Mercury in the structure of Crystal Structure of Bovine Rhodopsin (pdb 1hzx)

The binding sites of Mercury atom in the structure of Crystal Structure of Bovine Rhodopsin (pdb code 1hzx). This binding sites where shown with 5.0 Angstroms radius around Mercury atom. The 1hzx structure was solved by D.C.TELLER, T.OKADA, C.A.BEHNKE, K.PALCZEWSKI, R.E.STENKAMP, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-2.8 Space group P41 a (A) 97.246 b (A) 97.246 c (A) 149.544 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.5 Rfree (%) 21.2 Mercury Binding Sites: Mercury binding site 1 out of 6 in 1hzx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Mercury in the PDB 1hzx. 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: Ala260, A: Ile263, A: Cys264, A: Phe294, A: Thr297, A: Tyr301, conact list: Atom Atom Distance (A) Hg O A:Ala260 3.79 Hg C A:Ala260 4.85 Hg CB A:Ile263 4.98 Hg CG2 A:Ile263 4.99 Hg C A:Ile263 4.63 Hg N A:Cys264 3.92 Hg CB A:Cys264 3.01 Hg SG A:Cys264 2.20 Hg CA A:Cys264 3.66 Hg CE2 A:Phe294 4.46 Hg CZ A:Phe294 3.82 Hg CE1 A:Phe294 4.35 Hg CB A:Thr297 4.30 Hg OG1 A:Thr297 3.18 Hg C A:Thr297 5.00 Hg CB A:Tyr301 4.71 Hg CE2 A:Tyr301 3.96 Hg CD2 A:Tyr301 3.68 Hg CZ A:Tyr301 4.76 Hg CG A:Tyr301 4.27 interactive model: Mercury binding site 2 out of 6 in 1hzx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Mercury in the PDB 1hzx. 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: Ala132, A: Arg135, A: Tyr136, A: Ile219, A: Cys222, A: Tyr223, A: Leu226, conact list: Atom Atom Distance (A) Hg O A:Ala132 3.48 Hg C A:Ala132 4.12 Hg CB A:Ala132 4.19 Hg CA A:Ala132 3.93 Hg CB A:Arg135 4.46 Hg CG A:Arg135 4.61 Hg N A:Tyr136 4.82 Hg O A:Ile219 4.66 Hg O A:Cys222 3.37 Hg CB A:Cys222 3.82 Hg SG A:Cys222 2.51 Hg C A:Cys222 3.57 Hg CA A:Cys222 4.36 Hg N A:Tyr223 3.79 Hg CB A:Tyr223 4.55 Hg CA A:Tyr223 3.85 Hg CB A:Leu226 4.44 Hg CD1 A:Leu226 3.17 Hg CD2 A:Leu226 4.81 Hg CG A:Leu226 4.32 interactive model: Mercury binding site 3 out of 6 in 1hzx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Mercury in the PDB 1hzx. 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: His65, A: Gln312, A: Asn315, A: Cys316, A: Thr335, A: Thr336, A: Val337, conact list: Atom Atom Distance (A) Hg ND1 A:His65 4.99 Hg O A:Gln312 3.29 Hg C A:Gln312 4.28 Hg CG A:Gln312 4.19 Hg CA A:Gln312 4.74 Hg O A:Asn315 4.95 Hg CB A:Asn315 4.78 Hg C A:Asn315 4.48 Hg N A:Cys316 3.84 Hg CB A:Cys316 3.60 Hg SG A:Cys316 2.40 Hg CA A:Cys316 3.78 Hg O A:Thr335 4.49 Hg CB A:Thr336 4.86 Hg C A:Thr336 4.44 Hg CA A:Thr336 4.32 Hg O A:Val337 3.77 Hg N A:Val337 4.01 Hg CB A:Val337 4.78 Hg C A:Val337 4.65 Hg CG1 A:Val337 3.60 Hg CA A:Val337 4.71 interactive model: Mercury binding site 4 out of 6 in 1hzx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Mercury in the PDB 1hzx. 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: Ala260, B: Ile263, B: Cys264, B: Phe294, B: Thr297, B: Tyr301, conact list: Atom Atom Distance (A) Hg O B:Ala260 3.54 Hg C B:Ala260 4.60 Hg O B:Ile263 4.94 Hg CB B:Ile263 4.69 Hg CG2 B:Ile263 4.65 Hg C B:Ile263 4.45 Hg N B:Cys264 3.77 Hg CB B:Cys264 3.10 Hg SG B:Cys264 2.33 Hg CA B:Cys264 3.63 Hg CE2 B:Phe294 4.45 Hg CZ B:Phe294 3.80 Hg CE1 B:Phe294 4.42 Hg CB B:Thr297 4.41 Hg OG1 B:Thr297 3.20 Hg CB B:Tyr301 4.58 Hg CE2 B:Tyr301 4.07 Hg CD1 B:Tyr301 4.93 Hg CD2 B:Tyr301 3.71 Hg CZ B:Tyr301 4.81 Hg CG B:Tyr301 4.20 interactive model: Mercury binding site 5 out of 6 in 1hzx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Mercury in the PDB 1hzx. 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: Ala132, B: Arg135, B: Tyr136, B: Ile219, B: Cys222, B: Tyr223, B: Leu226, conact list: Atom Atom Distance (A) Hg O B:Ala132 3.46 Hg C B:Ala132 4.09 Hg CB B:Ala132 4.23 Hg CA B:Ala132 3.93 Hg CB B:Arg135 4.33 Hg CG B:Arg135 4.46 Hg N B:Tyr136 4.71 Hg O B:Ile219 4.50 Hg O B:Cys222 3.11 Hg CB B:Cys222 3.76 Hg SG B:Cys222 2.49 Hg C B:Cys222 3.32 Hg CA B:Cys222 4.19 Hg N B:Tyr223 3.51 Hg CB B:Tyr223 4.25 Hg CD1 B:Tyr223 4.91 Hg C B:Tyr223 4.75 Hg CA B:Tyr223 3.53 Hg CB B:Leu226 4.34 Hg CD1 B:Leu226 3.10 Hg CD2 B:Leu226 4.70 Hg CG B:Leu226 4.23 interactive model: Mercury binding site 6 out of 6 in 1hzx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Mercury in the PDB 1hzx. 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: His65, B: Lys66, B: Lys67, B: Cys316, B: Thr319, conact list: Atom Atom Distance (A) Hg NE2 B:His65 4.22 Hg CB B:His65 4.74 Hg ND1 B:His65 2.97 Hg CD2 B:His65 4.65 Hg CE1 B:His65 3.19 Hg CG B:His65 4.00 Hg NZ B:Lys66 3.92 Hg CE B:Lys67 3.71 Hg CD B:Lys67 3.10 Hg CG B:Lys67 3.96 Hg NZ B:Lys67 3.75 Hg O B:Cys316 4.52 Hg N B:Cys316 4.18 Hg CB B:Cys316 2.65 Hg SG B:Cys316 2.27 Hg C B:Cys316 4.39 Hg CA B:Cys316 3.25 Hg CB B:Thr319 4.58 Hg CG2 B:Thr319 4.55 Hg OG1 B:Thr319 4.53 interactive model: