Cadmium in the structure of R106G KDO8PS With Pep and A5P (pdb 1t8x)

The binding sites of Cadmium atom in the structure of R106G KDO8PS With Pep and A5P (pdb code 1t8x). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 1t8x structure was solved by D.L.GATTI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 54.0-1.8 Space group P3121 a (A) 84.375 b (A) 84.375 c (A) 160.459 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 19.7 Rfree (%) 24.2 Cadmium Binding Sites: Cadmium binding site 1 out of 2 in 1t8x Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 1t8x. 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: Pep1268, A: A5p1269, A: Hoh3006, conact list: Atom Atom Distance (A) Cd CB A:Cys1011 3.56 Cd SG A:Cys1011 2.63 Cd CA A:Cys1011 4.38 Cd NZ A:Lys1041 4.63 Cd CE A:Lys1046 4.90 Cd NZ A:Lys1046 4.11 Cd NE2 A:His1185 2.41 Cd ND1 A:His1185 4.40 Cd CD2 A:His1185 3.48 Cd CE1 A:His1185 3.23 Cd CG A:His1185 4.55 Cd OE1 A:Gln1188 4.52 Cd OE1 A:Glu1222 2.25 Cd CB A:Glu1222 4.97 Cd OE2 A:Glu1222 2.39 Cd CD A:Glu1222 2.61 Cd CG A:Glu1222 4.09 Cd CB A:Asp1233 4.02 Cd OD2 A:Asp1233 4.24 Cd OD1 A:Asp1233 2.15 Cd CG A:Asp1233 3.30 Cd C1 A:Pep1268 4.29 Cd O1 A:Pep1268 4.08 Cd O2' A:Pep1268 4.62 Cd C2 A:Pep1268 4.85 Cd O3 A:A5p1269 4.60 Cd O2 A:A5p1269 4.61 Cd C3 A:A5p1269 4.96 Cd O A:Hoh3006 2.28 interactive model: Cadmium binding site 2 out of 2 in 1t8x Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 1t8x. 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: Thr2184, B: His2185, B: Glu2222, B: Ser2232, B: Asp2233, B: Pep2268, B: Hoh3056, conact list: Atom Atom Distance (A) Cd CB B:Cys2011 3.60 Cd SG B:Cys2011 2.65 Cd CA B:Cys2011 4.38 Cd NZ B:Lys2041 4.78 Cd CE B:Lys2046 4.86 Cd NZ B:Lys2046 4.25 Cd CG2 B:Thr2184 4.96 Cd NE2 B:His2185 2.31 Cd ND1 B:His2185 4.26 Cd CD2 B:His2185 3.44 Cd CE1 B:His2185 3.06 Cd CG B:His2185 4.47 Cd OE1 B:Glu2222 2.25 Cd CB B:Glu2222 5.00 Cd OE2 B:Glu2222 2.63 Cd CD B:Glu2222 2.70 Cd CG B:Glu2222 4.11 Cd OG B:Ser2232 4.65 Cd CB B:Asp2233 3.91 Cd OD2 B:Asp2233 2.14 Cd OD1 B:Asp2233 4.11 Cd CG B:Asp2233 3.20 Cd C1 B:Pep2268 4.30 Cd O1 B:Pep2268 4.01 Cd O2' B:Pep2268 4.70 Cd C2 B:Pep2268 4.80 Cd O B:Hoh3056 2.59 interactive model: