Mercury in the structure of Structure Of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi (pdb 2d2n)

The binding sites of Mercury atom in the structure of Structure Of An Extracellular Giant Hemoglobin of the Gutless Beard Worm Oligobrachia Mashikoi (pdb code 2d2n). This binding sites where shown with 5.0 Angstroms radius around Mercury atom. The 2d2n structure was solved by N.NUMOTO, T.NAKAGAWA, A.KITA, Y.SASAYAMA, Y.FUKUMORI, K.MIKI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-3.2 Space group H32 a (A) 111.745 b (A) 111.745 c (A) 276.707 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 24.2 Rfree (%) 29.7 Mercury Binding Sites: Mercury binding site 1 out of 4 in 2d2n Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Mercury in the PDB 2d2n. 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: Phe32, A: Phe59, A: Thr60, A: His62, A: Cys63, A: Mmc500, conact list: Atom Atom Distance (A) Hg CB A:Phe32 4.15 Hg CD1 A:Phe32 3.53 Hg CD2 A:Phe32 4.59 Hg CZ A:Phe32 4.80 Hg CE1 A:Phe32 4.07 Hg CG A:Phe32 3.84 Hg O A:Phe59 3.47 Hg CB A:Phe59 4.56 Hg CE2 A:Phe59 2.96 Hg CD1 A:Phe59 2.95 Hg CD2 A:Phe59 3.35 Hg CZ A:Phe59 2.51 Hg C A:Phe59 4.15 Hg CE1 A:Phe59 2.49 Hg CG A:Phe59 3.36 Hg CA A:Phe59 4.62 Hg N A:Thr60 4.97 Hg CB A:His62 4.08 Hg CD2 A:His62 3.99 Hg C A:His62 4.60 Hg CG A:His62 4.30 Hg CA A:His62 4.88 Hg N A:Cys63 3.63 Hg CB A:Cys63 3.75 Hg SG A:Cys63 2.28 Hg CA A:Cys63 3.99 Hg HG A:Mmc500 0.00 Hg C A:Mmc500 2.67 interactive model: Mercury binding site 2 out of 4 in 2d2n Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Mercury in the PDB 2d2n. 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: Gly69, B: Leu70, B: Met72, B: Cys73, B: Leu86, B: Leu87, B: Leu90, B: Mmc1500, conact list: Atom Atom Distance (A) Hg O B:Gly69 3.51 Hg C B:Gly69 3.81 Hg CA B:Gly69 4.31 Hg N B:Leu70 4.37 Hg CA B:Leu70 4.70 Hg CB B:Met72 4.34 Hg CE B:Met72 3.68 Hg C B:Met72 4.65 Hg CA B:Met72 4.99 Hg N B:Cys73 3.67 Hg CB B:Cys73 3.52 Hg SG B:Cys73 2.21 Hg CA B:Cys73 3.91 Hg CB B:Leu86 4.30 Hg CD1 B:Leu86 4.59 Hg C B:Leu86 4.98 Hg N B:Leu87 4.93 Hg CD2 B:Leu87 4.39 Hg CD1 B:Leu90 2.89 Hg CD2 B:Leu90 4.31 Hg CG B:Leu90 4.09 Hg HG B:Mmc1500 0.00 Hg C B:Mmc1500 2.67 interactive model: Mercury binding site 3 out of 4 in 2d2n Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Mercury in the PDB 2d2n. 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: C: Phe36, C: Val53, C: Phe63, C: His66, C: Cys67, C: Mmc2500, conact list: Atom Atom Distance (A) Hg CE2 C:Phe36 3.63 Hg CD1 C:Phe36 4.75 Hg CD2 C:Phe36 3.65 Hg CZ C:Phe36 4.22 Hg CE1 C:Phe36 4.73 Hg CG C:Phe36 4.26 Hg CG1 C:Val53 4.81 Hg O C:Phe63 3.24 Hg CB C:Phe63 4.57 Hg CE2 C:Phe63 3.08 Hg CD1 C:Phe63 3.65 Hg CD2 C:Phe63 3.26 Hg CZ C:Phe63 3.21 Hg C C:Phe63 4.04 Hg CE1 C:Phe63 3.50 Hg CG C:Phe63 3.55 Hg CA C:Phe63 4.44 Hg O C:His66 4.91 Hg NE2 C:His66 4.79 Hg N C:His66 4.93 Hg CB C:His66 3.79 Hg CD2 C:His66 3.53 Hg C C:His66 4.17 Hg CG C:His66 4.00 Hg CA C:His66 4.53 Hg N C:Cys67 3.53 Hg CB C:Cys67 3.93 Hg SG C:Cys67 2.72 Hg CA C:Cys67 3.90 Hg HG C:Mmc2500 0.00 Hg C C:Mmc2500 2.67 interactive model: Mercury binding site 4 out of 4 in 2d2n Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Mercury in the PDB 2d2n. 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: D: Ser78, D: Leu79, D: Arg82, D: Cys85, D: Tyr136, D: Mmc3500, conact list: Atom Atom Distance (A) Hg O D:Ser78 4.95 Hg O D:Leu79 3.77 Hg CB D:Leu79 4.44 Hg CD2 D:Leu79 3.73 Hg C D:Leu79 4.40 Hg CG D:Leu79 4.75 Hg CA D:Leu79 4.10 Hg O D:Arg82 4.95 Hg CD D:Arg82 4.54 Hg CZ D:Arg82 4.19 Hg NE D:Arg82 4.57 Hg NH2 D:Arg82 4.87 Hg NH1 D:Arg82 3.64 Hg CA D:Arg82 4.88 Hg CB D:Cys85 3.32 Hg SG D:Cys85 2.74 Hg CA D:Cys85 4.80 Hg CE2 D:Tyr136 2.46 Hg CD1 D:Tyr136 4.96 Hg CD2 D:Tyr136 3.00 Hg CZ D:Tyr136 3.52 Hg CE1 D:Tyr136 4.66 Hg CG D:Tyr136 4.29 Hg OH D:Tyr136 3.89 Hg HG D:Mmc3500 0.00 Hg C D:Mmc3500 2.66 interactive model: