Cadmium in the structure of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 (pdb 2wxt)

The binding sites of Cadmium atom in the structure of Clostridium Perfringens Alpha-Toxin Strain NCTC8237 (pdb code 2wxt). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 2wxt structure was solved by N.JUSTIN, C.E.NAYLOR, A.K.BASAK, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 29.1-2.0 Space group C2221 a (A) 60.180 b (A) 174.370 c (A) 79.530 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.47 Rfree (%) 23.21 Cadmium Binding Sites: Cadmium binding site 1 out of 8 in 2wxt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 2wxt. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His46, A: Glu47, A: Leu50, A: Lys115, A: Hoh2039, A: Hoh2040, A: Hoh2042, A: Hoh2043, A: Hoh2098, conact list: Atom Atom Distance (A) Cd NE2 A:His46 3.57 Cd CB A:His46 3.85 Cd ND1 A:His46 2.37 Cd CD2 A:His46 3.81 Cd C A:His46 4.83 Cd CE1 A:His46 2.74 Cd CG A:His46 3.10 Cd CA A:His46 4.98 Cd N A:Glu47 4.61 Cd OE1 A:Glu47 2.95 Cd OE2 A:Glu47 2.39 Cd CD A:Glu47 3.04 Cd CG A:Glu47 4.48 Cd CD1 A:Leu50 4.31 Cd CD A:Lys115 4.76 Cd O A:Hoh2039 4.54 Cd O A:Hoh2040 4.75 Cd O A:Hoh2042 4.84 Cd O A:Hoh2043 4.06 Cd O A:Hoh2098 4.68 interactive model: Cadmium binding site 2 out of 8 in 2wxt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 2wxt. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His11, A: Asp56, A: His68, A: His126, A: Asp130, A: His136, A: Zn1371, A: Hoh2065, A: Hoh2243, conact list: Atom Atom Distance (A) Cd NE2 A:His11 4.62 Cd CB A:Asp56 4.77 Cd OD2 A:Asp56 3.63 Cd OD1 A:Asp56 2.46 Cd CG A:Asp56 3.39 Cd NE2 A:His68 4.17 Cd CB A:His68 3.74 Cd ND1 A:His68 2.16 Cd CD2 A:His68 4.34 Cd CE1 A:His68 2.97 Cd CG A:His68 3.29 Cd NE2 A:His126 2.43 Cd ND1 A:His126 4.42 Cd CD2 A:His126 3.50 Cd CE1 A:His126 3.24 Cd CG A:His126 4.57 Cd CB A:Asp130 4.66 Cd OD2 A:Asp130 3.46 Cd OD1 A:Asp130 2.38 Cd CG A:Asp130 3.27 Cd CE1 A:His136 4.42 Cd ZN A:Zn1371 3.62 Cd O A:Hoh2065 2.52 Cd O A:Hoh2243 1.94 interactive model: Cadmium binding site 3 out of 8 in 2wxt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 2wxt. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Trp1, A: His136, A: His148, A: Glu152, A: Zn1371, A: Hoh2001, A: Hoh2002, A: Hoh2065, A: Hoh2107, A: Hoh2113, A: Hoh2114, A: Hoh2243, conact list: Atom Atom Distance (A) Cd N A:Trp1 4.44 Cd NE2 A:His136 2.31 Cd ND1 A:His136 4.40 Cd CD2 A:His136 3.28 Cd CE1 A:His136 3.28 Cd CG A:His136 4.44 Cd NE2 A:His148 2.46 Cd ND1 A:His148 4.55 Cd CD2 A:His148 3.38 Cd CE1 A:His148 3.44 Cd CG A:His148 4.55 Cd OE1 A:Glu152 2.18 Cd OE2 A:Glu152 2.70 Cd CD A:Glu152 2.81 Cd CG A:Glu152 4.35 Cd ZN A:Zn1371 4.85 Cd O A:Hoh2001 4.71 Cd O A:Hoh2002 4.46 Cd O A:Hoh2065 3.87 Cd O A:Hoh2107 4.89 Cd O A:Hoh2113 4.57 Cd O A:Hoh2114 4.42 Cd O A:Hoh2243 4.44 interactive model: Cadmium binding site 4 out of 8 in 2wxt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 2wxt. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Glu157, A: Hoh2112, A: Hoh2118, conact list: Atom Atom Distance (A) Cd OE1 A:Glu157 2.43 Cd CB A:Glu157 4.83 Cd OE2 A:Glu157 2.51 Cd CD A:Glu157 2.70 Cd CG A:Glu157 4.13 Cd O A:Hoh2112 4.50 Cd O A:Hoh2118 2.97 interactive model: Cadmium binding site 5 out of 8 in 2wxt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 2wxt. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Gly168, A: Cys169, A: Cd1377, A: Hoh2053, A: Hoh2054, A: Hoh2124, A: Hoh2125, conact list: Atom Atom Distance (A) Cd O A:Gly168 2.74 Cd C A:Gly168 3.32 Cd CA A:Gly168 4.05 Cd N A:Cys169 4.03 Cd CB A:Cys169 3.59 Cd SG A:Cys169 2.58 Cd CA A:Cys169 4.12 Cd CD A:Cd1377 4.21 Cd O A:Hoh2053 4.47 Cd O A:Hoh2054 4.05 Cd O A:Hoh2124 2.72 Cd O A:Hoh2125 4.96 interactive model: Cadmium binding site 6 out of 8 in 2wxt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cadmium in the PDB 2wxt. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Gly168, A: Cys169, A: Lys170, A: Glu173, A: Cd1376, A: Cd1378, A: Hoh2055, A: Hoh2124, A: Hoh2125, A: Hoh2129, conact list: Atom Atom Distance (A) Cd O A:Gly168 4.25 Cd CB A:Cys169 4.13 Cd SG A:Cys169 2.88 Cd CA A:Cys169 4.19 Cd N A:Lys170 4.74 Cd OE1 A:Glu173 2.45 Cd CB A:Glu173 4.85 Cd OE2 A:Glu173 2.28 Cd CD A:Glu173 2.67 Cd CG A:Glu173 4.16 Cd CD A:Cd1376 4.21 Cd CD A:Cd1378 4.03 Cd O A:Hoh2055 4.52 Cd O A:Hoh2124 4.23 Cd O A:Hoh2125 2.79 Cd O A:Hoh2129 4.39 interactive model: Cadmium binding site 7 out of 8 in 2wxt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cadmium in the PDB 2wxt. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Cys169, A: Glu173, A: Cd1377, A: Hoh2129, A: Hoh2130, conact list: Atom Atom Distance (A) Cd SG A:Cys169 4.82 Cd OE1 A:Glu173 4.40 Cd CB A:Glu173 4.14 Cd OE2 A:Glu173 2.21 Cd CD A:Glu173 3.25 Cd CG A:Glu173 3.60 Cd CD A:Cd1377 4.03 Cd O A:Hoh2129 4.33 Cd O A:Hoh2130 4.46 interactive model: Cadmium binding site 8 out of 8 in 2wxt Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Cadmium in the PDB 2wxt. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cadmium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Leu180, A: Lys183, A: His241, A: Glu245, A: Asn247, A: Hoh2136, conact list: Atom Atom Distance (A) Cd CD1 A:Leu180 4.40 Cd NZ A:Lys183 4.94 Cd O A:His241 4.62 Cd NE2 A:His241 4.50 Cd CB A:His241 3.61 Cd ND1 A:His241 2.43 Cd CD2 A:His241 4.52 Cd C A:His241 4.82 Cd CE1 A:His241 3.39 Cd CG A:His241 3.37 Cd CA A:His241 4.44 Cd OE1 A:Glu245 2.35 Cd CB A:Glu245 4.92 Cd OE2 A:Glu245 2.40 Cd CD A:Glu245 2.62 Cd CG A:Glu245 4.02 Cd ND2 A:Asn247 4.90 Cd O A:Hoh2136 4.79 interactive model: