Hg282 0.00 interactive model: