Cadmium in the structure of Aquifex Aeolicus KDO8P Synthase in Complex With Pep, A5P and Cadmium (pdb 1fww)

The binding sites of Cadmium atom in the structure of Aquifex Aeolicus KDO8P Synthase in Complex With Pep, A5P and Cadmium (pdb code 1fww). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 1fww structure was solved by H.S.DUEWEL, S.RADAEV, J.WANG, R.W.WOODARD, D.L.GATTI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 27.1-1.9 Space group P3121 a (A) 84.108 b (A) 84.108 c (A) 159.780 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 20.5 Rfree (%) 23.8 Cadmium Binding Sites: Cadmium binding site 1 out of 2 in 1fww Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 1fww. 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: Cys1011, A: Lys1041, A: Lys1046, A: His1185, A: Glu1222, A: Asp1233, A: Pep1268, A: A5p1269, A: Hoh3189, A: Hoh3211, conact list: Atom Atom Distance (A) Cd CB A:Cys1011 3.54 Cd SG A:Cys1011 2.55 Cd CA A:Cys1011 4.34 Cd NZ A:Lys1041 4.65 Cd CE A:Lys1046 4.72 Cd NZ A:Lys1046 3.95 Cd NE2 A:His1185 2.52 Cd ND1 A:His1185 4.37 Cd CD2 A:His1185 3.60 Cd CE1 A:His1185 3.20 Cd CG A:His1185 4.59 Cd OE1 A:Glu1222 2.37 Cd OE2 A:Glu1222 2.45 Cd CD A:Glu1222 2.69 Cd CG A:Glu1222 4.14 Cd CB A:Asp1233 4.04 Cd OD2 A:Asp1233 2.25 Cd OD1 A:Asp1233 4.42 Cd CG A:Asp1233 3.41 Cd C1 A:Pep1268 4.29 Cd O1 A:Pep1268 4.12 Cd O2' A:Pep1268 4.63 Cd C2 A:Pep1268 4.72 Cd C2 A:A5p1269 4.85 Cd O2 A:A5p1269 4.01 Cd O4 A:A5p1269 4.92 Cd O A:Hoh3189 3.79 Cd O A:Hoh3211 2.34 interactive model: Cadmium binding site 2 out of 2 in 1fww Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 1fww. 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: B: Cys2011, B: Lys2041, B: Lys2046, B: His2185, B: Glu2222, B: Ser2232, B: Asp2233, B: Pep2268, B: Hoh3194, conact list: Atom Atom Distance (A) Cd CB B:Cys2011 3.62 Cd SG B:Cys2011 2.67 Cd CA B:Cys2011 4.39 Cd NZ B:Lys2041 4.76 Cd CE B:Lys2046 4.77 Cd NZ B:Lys2046 4.12 Cd NE2 B:His2185 2.32 Cd ND1 B:His2185 4.17 Cd CD2 B:His2185 3.45 Cd CE1 B:His2185 2.99 Cd CG B:His2185 4.42 Cd OE1 B:Glu2222 2.29 Cd OE2 B:Glu2222 2.45 Cd CD B:Glu2222 2.66 Cd CG B:Glu2222 4.14 Cd OG B:Ser2232 4.82 Cd CB B:Asp2233 3.94 Cd OD2 B:Asp2233 2.16 Cd OD1 B:Asp2233 4.28 Cd CG B:Asp2233 3.29 Cd C1 B:Pep2268 4.28 Cd O1 B:Pep2268 4.10 Cd O2' B:Pep2268 4.63 Cd C2 B:Pep2268 4.64 Cd O B:Hoh3194 2.52 interactive model: