Mercury in the structure of The Structure Of Major Capsid Protein of A Large, Lipid Containing, Dna Virus (pdb 1m3y)

The binding sites of Mercury atom in the structure of The Structure Of Major Capsid Protein of A Large, Lipid Containing, Dna Virus (pdb code 1m3y). This binding sites where shown with 5.0 Angstroms radius around Mercury atom. The 1m3y structure was solved by N.NANDHAGOPAL, A.A.SIMPSON, J.R.GURNON, X.YAN, T.S.BAKER, M.V.GRAVES, J.L.VAN ETTEN, M.G.ROSSMANN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 84.4-2.0 Space group P213 a (A) 188.792 b (A) 188.792 c (A) 188.792 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 34.2 Rfree (%) 35.2 Mercury Binding Sites: Mercury binding site 1 out of 8 in 1m3y Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Mercury in the PDB 1m3y. 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: Leu320, A: Arg325, A: Phe356, A: Cys369, A: Phe371, A: Ile374, A: Hoh459, conact list: Atom Atom Distance (A) Hg CD1 A:Leu320 3.86 Hg CD2 A:Leu320 3.37 Hg CG A:Leu320 4.20 Hg CD A:Arg325 4.73 Hg NE A:Arg325 4.63 Hg CE2 A:Phe356 3.90 Hg CD2 A:Phe356 4.58 Hg CZ A:Phe356 4.15 Hg CE1 A:Phe356 4.99 Hg CB A:Cys369 3.57 Hg SG A:Cys369 2.59 Hg CA A:Cys369 4.93 Hg CE2 A:Phe371 4.74 Hg CD1 A:Phe371 4.69 Hg CZ A:Phe371 4.03 Hg CE1 A:Phe371 4.00 Hg CD1 A:Ile374 3.26 Hg CG1 A:Ile374 4.69 Hg O A:Hoh459 4.49 interactive model: Mercury binding site 2 out of 8 in 1m3y Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Mercury in the PDB 1m3y. 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: Thr240, A: Pro241, A: Ser242, A: Ala243, A: Cys386, A: Asn406, A: Ala408, A: Thr409, A: Ndg442, conact list: Atom Atom Distance (A) Hg O A:Thr240 4.34 Hg OG1 A:Thr240 4.13 Hg C A:Thr240 4.93 Hg O A:Pro241 3.87 Hg C A:Pro241 3.94 Hg O A:Ser242 3.75 Hg N A:Ser242 3.54 Hg CB A:Ser242 3.59 Hg OG A:Ser242 3.64 Hg C A:Ser242 3.72 Hg CA A:Ser242 2.87 Hg N A:Ala243 4.88 Hg O A:Cys386 4.05 Hg N A:Cys386 4.97 Hg CB A:Cys386 3.25 Hg SG A:Cys386 3.72 Hg C A:Cys386 4.74 Hg CA A:Cys386 4.50 Hg O A:Asn406 3.50 Hg CB A:Asn406 4.66 Hg C A:Asn406 4.21 Hg CA A:Asn406 4.17 Hg C A:Ala408 4.77 Hg N A:Thr409 3.89 Hg CB A:Thr409 3.50 Hg CG2 A:Thr409 2.91 Hg OG1 A:Thr409 3.23 Hg CA A:Thr409 3.93 Hg C8 A:Ndg442 4.90 interactive model: Mercury binding site 3 out of 8 in 1m3y Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Mercury in the PDB 1m3y. 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: Leu320, B: Arg325, B: Phe356, B: Cys369, B: Phe371, B: Ile374, conact list: Atom Atom Distance (A) Hg CD1 B:Leu320 3.92 Hg CD2 B:Leu320 3.47 Hg CG B:Leu320 4.29 Hg CD B:Arg325 4.78 Hg NE B:Arg325 4.65 Hg CE2 B:Phe356 3.83 Hg CD2 B:Phe356 4.51 Hg CZ B:Phe356 4.07 Hg CE1 B:Phe356 4.92 Hg CB B:Cys369 3.48 Hg SG B:Cys369 2.54 Hg CA B:Cys369 4.84 Hg CE2 B:Phe371 4.74 Hg CD1 B:Phe371 4.62 Hg CZ B:Phe371 4.00 Hg CE1 B:Phe371 3.93 Hg CD1 B:Ile374 3.28 Hg CG1 B:Ile374 4.70 interactive model: Mercury binding site 4 out of 8 in 1m3y Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Mercury in the PDB 1m3y. 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: Thr240, B: Pro241, B: Ser242, B: Ala243, B: Cys386, B: Asn406, B: Ala408, B: Thr409, B: Ndg542, conact list: Atom Atom Distance (A) Hg O B:Thr240 4.77 Hg OG1 B:Thr240 4.46 Hg O B:Pro241 3.97 Hg C B:Pro241 4.16 Hg O B:Ser242 3.56 Hg N B:Ser242 3.79 Hg CB B:Ser242 3.74 Hg OG B:Ser242 3.92 Hg C B:Ser242 3.69 Hg CA B:Ser242 3.01 Hg N B:Ala243 4.89 Hg O B:Cys386 3.75 Hg N B:Cys386 4.89 Hg CB B:Cys386 3.09 Hg SG B:Cys386 3.72 Hg C B:Cys386 4.49 Hg CA B:Cys386 4.33 Hg O B:Asn406 3.23 Hg CB B:Asn406 4.26 Hg C B:Asn406 3.89 Hg CA B:Asn406 3.79 Hg C B:Ala408 4.86 Hg N B:Thr409 3.99 Hg CB B:Thr409 3.66 Hg CG2 B:Thr409 3.18 Hg OG1 B:Thr409 3.23 Hg CA B:Thr409 4.13 Hg C8 B:Ndg542 4.68 interactive model: Mercury binding site 5 out of 8 in 1m3y Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Mercury in the PDB 1m3y. 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: Leu320, C: Arg325, C: Phe356, C: Cys369, C: Phe371, C: Ile374, conact list: Atom Atom Distance (A) Hg CD1 C:Leu320 3.97 Hg CD2 C:Leu320 3.43 Hg CG C:Leu320 4.29 Hg CD C:Arg325 4.89 Hg NE C:Arg325 4.81 Hg CE2 C:Phe356 3.90 Hg CD2 C:Phe356 4.61 Hg CZ C:Phe356 4.09 Hg CE1 C:Phe356 4.93 Hg CB C:Cys369 3.55 Hg SG C:Cys369 2.57 Hg CA C:Cys369 4.91 Hg CE2 C:Phe371 4.59 Hg CD1 C:Phe371 4.50 Hg CZ C:Phe371 3.88 Hg CE1 C:Phe371 3.83 Hg CD1 C:Ile374 3.18 Hg CG1 C:Ile374 4.63 interactive model: Mercury binding site 6 out of 8 in 1m3y Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Mercury in the PDB 1m3y. 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: Thr240, C: Pro241, C: Ser242, C: Cys386, C: Asn406, C: Ala408, C: Thr409, conact list: Atom Atom Distance (A) Hg O C:Thr240 4.34 Hg OG1 C:Thr240 3.88 Hg C C:Thr240 4.84 Hg O C:Pro241 3.78 Hg C C:Pro241 3.94 Hg O C:Ser242 3.94 Hg N C:Ser242 3.66 Hg CB C:Ser242 3.90 Hg OG C:Ser242 3.97 Hg C C:Ser242 3.90 Hg CA C:Ser242 3.09 Hg O C:Cys386 4.06 Hg N C:Cys386 4.82 Hg CB C:Cys386 3.01 Hg SG C:Cys386 3.37 Hg C C:Cys386 4.68 Hg CA C:Cys386 4.33 Hg O C:Asn406 3.44 Hg CB C:Asn406 4.71 Hg C C:Asn406 4.12 Hg CA C:Asn406 4.11 Hg N C:Ala408 4.93 Hg C C:Ala408 4.51 Hg N C:Thr409 3.69 Hg CB C:Thr409 3.50 Hg CG2 C:Thr409 3.02 Hg OG1 C:Thr409 3.23 Hg CA C:Thr409 3.80 interactive model: Mercury binding site 7 out of 8 in 1m3y Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Mercury in the PDB 1m3y. 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: Leu320, D: Arg325, D: Phe356, D: Cys369, D: Phe371, D: Ile374, conact list: Atom Atom Distance (A) Hg CD1 D:Leu320 3.90 Hg CD2 D:Leu320 3.30 Hg CG D:Leu320 4.18 Hg CD D:Arg325 4.74 Hg NE D:Arg325 4.67 Hg CE2 D:Phe356 3.79 Hg CD2 D:Phe356 4.56 Hg CZ D:Phe356 4.00 Hg CE1 D:Phe356 4.90 Hg CB D:Cys369 3.68 Hg SG D:Cys369 2.70 Hg CE2 D:Phe371 4.63 Hg CD1 D:Phe371 4.67 Hg CZ D:Phe371 3.93 Hg CE1 D:Phe371 3.95 Hg CD1 D:Ile374 3.32 Hg CG1 D:Ile374 4.75 interactive model: Mercury binding site 8 out of 8 in 1m3y Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Mercury in the PDB 1m3y. 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: Thr240, D: Pro241, D: Ser242, D: Ala243, D: Cys386, D: Asn406, D: Thr409, D: Ndg742, conact list: Atom Atom Distance (A) Hg O D:Thr240 4.60 Hg OG1 D:Thr240 4.40 Hg O D:Pro241 3.65 Hg C D:Pro241 3.84 Hg O D:Ser242 3.36 Hg N D:Ser242 3.52 Hg CB D:Ser242 3.63 Hg OG D:Ser242 3.87 Hg C D:Ser242 3.43 Hg CA D:Ser242 2.77 Hg N D:Ala243 4.59 Hg O D:Cys386 3.59 Hg N D:Cys386 4.61 Hg CB D:Cys386 2.94 Hg SG D:Cys386 3.58 Hg C D:Cys386 4.30 Hg CA D:Cys386 4.12 Hg O D:Asn406 3.53 Hg CB D:Asn406 4.43 Hg C D:Asn406 4.13 Hg CA D:Asn406 3.95 Hg N D:Thr409 4.19 Hg CB D:Thr409 3.92 Hg CG2 D:Thr409 3.35 Hg OG1 D:Thr409 3.58 Hg CA D:Thr409 4.33 Hg C8 D:Ndg742 4.95 interactive model: