Cadmium in the structure of Phosphorylation of Self-Peptides Alters Human Leukocyte Antigen Class I-Restricted Antigen Presentation and Generates Tumor Specific Epitopes (pdb 3fqx)

The binding sites of Cadmium atom in the structure of Phosphorylation of Self-Peptides Alters Human Leukocyte Antigen Class I-Restricted Antigen Presentation and Generates Tumor Specific Epitopes (pdb code 3fqx). This binding sites where shown with 5.0 Angstroms radius around Cadmium atom. The 3fqx structure was solved by J.PETERSEN, J.ROSSJOHN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 24.0-1.7 Space group P212121 a (A) 59.846 b (A) 79.684 c (A) 110.997 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 17.2 Rfree (%) 19.7 Cadmium Binding Sites: Cadmium binding site 1 out of 5 in 3fqx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cadmium in the PDB 3fqx. 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: His191, A: His192, A: Ala193, A: Hoh328, conact list: Atom Atom Distance (A) Cd O A:His191 2.49 Cd NE2 A:His191 4.36 Cd N A:His191 4.65 Cd CB A:His191 3.67 Cd ND1 A:His191 2.30 Cd CD2 A:His191 4.45 Cd C A:His191 3.23 Cd CE1 A:His191 3.20 Cd CG A:His191 3.34 Cd CA A:His191 4.03 Cd N A:His192 3.97 Cd C A:His192 4.85 Cd CA A:His192 4.23 Cd N A:Ala193 4.42 Cd O A:Hoh328 4.46 interactive model: Cadmium binding site 2 out of 5 in 3fqx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cadmium in the PDB 3fqx. 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: Trp107, A: Hoh398, A: Hoh413, A: Hoh414, A: Hoh487, conact list: Atom Atom Distance (A) Cd O A:Gly1 2.63 Cd N A:Gly1 2.41 Cd C A:Gly1 3.24 Cd CA A:Gly1 3.27 Cd O A:Ser2 4.76 Cd N A:Ser2 4.46 Cd NE2 A:His3 2.32 Cd ND1 A:His3 4.29 Cd CD2 A:His3 3.27 Cd CE1 A:His3 3.20 Cd CG A:His3 4.36 Cd NE1 A:Trp107 4.37 Cd O A:Hoh398 2.36 Cd O A:Hoh413 4.01 Cd O A:Hoh414 2.89 Cd O A:Hoh487 2.41 interactive model: Cadmium binding site 3 out of 5 in 3fqx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cadmium in the PDB 3fqx. 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: His197, A: Glu198, A: Hoh301, A: Hoh340, A: Hoh361, A: Hoh500, A: Hoh552, conact list: Atom Atom Distance (A) Cd NE2 A:His197 4.63 Cd CB A:His197 3.91 Cd ND1 A:His197 2.59 Cd CD2 A:His197 4.73 Cd CE1 A:His197 3.46 Cd CG A:His197 3.63 Cd OE1 A:Glu198 4.26 Cd OE2 A:Glu198 4.31 Cd CD A:Glu198 4.74 Cd O A:Hoh301 2.43 Cd O A:Hoh340 4.32 Cd O A:Hoh361 2.26 Cd O A:Hoh500 2.51 Cd O A:Hoh552 2.18 interactive model: Cadmium binding site 4 out of 5 in 3fqx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cadmium in the PDB 3fqx. 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: Asp30, A: Pro210, A: Ala211, A: Glu212, A: Gol281, A: Hoh346, A: Hoh415, A: Hoh416, A: Hoh518, A: Hoh533, A: Hoh537, A: Hoh550, conact list: Atom Atom Distance (A) Cd N A:Asp30 4.83 Cd CB A:Asp30 4.35 Cd OD2 A:Asp30 2.53 Cd OD1 A:Asp30 2.53 Cd CG A:Asp30 2.86 Cd CB A:Pro210 4.55 Cd N A:Ala211 4.49 Cd CB A:Ala211 4.61 Cd CA A:Ala211 4.99 Cd N A:Glu212 4.56 Cd C3 A:Gol281 4.91 Cd O A:Hoh346 2.05 Cd O A:Hoh415 2.31 Cd O A:Hoh416 2.69 Cd O A:Hoh518 4.79 Cd O A:Hoh533 3.31 Cd O A:Hoh537 3.76 Cd O A:Hoh550 3.80 interactive model: Cadmium binding site 5 out of 5 in 3fqx Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cadmium in the PDB 3fqx. 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: His50, A: Hoh345, A: Hoh564, B: Hoh147, B: Hoh418, conact list: Atom Atom Distance (A) Cd NE2 B:His50 2.34 Cd ND1 B:His50 4.45 Cd CD2 B:His50 3.24 Cd CE1 B:His50 3.37 Cd CG B:His50 4.43 Cd O A:Hoh345 2.45 Cd O A:Hoh564 4.66 Cd O B:Hoh147 4.52 Cd O B:Hoh418 2.73 interactive model: