Mercury in the structure of Portal Protein From Bacteriophage SPP1 (pdb 2jes)

The binding sites of Mercury atom in the structure of Portal Protein From Bacteriophage SPP1 (pdb code 2jes). This binding sites where shown with 5.0 Angstroms radius around Mercury atom. The 2jes structure was solved by A.A.LEBEDEV, M.H.KRAUSE, A.L.ISIDRO, A.A.VAGIN, E.V.ORLOVA, J.TURNER, E.J.DODSON, P.TAVARES, A.A.ANTSON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 39.8-3.4 Space group C22211 a (A) 174.314 b (A) 221.405 c (A) 421.866 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 28.8 Rfree (%) 31.9 Mercury Binding Sites: Mercury binding site 1 out of 13 in 2jes Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Mercury in the PDB 2jes. 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: Cys55, A: Ser85, A: His86, A: Ala87, C: Lys258, C: Phe259, C: Tyr260, C: Lys261, C: Asp262, C: Leu263, conact list: Atom Atom Distance (A) Hg CB A:Cys55 3.84 Hg SG A:Cys55 3.35 Hg O A:Ser85 3.04 Hg OG A:Ser85 4.88 Hg C A:Ser85 4.25 Hg C A:His86 4.95 Hg CA A:His86 4.83 Hg N A:Ala87 4.49 Hg CB A:Ala87 4.69 Hg O C:Lys258 4.26 Hg O C:Phe259 3.03 Hg C C:Phe259 3.38 Hg CA C:Phe259 4.26 Hg O C:Tyr260 4.93 Hg N C:Tyr260 3.67 Hg CB C:Tyr260 4.89 Hg C C:Tyr260 4.15 Hg CA C:Tyr260 3.63 Hg N C:Lys261 4.25 Hg N C:Asp262 4.21 Hg CB C:Asp262 3.84 Hg OD2 C:Asp262 3.68 Hg CG C:Asp262 4.15 Hg CA C:Asp262 4.64 Hg N C:Leu263 4.91 interactive model: Mercury binding site 2 out of 13 in 2jes Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Mercury in the PDB 2jes. 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: Cys55, C: Ser85, C: His86, C: Ala87, E: Lys258, E: Phe259, E: Tyr260, E: Lys261, E: Asp262, E: Leu263, conact list: Atom Atom Distance (A) Hg CB C:Cys55 3.97 Hg SG C:Cys55 3.57 Hg O C:Ser85 2.89 Hg OG C:Ser85 4.96 Hg C C:Ser85 4.10 Hg N C:His86 4.81 Hg C C:His86 4.74 Hg CA C:His86 4.57 Hg N C:Ala87 4.29 Hg CB C:Ala87 4.57 Hg CA C:Ala87 4.95 Hg O E:Lys258 4.62 Hg O E:Phe259 2.95 Hg C E:Phe259 3.45 Hg CA E:Phe259 4.42 Hg N E:Tyr260 3.79 Hg CB E:Tyr260 4.86 Hg C E:Tyr260 4.28 Hg CA E:Tyr260 3.69 Hg N E:Lys261 4.48 Hg N E:Asp262 4.31 Hg CB E:Asp262 3.80 Hg OD2 E:Asp262 4.13 Hg CG E:Asp262 4.42 Hg CA E:Asp262 4.62 Hg N E:Leu263 4.77 Hg CG E:Leu263 4.72 interactive model: Mercury binding site 3 out of 13 in 2jes Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Mercury in the PDB 2jes. 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: E: Cys55, E: Ser85, E: His86, E: Ala87, G: Lys258, G: Phe259, G: Tyr260, G: Lys261, G: Asp262, conact list: Atom Atom Distance (A) Hg CB E:Cys55 3.78 Hg SG E:Cys55 3.40 Hg O E:Ser85 2.98 Hg OG E:Ser85 5.00 Hg C E:Ser85 4.17 Hg N E:His86 4.86 Hg C E:His86 4.68 Hg CA E:His86 4.63 Hg N E:Ala87 4.20 Hg CB E:Ala87 4.27 Hg CA E:Ala87 4.74 Hg O G:Lys258 4.48 Hg O G:Phe259 2.89 Hg C G:Phe259 3.29 Hg CA G:Phe259 4.15 Hg N G:Tyr260 3.68 Hg CB G:Tyr260 4.89 Hg C G:Tyr260 4.32 Hg CA G:Tyr260 3.70 Hg N G:Lys261 4.50 Hg N G:Asp262 4.47 Hg CB G:Asp262 4.09 Hg OD2 G:Asp262 4.69 Hg CG G:Asp262 4.78 Hg CA G:Asp262 4.88 interactive model: Mercury binding site 4 out of 13 in 2jes Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Mercury in the PDB 2jes. 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: G: Cys55, G: Ser85, G: His86, G: Ala87, I: Lys258, I: Phe259, I: Tyr260, I: Lys261, I: Asp262, I: Leu263, conact list: Atom Atom Distance (A) Hg CB G:Cys55 4.07 Hg SG G:Cys55 3.52 Hg O G:Ser85 2.90 Hg C G:Ser85 4.10 Hg N G:His86 4.77 Hg C G:His86 4.69 Hg CA G:His86 4.50 Hg N G:Ala87 4.18 Hg CB G:Ala87 4.50 Hg CA G:Ala87 4.86 Hg O I:Lys258 4.64 Hg O I:Phe259 3.04 Hg C I:Phe259 3.41 Hg CA I:Phe259 4.38 Hg O I:Tyr260 4.88 Hg N I:Tyr260 3.65 Hg CB I:Tyr260 4.66 Hg C I:Tyr260 4.14 Hg CA I:Tyr260 3.50 Hg N I:Lys261 4.37 Hg N I:Asp262 4.34 Hg CB I:Asp262 3.97 Hg OD2 I:Asp262 4.01 Hg CG I:Asp262 4.50 Hg CA I:Asp262 4.75 Hg N I:Leu263 4.83 Hg CD2 I:Leu263 4.97 Hg CG I:Leu263 4.68 interactive model: Mercury binding site 5 out of 13 in 2jes Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Mercury in the PDB 2jes. 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: I: Cys55, I: Ser85, I: His86, I: Ala87, K: Lys258, K: Phe259, K: Tyr260, K: Lys261, K: Asp262, K: Leu263, conact list: Atom Atom Distance (A) Hg CB I:Cys55 3.93 Hg SG I:Cys55 3.38 Hg O I:Ser85 3.07 Hg C I:Ser85 4.21 Hg N I:His86 4.85 Hg C I:His86 4.59 Hg CA I:His86 4.51 Hg N I:Ala87 4.08 Hg CB I:Ala87 4.40 Hg CA I:Ala87 4.78 Hg O K:Lys258 4.60 Hg O K:Phe259 2.99 Hg C K:Phe259 3.37 Hg CA K:Phe259 4.35 Hg O K:Tyr260 4.73 Hg N K:Tyr260 3.63 Hg CB K:Tyr260 4.74 Hg C K:Tyr260 4.09 Hg CA K:Tyr260 3.52 Hg N K:Lys261 4.43 Hg N K:Asp262 4.44 Hg CB K:Asp262 3.99 Hg OD2 K:Asp262 4.41 Hg CG K:Asp262 4.64 Hg CA K:Asp262 4.81 Hg N K:Leu263 4.95 Hg CG K:Leu263 4.90 interactive model: Mercury binding site 6 out of 13 in 2jes Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Mercury in the PDB 2jes. 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: K: Cys55, K: Ser85, K: His86, K: Ala87, M: Lys258, M: Phe259, M: Tyr260, M: Lys261, M: Asp262, M: Leu263, conact list: Atom Atom Distance (A) Hg CB K:Cys55 3.93 Hg SG K:Cys55 3.41 Hg O K:Ser85 2.93 Hg C K:Ser85 4.14 Hg N K:His86 4.87 Hg C K:His86 4.76 Hg CA K:His86 4.63 Hg N K:Ala87 4.14 Hg CB K:Ala87 4.48 Hg CA K:Ala87 4.87 Hg O M:Lys258 4.49 Hg O M:Phe259 3.04 Hg C M:Phe259 3.38 Hg CA M:Phe259 4.36 Hg O M:Tyr260 4.83 Hg N M:Tyr260 3.58 Hg CB M:Tyr260 4.70 Hg C M:Tyr260 4.09 Hg CA M:Tyr260 3.49 Hg N M:Lys261 4.31 Hg N M:Asp262 4.25 Hg CB M:Asp262 3.72 Hg OD2 M:Asp262 3.90 Hg CG M:Asp262 4.25 Hg CA M:Asp262 4.59 Hg N M:Leu263 4.82 Hg CG M:Leu263 4.97 interactive model: Mercury binding site 7 out of 13 in 2jes Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Mercury in the PDB 2jes. 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: M: Cys55, M: Ser85, M: His86, M: Ala87, O: Lys258, O: Phe259, O: Tyr260, O: Lys261, O: Asp262, O: Leu263, conact list: Atom Atom Distance (A) Hg CB M:Cys55 3.85 Hg SG M:Cys55 3.35 Hg O M:Ser85 2.92 Hg C M:Ser85 4.11 Hg N M:His86 4.84 Hg C M:His86 4.69 Hg CA M:His86 4.57 Hg N M:Ala87 4.19 Hg CB M:Ala87 4.54 Hg CA M:Ala87 4.86 Hg O O:Lys258 4.68 Hg O O:Phe259 2.98 Hg C O:Phe259 3.53 Hg CA O:Phe259 4.48 Hg O O:Tyr260 4.96 Hg N O:Tyr260 3.92 Hg C O:Tyr260 4.33 Hg CA O:Tyr260 3.83 Hg N O:Lys261 4.60 Hg N O:Asp262 4.31 Hg CB O:Asp262 3.56 Hg OD2 O:Asp262 3.89 Hg CG O:Asp262 4.09 Hg CA O:Asp262 4.55 Hg N O:Leu263 4.90 interactive model: Mercury binding site 8 out of 13 in 2jes Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Mercury in the PDB 2jes. 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: O: Cys55, O: Ser85, O: His86, O: Ala87, Q: Lys258, Q: Phe259, Q: Tyr260, Q: Lys261, Q: Asp262, conact list: Atom Atom Distance (A) Hg CB O:Cys55 3.56 Hg SG O:Cys55 2.93 Hg CA O:Cys55 4.94 Hg O O:Ser85 2.83 Hg OG O:Ser85 4.89 Hg C O:Ser85 4.01 Hg N O:His86 4.70 Hg C O:His86 4.50 Hg CA O:His86 4.45 Hg N O:Ala87 4.14 Hg CB O:Ala87 4.39 Hg CA O:Ala87 4.75 Hg O Q:Lys258 4.45 Hg O Q:Phe259 3.09 Hg C Q:Phe259 3.63 Hg CA Q:Phe259 4.46 Hg N Q:Tyr260 4.10 Hg C Q:Tyr260 4.56 Hg CA Q:Tyr260 4.05 Hg N Q:Lys261 4.75 Hg N Q:Asp262 4.56 Hg CB Q:Asp262 3.87 Hg OD2 Q:Asp262 4.40 Hg CG Q:Asp262 4.62 Hg CA Q:Asp262 4.82 interactive model: Mercury binding site 9 out of 13 in 2jes Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Mercury in the PDB 2jes. 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: Q: Cys55, Q: Ser85, Q: His86, Q: Ala87, S: Lys258, S: Phe259, S: Tyr260, S: Lys261, S: Asp262, conact list: Atom Atom Distance (A) Hg CB Q:Cys55 3.37 Hg SG Q:Cys55 2.85 Hg CA Q:Cys55 4.85 Hg O Q:Ser85 2.96 Hg OG Q:Ser85 4.95 Hg C Q:Ser85 4.16 Hg N Q:His86 4.89 Hg C Q:His86 4.57 Hg CA Q:His86 4.64 Hg N Q:Ala87 4.11 Hg CB Q:Ala87 4.28 Hg CA Q:Ala87 4.60 Hg O S:Lys258 4.32 Hg O S:Phe259 3.11 Hg C S:Phe259 3.51 Hg CA S:Phe259 4.23 Hg N S:Tyr260 3.99 Hg C S:Tyr260 4.62 Hg CA S:Tyr260 4.06 Hg N S:Lys261 4.75 Hg N S:Asp262 4.67 Hg CB S:Asp262 4.15 Hg OD2 S:Asp262 4.90 Hg CG S:Asp262 4.81 interactive model: Mercury binding site 10 out of 13 in 2jes Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Mercury in the PDB 2jes. 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: S: Cys55, S: Ser85, S: His86, S: Ala87, U: Lys258, U: Phe259, U: Tyr260, U: Lys261, U: Asp262, U: Leu263, conact list: Atom Atom Distance (A) Hg CB S:Cys55 4.02 Hg SG S:Cys55 3.45 Hg O S:Ser85 3.11 Hg C S:Ser85 4.26 Hg N S:His86 4.91 Hg C S:His86 4.70 Hg CA S:His86 4.61 Hg N S:Ala87 4.16 Hg CB S:Ala87 4.37 Hg CA S:Ala87 4.78 Hg O U:Lys258 4.79 Hg O U:Phe259 3.03 Hg C U:Phe259 3.51 Hg CA U:Phe259 4.47 Hg O U:Tyr260 4.75 Hg N U:Tyr260 3.81 Hg CB U:Tyr260 4.75 Hg C U:Tyr260 4.17 Hg CA U:Tyr260 3.60 Hg N U:Lys261 4.55 Hg N U:Asp262 4.44 Hg CB U:Asp262 3.88 Hg OD2 U:Asp262 4.74 Hg CG U:Asp262 4.81 Hg CA U:Asp262 4.71 Hg N U:Leu263 4.78 Hg CG U:Leu263 4.68 interactive model: Mercury binding site 11 out of 13 in 2jes Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Mercury in the PDB 2jes. 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: U: Cys55, U: Ser85, U: His86, U: Ala87, W: Lys258, W: Phe259, W: Tyr260, W: Lys261, W: Asp262, conact list: Atom Atom Distance (A) Hg CB U:Cys55 3.72 Hg SG U:Cys55 3.11 Hg O U:Ser85 3.03 Hg OG U:Ser85 4.98 Hg C U:Ser85 4.23 Hg N U:His86 4.94 Hg C U:His86 4.63 Hg CA U:His86 4.66 Hg N U:Ala87 4.19 Hg CB U:Ala87 4.33 Hg CA U:Ala87 4.75 Hg O W:Lys258 4.46 Hg O W:Phe259 3.04 Hg C W:Phe259 3.36 Hg CA W:Phe259 4.22 Hg O W:Tyr260 4.92 Hg N W:Tyr260 3.65 Hg CB W:Tyr260 4.85 Hg C W:Tyr260 4.24 Hg CA W:Tyr260 3.63 Hg N W:Lys261 4.54 Hg N W:Asp262 4.54 Hg CB W:Asp262 4.07 Hg OD2 W:Asp262 4.37 Hg CG W:Asp262 4.70 Hg CA W:Asp262 4.92 interactive model: Mercury binding site 12 out of 13 in 2jes Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Mercury in the PDB 2jes. 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: W: Cys55, W: Ser85, W: His86, W: Ala87, Y: Lys258, Y: Phe259, Y: Tyr260, Y: Lys261, Y: Asp262, Y: Leu263, conact list: Atom Atom Distance (A) Hg CB W:Cys55 3.80 Hg SG W:Cys55 3.27 Hg O W:Ser85 2.81 Hg OG W:Ser85 4.59 Hg C W:Ser85 4.01 Hg N W:His86 4.72 Hg C W:His86 4.54 Hg CA W:His86 4.45 Hg N W:Ala87 4.17 Hg CB W:Ala87 4.56 Hg CA W:Ala87 4.89 Hg O Y:Lys258 4.69 Hg O Y:Phe259 2.97 Hg C Y:Phe259 3.43 Hg CA Y:Phe259 4.36 Hg N Y:Tyr260 3.81 Hg CB Y:Tyr260 4.97 Hg C Y:Tyr260 4.28 Hg CA Y:Tyr260 3.74 Hg N Y:Lys261 4.42 Hg N Y:Asp262 4.31 Hg CB Y:Asp262 3.83 Hg OD2 Y:Asp262 3.80 Hg CG Y:Asp262 4.26 Hg CA Y:Asp262 4.69 Hg N Y:Leu263 4.99 interactive model: Mercury binding site 13 out of 13 in 2jes Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Mercury in the PDB 2jes. 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: Lys258, A: Phe259, A: Tyr260, A: Lys261, A: Asp262, A: Leu263, Y: Cys55, Y: Ser85, Y: His86, Y: Ala87, conact list: Atom Atom Distance (A) Hg O A:Lys258 4.42 Hg O A:Phe259 2.86 Hg C A:Phe259 3.27 Hg CA A:Phe259 4.17 Hg O A:Tyr260 4.85 Hg N A:Tyr260 3.61 Hg CB A:Tyr260 4.85 Hg C A:Tyr260 4.12 Hg CA A:Tyr260 3.59 Hg N A:Lys261 4.32 Hg N A:Asp262 4.31 Hg CB A:Asp262 3.98 Hg OD2 A:Asp262 4.04 Hg CG A:Asp262 4.45 Hg CA A:Asp262 4.76 Hg N A:Leu263 4.99 Hg CB Y:Cys55 3.82 Hg SG Y:Cys55 3.44 Hg O Y:Ser85 3.03 Hg C Y:Ser85 4.24 Hg N Y:His86 4.94 Hg C Y:His86 4.77 Hg CA Y:His86 4.68 Hg N Y:Ala87 4.17 Hg CB Y:Ala87 4.49 Hg CA Y:Ala87 4.87 interactive model: