Mercury in the structure of Crystal Structure of Bovine Rhodopsin At 2.2 Angstroms Resolution (pdb 1u19)

The binding sites of Mercury atom in the structure of Crystal Structure of Bovine Rhodopsin At 2.2 Angstroms Resolution (pdb code 1u19). This binding sites where shown with 5.0 Angstroms radius around Mercury atom. The 1u19 structure was solved by T.OKADA, M.SUGIHARA, A.N.BONDAR, M.ELSTNER, P.ENTEL, V.BUSS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-2.2 Space group P41 a (A) 96.680 b (A) 96.680 c (A) 150.200 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20 Rfree (%) 22.2 Mercury Binding Sites: Mercury binding site 1 out of 6 in 1u19 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Mercury in the PDB 1u19. 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 3.98 Hg CG2 A:Ile263 4.96 Hg C A:Ile263 4.96 Hg N A:Cys264 4.13 Hg CB A:Cys264 3.03 Hg SG A:Cys264 2.82 Hg CA A:Cys264 3.69 Hg O A:Phe294 4.81 Hg CE2 A:Phe294 4.44 Hg CZ A:Phe294 3.89 Hg CE1 A:Phe294 4.35 Hg O A:Thr297 4.84 Hg CB A:Thr297 4.23 Hg OG1 A:Thr297 3.08 Hg C A:Thr297 4.65 Hg N A:Ser298 4.74 Hg CB A:Tyr301 4.81 Hg CE2 A:Tyr301 3.93 Hg CD2 A:Tyr301 3.58 Hg CZ A:Tyr301 4.97 Hg CG A:Tyr301 4.40 interactive model: Mercury binding site 2 out of 6 in 1u19 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Mercury in the PDB 1u19. 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 3.41 Hg C A:Ala132 4.05 Hg CB A:Ala132 4.16 Hg CA A:Ala132 3.87 Hg CB A:Arg135 4.22 Hg CG A:Arg135 4.33 Hg N A:Tyr136 4.64 Hg CB A:Tyr136 4.88 Hg CA A:Tyr136 4.99 Hg O A:Ile219 4.59 Hg O A:Cys222 3.40 Hg CB A:Cys222 3.51 Hg SG A:Cys222 2.35 Hg C A:Cys222 3.49 Hg CA A:Cys222 4.14 Hg N A:Tyr223 3.75 Hg CB A:Tyr223 4.76 Hg CA A:Tyr223 3.97 Hg CB A:Leu226 4.62 Hg CD1 A:Leu226 4.12 Hg CD2 A:Leu226 3.82 Hg CG A:Leu226 4.40 interactive model: Mercury binding site 3 out of 6 in 1u19 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Mercury in the PDB 1u19. 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: Thr336, A: Val337, A: Hoh2061, conact list: Atom Atom Distance (A) Hg ND1 A:His65 4.85 Hg O A:Gln312 3.17 Hg NE2 A:Gln312 4.74 Hg CB A:Gln312 4.81 Hg CD A:Gln312 4.78 Hg C A:Gln312 4.19 Hg CG A:Gln312 3.82 Hg CA A:Gln312 4.55 Hg O A:Asn315 4.84 Hg CB A:Asn315 4.06 Hg C A:Asn315 4.21 Hg CA A:Asn315 4.75 Hg N A:Cys316 3.54 Hg CB A:Cys316 3.58 Hg SG A:Cys316 2.47 Hg CA A:Cys316 3.70 Hg O A:Thr336 4.82 Hg N A:Thr336 4.98 Hg CB A:Thr336 4.12 Hg CG2 A:Thr336 4.05 Hg C A:Thr336 3.80 Hg CA A:Thr336 3.69 Hg O A:Val337 3.67 Hg N A:Val337 3.32 Hg CB A:Val337 4.60 Hg C A:Val337 4.40 Hg CG1 A:Val337 3.66 Hg CA A:Val337 4.25 Hg O A:Hoh2061 2.60 interactive model: Mercury binding site 4 out of 6 in 1u19 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Mercury in the PDB 1u19. 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 3.55 Hg C B:Ala260 4.47 Hg CA B:Ala260 4.93 Hg O B:Ile263 4.96 Hg CB B:Ile263 4.99 Hg CG2 B:Ile263 4.90 Hg C B:Ile263 4.65 Hg N B:Cys264 4.09 Hg CB B:Cys264 3.27 Hg SG B:Cys264 2.68 Hg CA B:Cys264 3.83 Hg CE2 B:Phe294 4.62 Hg CZ B:Phe294 4.22 Hg CE1 B:Phe294 4.85 Hg CB B:Thr297 4.71 Hg OG1 B:Thr297 3.52 Hg CB B:Tyr301 4.77 Hg CE2 B:Tyr301 3.94 Hg CD2 B:Tyr301 3.66 Hg CZ B:Tyr301 4.77 Hg CG B:Tyr301 4.30 interactive model: Mercury binding site 5 out of 6 in 1u19 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Mercury in the PDB 1u19. 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 3.35 Hg C B:Ala132 3.97 Hg CB B:Ala132 4.18 Hg CA B:Ala132 3.78 Hg CB B:Arg135 3.97 Hg CG B:Arg135 4.31 Hg N B:Tyr136 4.72 Hg O B:Ile219 4.53 Hg O B:Cys222 3.27 Hg CB B:Cys222 3.58 Hg SG B:Cys222 2.27 Hg C B:Cys222 3.40 Hg CA B:Cys222 4.13 Hg N B:Tyr223 3.64 Hg CB B:Tyr223 4.57 Hg C B:Tyr223 4.97 Hg CA B:Tyr223 3.79 Hg CB B:Leu226 4.89 Hg CD1 B:Leu226 4.21 Hg CD2 B:Leu226 4.13 Hg CG B:Leu226 4.64 interactive model: Mercury binding site 6 out of 6 in 1u19 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Mercury in the PDB 1u19. 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: Lys67, B: Leu68, B: Gln312, B: Asn315, B: Cys316, B: Thr319, B: Thr336, B: Val337, B: Ser338, B: Thr342, conact list: Atom Atom Distance (A) Hg NE2 B:His65 4.70 Hg CB B:His65 4.21 Hg ND1 B:His65 2.72 Hg CD2 B:His65 4.89 Hg CE1 B:His65 3.48 Hg CG B:His65 3.83 Hg CE B:Lys67 4.24 Hg CD B:Lys67 4.91 Hg NZ B:Lys67 4.65 Hg CD1 B:Leu68 4.88 Hg O B:Gln312 4.96 Hg C B:Asn315 4.94 Hg O B:Cys316 3.97 Hg N B:Cys316 4.04 Hg CB B:Cys316 2.30 Hg SG B:Cys316 2.37 Hg C B:Cys316 3.93 Hg CA B:Cys316 2.95 Hg OG1 B:Thr319 4.75 Hg O B:Thr336 2.05 Hg CB B:Thr336 4.75 Hg C B:Thr336 3.13 Hg CA B:Thr336 4.15 Hg O B:Val337 1.99 Hg N B:Val337 3.92 Hg CG2 B:Val337 4.78 Hg C B:Val337 3.16 Hg CA B:Val337 4.05 Hg N B:Ser338 4.15 Hg CB B:Ser338 4.55 Hg OG B:Ser338 3.61 Hg CA B:Ser338 4.37 Hg CG2 B:Thr342 4.75 interactive model: