Mercury in the structure of Crystal Structure Of Mercury Derivative of Retinol Dehydratase in A Complex With Retinol and Pap (pdb 1fmj)

The binding sites of Mercury atom in the structure of Crystal Structure Of Mercury Derivative of Retinol Dehydratase in A Complex With Retinol and Pap (pdb code 1fmj). This binding sites where shown with 5.0 Angstroms radius around Mercury atom. The 1fmj structure was solved by S.PAKHOMOVA, M.KOBAYASHI, J.BUCK, M.E.NEWCOMER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-2.0 Space group P1211 a (A) 79.429 b (A) 66.183 c (A) 83.336 alpha (°) 90.00 beta (°) 108.89 gamma (°) 90.00 Rfactor (%) 23.1 Rfree (%) 26.4 Mercury Binding Sites: Mercury binding site 1 out of 8 in 1fmj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Mercury in the PDB 1fmj. 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: A: Asp250, A: Asp254, A: Leu255, A: Gly257, A: Cys258, A: Hg451, conact list: Atom Atom Distance (A) Hg O A:Asp250 3.60 Hg CB A:Asp250 4.01 Hg C A:Asp250 4.22 Hg CG A:Asp250 4.90 Hg CA A:Asp250 4.65 Hg O A:Asp254 2.77 Hg N A:Asp254 4.68 Hg CB A:Asp254 4.02 Hg C A:Asp254 3.80 Hg CG A:Asp254 4.76 Hg CA A:Asp254 4.39 Hg N A:Leu255 4.84 Hg O A:Gly257 4.39 Hg N A:Gly257 4.67 Hg C A:Gly257 3.70 Hg CA A:Gly257 4.19 Hg N A:Cys258 3.09 Hg CB A:Cys258 3.36 Hg SG A:Cys258 2.42 Hg C A:Cys258 4.95 Hg CA A:Cys258 3.43 Hg HG A:Hg451 0.00 Hg HG A:Hg451 2.59 interactive model: Mercury binding site 2 out of 8 in 1fmj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Mercury in the PDB 1fmj. 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: A: Leu246, A: Asp250, A: Gly257, A: Cys258, A: Arg261, A: Hg451, A: Hoh482, conact list: Atom Atom Distance (A) Hg CD2 A:Leu246 4.20 Hg CB A:Asp250 3.84 Hg OD2 A:Asp250 4.51 Hg CG A:Asp250 4.49 Hg O A:Gly257 4.86 Hg C A:Gly257 4.78 Hg N A:Cys258 4.23 Hg CB A:Cys258 3.63 Hg SG A:Cys258 2.52 Hg C A:Cys258 4.97 Hg CA A:Cys258 3.67 Hg CB A:Arg261 4.94 Hg CD A:Arg261 3.46 Hg CZ A:Arg261 4.42 Hg CG A:Arg261 4.44 Hg NE A:Arg261 4.37 Hg NH1 A:Arg261 3.57 Hg HG A:Hg451 2.59 Hg HG A:Hg451 0.00 Hg O A:Hoh482 3.68 interactive model: Mercury binding site 3 out of 8 in 1fmj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Mercury in the PDB 1fmj. 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: A: Gln276, A: Cys279, A: Glu280, A: Hoh548, conact list: Atom Atom Distance (A) Hg O A:Gln276 4.40 Hg O A:Cys279 3.75 Hg N A:Cys279 4.88 Hg CB A:Cys279 2.90 Hg SG A:Cys279 2.52 Hg C A:Cys279 3.40 Hg CA A:Cys279 3.76 Hg N A:Glu280 3.49 Hg CB A:Glu280 4.58 Hg CA A:Glu280 3.99 Hg O A:Hoh548 4.00 interactive model: Mercury binding site 4 out of 8 in 1fmj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Mercury in the PDB 1fmj. 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: A: Lys315, A: Gly317, A: Cys318, A: Asp321, conact list: Atom Atom Distance (A) Hg CB A:Lys315 4.95 Hg C A:Gly317 4.99 Hg O A:Cys318 5.00 Hg N A:Cys318 4.42 Hg CB A:Cys318 3.51 Hg SG A:Cys318 2.65 Hg C A:Cys318 4.88 Hg CA A:Cys318 3.70 Hg OD2 A:Asp321 3.30 Hg CG A:Asp321 4.53 interactive model: Mercury binding site 5 out of 8 in 1fmj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Mercury in the PDB 1fmj. 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: B: Asp250, B: Tyr251, B: Asp254, B: Leu255, B: Gly257, B: Cys258, B: Hg551, conact list: Atom Atom Distance (A) Hg O B:Asp250 3.83 Hg CB B:Asp250 3.97 Hg C B:Asp250 4.26 Hg CG B:Asp250 4.78 Hg CA B:Asp250 4.63 Hg N B:Tyr251 5.00 Hg O B:Asp254 2.94 Hg N B:Asp254 4.62 Hg CB B:Asp254 3.85 Hg OD2 B:Asp254 4.90 Hg C B:Asp254 3.85 Hg CG B:Asp254 4.53 Hg CA B:Asp254 4.34 Hg N B:Leu255 4.86 Hg O B:Gly257 4.58 Hg N B:Gly257 4.67 Hg C B:Gly257 3.75 Hg CA B:Gly257 4.12 Hg N B:Cys258 3.04 Hg CB B:Cys258 3.49 Hg SG B:Cys258 2.39 Hg CA B:Cys258 3.50 Hg HG B:Hg551 0.00 Hg HG B:Hg551 1.92 interactive model: Mercury binding site 6 out of 8 in 1fmj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Mercury in the PDB 1fmj. 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: B: Leu246, B: Asp250, B: Asp254, B: Gly257, B: Cys258, B: Arg261, B: Hg551, B: Hoh589, conact list: Atom Atom Distance (A) Hg CD2 B:Leu246 4.71 Hg O B:Asp250 4.86 Hg CB B:Asp250 3.66 Hg OD2 B:Asp250 4.53 Hg C B:Asp250 4.82 Hg CG B:Asp250 4.29 Hg CA B:Asp250 4.83 Hg O B:Asp254 4.73 Hg O B:Gly257 4.95 Hg C B:Gly257 4.54 Hg N B:Cys258 3.84 Hg CB B:Cys258 3.56 Hg SG B:Cys258 2.39 Hg CA B:Cys258 3.60 Hg CD B:Arg261 4.25 Hg NH1 B:Arg261 4.25 Hg HG B:Hg551 1.92 Hg HG B:Hg551 0.00 Hg O B:Hoh589 3.73 interactive model: Mercury binding site 7 out of 8 in 1fmj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Mercury in the PDB 1fmj. 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: B: Gln276, B: Cys279, B: Glu280, conact list: Atom Atom Distance (A) Hg O B:Gln276 4.75 Hg NE2 B:Gln276 4.18 Hg O B:Cys279 4.08 Hg CB B:Cys279 3.08 Hg SG B:Cys279 2.53 Hg C B:Cys279 3.69 Hg CA B:Cys279 3.98 Hg N B:Glu280 3.75 Hg CB B:Glu280 4.86 Hg CA B:Glu280 4.26 interactive model: Mercury binding site 8 out of 8 in 1fmj Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Mercury in the PDB 1fmj. 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: B: Gly317, B: Cys318, B: Asp321, B: Hoh665, conact list: Atom Atom Distance (A) Hg O B:Gly317 4.58 Hg C B:Gly317 4.58 Hg O B:Cys318 4.60 Hg N B:Cys318 4.02 Hg CB B:Cys318 3.23 Hg SG B:Cys318 2.51 Hg C B:Cys318 4.45 Hg CA B:Cys318 3.28 Hg OD2 B:Asp321 3.54 Hg CG B:Asp321 4.53 Hg O B:Hoh665 3.60 interactive model: