Mercury in the structure of Crystal Structure of Bovine Rhodopsin With Beta-Ionone (pdb 3oax)

The binding sites of Mercury atom in the structure of Crystal Structure of Bovine Rhodopsin With Beta-Ionone (pdb code 3oax). This binding sites where shown with 5.0 Angstroms radius around Mercury atom. The 3oax structure was solved by C.L.MAKINO, C.K.RILEY, J.LOONEY, R.K.CROUCH, T.OKADA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-2.6 Space group P41 a (A) 96.990 b (A) 96.990 c (A) 149.800 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 22.4 Rfree (%) 26.2 Mercury Binding Sites: Mercury binding site 1 out of 6 in 3oax Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Mercury in the PDB 3oax. 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: Ser298, A: Tyr301, conact list: Atom Atom Distance (A) Hg O A:Ala260 4.31 Hg C A:Ile263 4.91 Hg N A:Cys264 4.21 Hg CB A:Cys264 2.88 Hg SG A:Cys264 2.64 Hg C A:Cys264 4.96 Hg CA A:Cys264 3.66 Hg O A:Phe294 4.72 Hg CE2 A:Phe294 4.38 Hg CZ A:Phe294 3.81 Hg CE1 A:Phe294 4.24 Hg O A:Thr297 4.97 Hg CB A:Thr297 4.10 Hg OG1 A:Thr297 2.90 Hg C A:Thr297 4.70 Hg CA A:Thr297 5.00 Hg N A:Ser298 4.72 Hg CB A:Tyr301 4.81 Hg CE2 A:Tyr301 4.01 Hg CD2 A:Tyr301 3.67 Hg CZ A:Tyr301 4.95 Hg CG A:Tyr301 4.39 interactive model: Mercury binding site 2 out of 6 in 3oax Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Mercury in the PDB 3oax. 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 3.43 Hg C A:Ala132 4.14 Hg CB A:Ala132 4.10 Hg CA A:Ala132 4.02 Hg CB A:Arg135 4.51 Hg N A:Tyr136 4.77 Hg CB A:Tyr136 4.96 Hg O A:Ile219 4.69 Hg O A:Cys222 3.67 Hg CB A:Cys222 3.46 Hg SG A:Cys222 2.33 Hg C A:Cys222 3.57 Hg CA A:Cys222 4.15 Hg N A:Tyr223 3.66 Hg CB A:Tyr223 4.73 Hg CA A:Tyr223 3.95 Hg CD1 A:Leu226 3.87 Hg CD2 A:Leu226 4.02 Hg CG A:Leu226 4.50 interactive model: Mercury binding site 3 out of 6 in 3oax Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Mercury in the PDB 3oax. 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: Asp331, A: Glu332, A: Thr335, A: Thr336, A: Val337, A: Hoh2061, conact list: Atom Atom Distance (A) Hg ND1 A:His65 4.96 Hg O A:Gln312 3.19 Hg CB A:Gln312 4.75 Hg CD A:Gln312 4.91 Hg C A:Gln312 4.05 Hg CG A:Gln312 3.83 Hg CA A:Gln312 4.41 Hg O A:Asn315 4.71 Hg CB A:Asn315 4.04 Hg C A:Asn315 4.09 Hg CA A:Asn315 4.62 Hg N A:Cys316 3.49 Hg CB A:Cys316 3.48 Hg SG A:Cys316 2.23 Hg CA A:Cys316 3.69 Hg O A:Asp331 4.80 Hg CG A:Glu332 4.42 Hg O A:Thr335 4.91 Hg CB A:Thr336 3.60 Hg CG2 A:Thr336 3.26 Hg C A:Thr336 4.02 Hg CA A:Thr336 3.68 Hg O A:Val337 3.93 Hg N A:Val337 3.59 Hg CB A:Val337 4.96 Hg C A:Val337 4.70 Hg CG1 A:Val337 3.99 Hg CA A:Val337 4.59 Hg O A:Hoh2061 2.46 interactive model: Mercury binding site 4 out of 6 in 3oax Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Mercury in the PDB 3oax. 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, B: Hoh2094, B: Hoh2112, conact list: Atom Atom Distance (A) Hg O B:Ala260 3.65 Hg C B:Ala260 4.62 Hg C B:Ile263 4.72 Hg N B:Cys264 3.99 Hg CB B:Cys264 3.01 Hg SG B:Cys264 2.63 Hg CA B:Cys264 3.66 Hg CE2 B:Phe294 4.28 Hg CZ B:Phe294 4.22 Hg CB B:Thr297 4.75 Hg OG1 B:Thr297 3.47 Hg CB B:Tyr301 4.88 Hg CE2 B:Tyr301 3.81 Hg CD2 B:Tyr301 3.61 Hg CZ B:Tyr301 4.67 Hg CG B:Tyr301 4.36 Hg O B:Hoh2094 3.12 Hg O B:Hoh2112 2.30 interactive model: Mercury binding site 5 out of 6 in 3oax Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Mercury in the PDB 3oax. 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 4.00 Hg C B:Ala132 4.55 Hg CB B:Ala132 4.42 Hg CA B:Ala132 4.17 Hg CB B:Arg135 4.06 Hg CG B:Arg135 4.21 Hg N B:Tyr136 4.60 Hg CB B:Tyr136 4.98 Hg O B:Ile219 4.71 Hg O B:Cys222 2.40 Hg N B:Cys222 4.81 Hg CB B:Cys222 3.15 Hg SG B:Cys222 2.11 Hg C B:Cys222 2.97 Hg CA B:Cys222 3.64 Hg N B:Tyr223 3.71 Hg CB B:Tyr223 4.81 Hg CA B:Tyr223 4.03 Hg CD1 B:Leu226 4.13 Hg CD2 B:Leu226 4.00 Hg CG B:Leu226 4.60 interactive model: Mercury binding site 6 out of 6 in 3oax Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Mercury in the PDB 3oax. 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: Gln312, B: Asn315, B: Cys316, B: Asp331, B: Glu332, B: Thr335, B: Thr336, B: Val337, B: Glu341, conact list: Atom Atom Distance (A) Hg O B:Gln312 3.23 Hg CB B:Gln312 4.95 Hg C B:Gln312 4.16 Hg CG B:Gln312 4.21 Hg CA B:Gln312 4.46 Hg O B:Asn315 4.46 Hg CB B:Asn315 4.00 Hg C B:Asn315 3.90 Hg CA B:Asn315 4.51 Hg N B:Cys316 3.35 Hg CB B:Cys316 3.44 Hg SG B:Cys316 2.37 Hg CA B:Cys316 3.53 Hg O B:Asp331 4.60 Hg CB B:Glu332 4.64 Hg CD B:Glu332 4.75 Hg CG B:Glu332 3.69 Hg O B:Thr335 4.39 Hg C B:Thr335 4.85 Hg O B:Thr336 4.46 Hg N B:Thr336 4.40 Hg CB B:Thr336 3.45 Hg CG2 B:Thr336 2.66 Hg OG1 B:Thr336 4.41 Hg C B:Thr336 3.31 Hg CA B:Thr336 3.08 Hg O B:Val337 3.72 Hg N B:Val337 2.79 Hg CB B:Val337 4.20 Hg CG2 B:Val337 4.00 Hg C B:Val337 4.27 Hg CA B:Val337 3.88 Hg OE1 B:Glu341 4.13 interactive model: