Cadmium in the structure of Crystal Structure of CF34 Tcr in Complex With Hla-B8/Flr (pdb 3ffc)

The binding sites of Cadmium atom in the structure of Crystal Structure of CF34 Tcr in Complex With Hla-B8/Flr (pdb code 3ffc). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 3ffc structure was solved by S.GRAS, S.R.BURROWS, L.KJER-NIELSEN, C.S.CLEMENTS, Y.C.LIU, L.C.SULLIVAN, A.G.BROOKS, A.W.PURCELL, J.MCCLUSKEY, J.ROSSJOHN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 15.0-2.8 Space group I222 a (A) 111.564 b (A) 171.807 c (A) 272.690 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 22.1 Rfree (%) 26.8 Cadmium Binding Sites: Cadmium binding site 1 out of 10 in 3ffc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 3ffc. 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: Gly1, A: Ser2, A: His3, A: Glu180, conact list: Atom Atom Distance (A) Cd O A:Gly1 2.50 Cd N A:Gly1 2.40 Cd C A:Gly1 3.18 Cd CA A:Gly1 3.20 Cd N A:Ser2 4.43 Cd NE2 A:His3 2.41 Cd ND1 A:His3 4.54 Cd CD2 A:His3 3.19 Cd CE1 A:His3 3.50 Cd CG A:His3 4.43 Cd OE1 A:Glu180 2.21 Cd OE2 A:Glu180 2.66 Cd CD A:Glu180 2.78 Cd CG A:Glu180 4.29 interactive model: Cadmium binding site 2 out of 10 in 3ffc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 3ffc. 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: Glu36, B: Asp38, B: Arg45, B: Arg81, F: Glu19, F: Pro20, F: Arg75, conact list: Atom Atom Distance (A) Cd OE1 B:Glu36 4.46 Cd OE2 B:Glu36 2.30 Cd CD B:Glu36 3.42 Cd CG B:Glu36 3.94 Cd CB B:Asp38 4.35 Cd OD2 B:Asp38 2.32 Cd OD1 B:Asp38 2.85 Cd CG B:Asp38 2.90 Cd CD B:Arg45 4.29 Cd NE B:Arg45 4.19 Cd NH2 B:Arg81 4.93 Cd OE1 F:Glu19 2.32 Cd OE2 F:Glu19 2.85 Cd CD F:Glu19 2.95 Cd CG F:Glu19 4.47 Cd CA F:Glu19 4.99 Cd CD F:Pro20 4.80 Cd CZ F:Arg75 4.85 Cd NH2 F:Arg75 3.57 interactive model: Cadmium binding site 3 out of 10 in 3ffc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 3ffc. 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: Ala41, B: His51, B: Asp53, B: Cl102, conact list: Atom Atom Distance (A) Cd CB A:Ala41 4.80 Cd NE2 B:His51 3.83 Cd ND1 B:His51 3.59 Cd CD2 B:His51 4.94 Cd CE1 B:His51 2.82 Cd CG B:His51 4.83 Cd CB B:Asp53 4.66 Cd OD2 B:Asp53 2.81 Cd OD1 B:Asp53 2.86 Cd CG B:Asp53 3.18 Cd CL B:Cl102 4.76 interactive model: Cadmium binding site 4 out of 10 in 3ffc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 3ffc. 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: D: Asp128, E: His153, conact list: Atom Atom Distance (A) Cd CB D:Asp128 3.71 Cd OD2 D:Asp128 4.33 Cd CG D:Asp128 4.54 Cd CA D:Asp128 4.89 Cd NE2 E:His153 2.69 Cd ND1 E:His153 4.61 Cd CD2 E:His153 3.79 Cd CE1 E:His153 3.42 Cd CG E:His153 4.82 interactive model: Cadmium binding site 5 out of 10 in 3ffc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 3ffc. 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: E: Glu181, conact list: Atom Atom Distance (A) Cd OE1 E:Glu181 3.80 Cd OE2 E:Glu181 4.99 Cd CD E:Glu181 4.74 interactive model: Cadmium binding site 6 out of 10 in 3ffc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cadmium in the PDB 3ffc. 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: F: Gly1, F: Ser2, F: His3, F: Glu180, conact list: Atom Atom Distance (A) Cd O F:Gly1 2.41 Cd N F:Gly1 2.52 Cd C F:Gly1 3.14 Cd CA F:Gly1 3.26 Cd N F:Ser2 4.35 Cd CA F:Ser2 4.94 Cd NE2 F:His3 2.40 Cd ND1 F:His3 4.55 Cd CD2 F:His3 3.11 Cd CE1 F:His3 3.55 Cd CG F:His3 4.37 Cd OE1 F:Glu180 2.21 Cd OE2 F:Glu180 2.90 Cd CD F:Glu180 2.78 Cd CG F:Glu180 4.06 interactive model: Cadmium binding site 7 out of 10 in 3ffc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cadmium in the PDB 3ffc. 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: Gly18, A: Glu19, A: Pro20, A: Arg75, G: Glu36, G: Val37, G: Asp38, G: Arg45, A: Cl283, conact list: Atom Atom Distance (A) Cd O A:Gly18 4.57 Cd OE1 A:Glu19 2.29 Cd OE2 A:Glu19 2.74 Cd CD A:Glu19 2.86 Cd CG A:Glu19 4.38 Cd CA A:Glu19 4.79 Cd CD A:Pro20 4.97 Cd NH2 A:Arg75 3.98 Cd OE1 G:Glu36 2.31 Cd CB G:Glu36 4.90 Cd OE2 G:Glu36 4.11 Cd CD G:Glu36 3.09 Cd CG G:Glu36 3.39 Cd O G:Val37 4.63 Cd C G:Val37 4.94 Cd CB G:Asp38 4.18 Cd OD2 G:Asp38 2.28 Cd OD1 G:Asp38 2.36 Cd CG G:Asp38 2.66 Cd CA G:Asp38 4.99 Cd CD G:Arg45 4.48 Cd NE G:Arg45 4.13 Cd CL A:Cl283 2.43 interactive model: Cadmium binding site 8 out of 10 in 3ffc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Cadmium in the PDB 3ffc. 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: G: His51, G: Asp53, G: Na104, conact list: Atom Atom Distance (A) Cd NE2 G:His51 3.76 Cd ND1 G:His51 3.53 Cd CD2 G:His51 4.77 Cd CE1 G:His51 2.86 Cd CG G:His51 4.66 Cd CB G:Asp53 4.72 Cd OD2 G:Asp53 2.72 Cd OD1 G:Asp53 4.61 Cd CG G:Asp53 3.84 Cd NA G:Na104 4.88 interactive model: Cadmium binding site 9 out of 10 in 3ffc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Cadmium in the PDB 3ffc. 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: I: Asp128, I: Phe209, J: His153, conact list: Atom Atom Distance (A) Cd CB I:Asp128 4.48 Cd OD2 I:Asp128 3.03 Cd OD1 I:Asp128 2.23 Cd CG I:Asp128 3.00 Cd CD2 I:Phe209 4.96 Cd NE2 J:His153 2.82 Cd ND1 J:His153 4.69 Cd CD2 J:His153 4.00 Cd CE1 J:His153 3.45 Cd CG J:His153 4.99 interactive model: Cadmium binding site 10 out of 10 in 3ffc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Cadmium in the PDB 3ffc. 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: J: Glu181, J: Cl263, conact list: Atom Atom Distance (A) Cd OE2 J:Glu181 4.06 Cd CD J:Glu181 4.95 Cd CL J:Cl263 3.73 interactive model: