Mercury in the structure of Crystal Structure of Norovirus 3C-Like Protease (pdb 1wqs)

The binding sites of Mercury atom in the structure of Crystal Structure of Norovirus 3C-Like Protease (pdb code 1wqs). This binding sites where shown with 5.0 Angstroms radius around Mercury atom. The 1wqs structure was solved by K.NAKAMURA, Y.SOMEYA, T.KUMASAKA, N.TANAKA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 8.0-2.8 Space group P61 a (A) 128.890 b (A) 128.890 c (A) 118.080 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 20.6 Rfree (%) 24 Mercury Binding Sites: Mercury binding site 1 out of 8 in 1wqs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Mercury in the PDB 1wqs. 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: Gly76, A: Cys77, A: Cys83, A: Met101, A: Gln117, A: Tyr143, A: Cys154, A: Gly155, A: Cys169, A: Val171, A: Hg1002, conact list: Atom Atom Distance (A) Hg C A:Gly76 4.56 Hg CA A:Gly76 4.82 Hg N A:Cys77 3.57 Hg CB A:Cys77 3.52 Hg CA A:Cys77 4.07 Hg SG A:Cys83 4.89 Hg CE A:Met101 4.11 Hg CG A:Met101 4.32 Hg SD A:Met101 4.55 Hg OE1 A:Gln117 3.88 Hg CB A:Gln117 4.91 Hg CD A:Gln117 4.50 Hg CB A:Tyr143 3.98 Hg CD1 A:Tyr143 4.24 Hg CG A:Tyr143 4.32 Hg O A:Cys154 4.76 Hg CB A:Cys154 2.92 Hg SG A:Cys154 3.87 Hg C A:Cys154 4.22 Hg CA A:Cys154 4.20 Hg N A:Gly155 4.18 Hg CA A:Gly155 4.80 Hg CB A:Cys169 3.93 Hg SG A:Cys169 2.79 Hg CG1 A:Val171 4.80 Hg HG A:Hg1002 3.60 interactive model: Mercury binding site 2 out of 8 in 1wqs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Mercury in the PDB 1wqs. 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: Cys77, A: Val81, A: Cys83, A: Met101, A: Tyr143, A: Val144, A: Tyr145, A: Cys154, A: Hg1001, conact list: Atom Atom Distance (A) Hg N A:Cys77 4.54 Hg CB A:Cys77 2.86 Hg SG A:Cys77 3.60 Hg CA A:Cys77 3.95 Hg CG2 A:Val81 4.84 Hg CB A:Cys83 3.49 Hg SG A:Cys83 2.05 Hg CA A:Cys83 4.61 Hg CG A:Met101 4.42 Hg O A:Tyr143 4.04 Hg CB A:Tyr143 4.51 Hg C A:Tyr143 4.54 Hg C A:Val144 4.92 Hg N A:Tyr145 4.82 Hg CB A:Tyr145 4.58 Hg CE2 A:Tyr145 3.51 Hg CD2 A:Tyr145 3.06 Hg CZ A:Tyr145 4.85 Hg CG A:Tyr145 4.16 Hg N A:Cys154 4.77 Hg CB A:Cys154 3.35 Hg SG A:Cys154 2.23 Hg CA A:Cys154 4.70 Hg HG A:Hg1001 3.60 interactive model: Mercury binding site 3 out of 8 in 1wqs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Mercury in the PDB 1wqs. 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: Cys77, B: Met101, B: Gln117, B: Tyr143, B: Cys154, B: Gly155, B: Cys169, B: Val171, B: Hg1004, conact list: Atom Atom Distance (A) Hg SG B:Cys77 4.12 Hg CE B:Met101 4.09 Hg CG B:Met101 4.69 Hg SD B:Met101 4.57 Hg CB B:Gln117 4.88 Hg CG B:Gln117 4.21 Hg O B:Tyr143 4.62 Hg CB B:Tyr143 3.40 Hg CD1 B:Tyr143 3.56 Hg CD2 B:Tyr143 4.62 Hg CE1 B:Tyr143 4.61 Hg CG B:Tyr143 3.62 Hg CA B:Tyr143 4.88 Hg O B:Cys154 3.40 Hg CB B:Cys154 3.61 Hg SG B:Cys154 2.63 Hg C B:Cys154 3.49 Hg CA B:Cys154 4.15 Hg N B:Gly155 3.86 Hg C B:Gly155 4.78 Hg CA B:Gly155 4.04 Hg CB B:Cys169 3.98 Hg SG B:Cys169 2.34 Hg CG1 B:Val171 4.60 Hg HG B:Hg1004 3.22 interactive model: Mercury binding site 4 out of 8 in 1wqs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Mercury in the PDB 1wqs. 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: Cys77, B: Cys83, B: Met101, B: Tyr143, B: Val144, B: Tyr145, B: Cys154, B: Hg1003, conact list: Atom Atom Distance (A) Hg CB B:Cys77 4.00 Hg SG B:Cys77 2.16 Hg N B:Cys83 4.90 Hg CB B:Cys83 2.54 Hg SG B:Cys83 2.39 Hg CA B:Cys83 4.19 Hg CE B:Met101 4.75 Hg CG B:Met101 3.63 Hg SD B:Met101 3.97 Hg O B:Tyr143 3.59 Hg CB B:Tyr143 3.41 Hg CD1 B:Tyr143 4.01 Hg C B:Tyr143 4.08 Hg CG B:Tyr143 4.18 Hg CA B:Tyr143 4.33 Hg O B:Val144 4.48 Hg N B:Val144 4.92 Hg CD2 B:Tyr145 4.73 Hg CB B:Cys154 3.25 Hg SG B:Cys154 2.48 Hg CA B:Cys154 4.68 Hg HG B:Hg1003 3.22 interactive model: Mercury binding site 5 out of 8 in 1wqs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Mercury in the PDB 1wqs. 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: Gly76, C: Cys77, C: Met101, C: Gln117, C: Tyr143, C: Cys154, C: Gly155, C: Cys169, C: Val171, C: Hg1006, conact list: Atom Atom Distance (A) Hg C C:Gly76 4.57 Hg CA C:Gly76 4.57 Hg N C:Cys77 3.97 Hg SG C:Cys77 4.59 Hg CE C:Met101 2.95 Hg SD C:Met101 4.77 Hg OE1 C:Gln117 4.00 Hg CB C:Gln117 4.72 Hg CD C:Gln117 4.66 Hg CG C:Gln117 4.94 Hg O C:Tyr143 4.97 Hg CB C:Tyr143 3.91 Hg CD1 C:Tyr143 3.93 Hg CE1 C:Tyr143 4.68 Hg CG C:Tyr143 4.12 Hg O C:Cys154 3.83 Hg CB C:Cys154 3.99 Hg SG C:Cys154 2.65 Hg C C:Cys154 3.72 Hg CA C:Cys154 4.39 Hg N C:Gly155 4.03 Hg C C:Gly155 4.93 Hg CA C:Gly155 4.21 Hg CB C:Cys169 3.62 Hg SG C:Cys169 2.51 Hg CG1 C:Val171 4.33 Hg HG C:Hg1006 4.48 interactive model: Mercury binding site 6 out of 8 in 1wqs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Mercury in the PDB 1wqs. 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: Cys77, C: Cys83, C: Tyr143, C: Val144, C: Tyr145, C: Cys154, C: Hg1005, conact list: Atom Atom Distance (A) Hg N C:Cys77 4.57 Hg CB C:Cys77 3.38 Hg SG C:Cys77 3.87 Hg CA C:Cys77 4.40 Hg CB C:Cys83 3.56 Hg SG C:Cys83 2.22 Hg CA C:Cys83 4.63 Hg O C:Tyr143 3.74 Hg CB C:Tyr143 4.62 Hg C C:Tyr143 4.29 Hg O C:Val144 4.02 Hg N C:Val144 4.64 Hg C C:Val144 4.10 Hg CA C:Val144 4.59 Hg N C:Tyr145 4.36 Hg CB C:Tyr145 3.94 Hg CE2 C:Tyr145 3.55 Hg CD1 C:Tyr145 4.62 Hg CD2 C:Tyr145 2.98 Hg CZ C:Tyr145 4.55 Hg CG C:Tyr145 3.62 Hg CA C:Tyr145 4.73 Hg N C:Cys154 4.43 Hg CB C:Cys154 2.86 Hg SG C:Cys154 2.13 Hg CA C:Cys154 4.34 Hg HG C:Hg1005 4.48 interactive model: Mercury binding site 7 out of 8 in 1wqs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Mercury in the PDB 1wqs. 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: Gly76, D: Cys77, D: Cys83, D: Met101, D: Gln117, D: Tyr143, D: Cys154, D: Gly155, D: Cys169, D: Val171, D: Hg1008, conact list: Atom Atom Distance (A) Hg CA D:Gly76 4.87 Hg N D:Cys77 4.95 Hg SG D:Cys77 4.85 Hg SG D:Cys83 4.57 Hg CE D:Met101 3.42 Hg CG D:Met101 4.95 Hg SD D:Met101 4.77 Hg NE2 D:Gln117 4.45 Hg CD D:Gln117 4.88 Hg CG D:Gln117 4.77 Hg CB D:Tyr143 3.90 Hg CD1 D:Tyr143 3.85 Hg CE1 D:Tyr143 4.77 Hg CG D:Tyr143 4.04 Hg O D:Cys154 3.66 Hg CB D:Cys154 3.59 Hg SG D:Cys154 2.96 Hg C D:Cys154 3.68 Hg CA D:Cys154 4.21 Hg N D:Gly155 4.13 Hg CA D:Gly155 4.38 Hg CB D:Cys169 3.46 Hg SG D:Cys169 2.53 Hg CA D:Cys169 4.89 Hg CG1 D:Val171 4.87 Hg HG D:Hg1008 2.91 interactive model: Mercury binding site 8 out of 8 in 1wqs Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Mercury in the PDB 1wqs. 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: Cys77, D: Cys83, D: Met101, D: Tyr143, D: Cys154, D: Hg1007, conact list: Atom Atom Distance (A) Hg N D:Cys77 4.69 Hg CB D:Cys77 3.47 Hg SG D:Cys77 2.70 Hg CA D:Cys77 4.69 Hg N D:Cys83 4.95 Hg CB D:Cys83 3.13 Hg SG D:Cys83 1.94 Hg CA D:Cys83 4.65 Hg CB D:Met101 4.28 Hg CE D:Met101 3.57 Hg CG D:Met101 3.18 Hg SD D:Met101 3.95 Hg CB D:Tyr143 4.30 Hg CD1 D:Tyr143 4.40 Hg CG D:Tyr143 4.83 Hg CB D:Cys154 3.54 Hg SG D:Cys154 1.85 Hg HG D:Hg1007 2.91 interactive model: