Cadmium in the structure of Aquifex Aeolicus KDO8PS R106G Mutant in Complex With 2PGA and R5P (pdb 1zji)

The binding sites of Cadmium atom in the structure of Aquifex Aeolicus KDO8PS R106G Mutant in Complex With 2PGA and R5P (pdb code 1zji). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 1zji structure was solved by X.XU, F.KONA, J.WANG, J.LU, T.STEMMLER, D.L.GATTI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.3-2.2 Space group P3121 a (A) 84.741 b (A) 84.741 c (A) 160.600 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 20.3 Rfree (%) 24.2 Cadmium Binding Sites: Cadmium binding site 1 out of 2 in 1zji Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 1zji. 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: Gln1188, A: Glu1222, A: Asp1233, A: R5p1269, A: 2pg1268, conact list: Atom Atom Distance (A) Cd CB A:Cys1011 3.72 Cd SG A:Cys1011 2.81 Cd CA A:Cys1011 4.45 Cd NZ A:Lys1041 4.71 Cd CE A:Lys1046 4.84 Cd NZ A:Lys1046 3.97 Cd NE2 A:His1185 2.39 Cd ND1 A:His1185 4.33 Cd CD2 A:His1185 3.52 Cd CE1 A:His1185 3.13 Cd CG A:His1185 4.54 Cd OE1 A:Gln1188 4.80 Cd OE1 A:Glu1222 2.32 Cd OE2 A:Glu1222 2.26 Cd CD A:Glu1222 2.56 Cd CG A:Glu1222 4.00 Cd CB A:Asp1233 4.25 Cd OD2 A:Asp1233 4.08 Cd OD1 A:Asp1233 2.17 Cd CG A:Asp1233 3.31 Cd O3 A:R5p1269 3.54 Cd C3 A:R5p1269 4.65 Cd O2 A:2pg1268 4.75 Cd C1 A:2pg1268 4.37 Cd O1 A:2pg1268 3.74 interactive model: Cadmium binding site 2 out of 2 in 1zji Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 1zji. 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: Asp2233, B: 2pg2268, conact list: Atom Atom Distance (A) Cd CB B:Cys2011 3.83 Cd SG B:Cys2011 2.95 Cd CA B:Cys2011 4.56 Cd NZ B:Lys2041 4.84 Cd CE B:Lys2046 5.00 Cd NZ B:Lys2046 4.32 Cd NE2 B:His2185 2.21 Cd ND1 B:His2185 4.03 Cd CD2 B:His2185 3.38 Cd CE1 B:His2185 2.83 Cd CG B:His2185 4.32 Cd OE1 B:Glu2222 2.39 Cd OE2 B:Glu2222 2.47 Cd CD B:Glu2222 2.71 Cd CG B:Glu2222 4.16 Cd CB B:Asp2233 4.27 Cd OD2 B:Asp2233 2.26 Cd OD1 B:Asp2233 4.24 Cd CG B:Asp2233 3.42 Cd O2 B:2pg2268 4.64 Cd C1 B:2pg2268 4.21 Cd O1 B:2pg2268 3.55 interactive model: