Copper in the structure of Structure of the Alzheimer'S Amyloid Precursor Protein (App) Copper Binding Domain in 'Large Unit Cell' Form (pdb 2fk3)

The binding sites of Copper atom in the structure of Structure of the Alzheimer'S Amyloid Precursor Protein (App) Copper Binding Domain in 'Large Unit Cell' Form (pdb code 2fk3). This binding sites where shown with 5.0 Angstroms radius around Copper atom. The 2fk3 structure was solved by G.K.-W.KONG, M.W.PARKER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.9-2.4 Space group P212121 a (A) 59.623 b (A) 67.437 c (A) 127.656 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.8 Rfree (%) 24.8 Copper Binding Sites: Copper binding site 1 out of 19 in 2fk3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Copper in the PDB 2fk3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His137, A: Glu139, G: Glu131, G: Ala132, A: Cu211, A: Hoh237, conact list: Atom Atom Distance (A) Cu NE2 A:His137 2.27 Cu ND1 A:His137 4.41 Cu CD2 A:His137 3.04 Cu CE1 A:His137 3.40 Cu CG A:His137 4.28 Cu OE1 A:Glu139 3.93 Cu OE2 A:Glu139 2.05 Cu CD A:Glu139 3.25 Cu CG A:Glu139 4.32 Cu O G:Glu131 2.54 Cu N G:Glu131 2.20 Cu CB G:Glu131 4.35 Cu C G:Glu131 2.91 Cu CA G:Glu131 2.98 Cu N G:Ala132 3.96 Cu CB G:Ala132 4.64 Cu CA G:Ala132 4.68 Cu CU A:Cu211 4.82 Cu O A:Hoh237 1.86 interactive model: Copper binding site 2 out of 19 in 2fk3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Copper in the PDB 2fk3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His151, A: Lys155, F: His151, A: Cu213, A: Hoh214, A: Hoh217, A: Hoh218, F: Hoh220, F: Hoh221, conact list: Atom Atom Distance (A) Cu CE1 A:His151 4.89 Cu CE A:Lys155 4.74 Cu CE1 F:His151 4.94 Cu CU A:Cu213 4.48 Cu O A:Hoh214 2.67 Cu O A:Hoh217 2.71 Cu O A:Hoh218 2.66 Cu O F:Hoh220 2.90 Cu O F:Hoh221 2.70 interactive model: Copper binding site 3 out of 19 in 2fk3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Copper in the PDB 2fk3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His137, A: Cu204, A: Hoh235, A: Hoh236, A: Hoh237, conact list: Atom Atom Distance (A) Cu CE1 A:His137 4.73 Cu CU A:Cu204 4.82 Cu O A:Hoh235 1.85 Cu O A:Hoh236 1.86 Cu O A:Hoh237 3.01 interactive model: Copper binding site 4 out of 19 in 2fk3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Copper in the PDB 2fk3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Leu165, A: His166, A: Tyr168, F: Leu165, F: His166, F: Asp167, F: Tyr168, A: Cu208, A: Hoh217, F: Hoh220, conact list: Atom Atom Distance (A) Cu O A:Leu165 2.87 Cu CB A:Leu165 4.57 Cu CD2 A:Leu165 4.74 Cu C A:Leu165 3.74 Cu CG A:Leu165 4.25 Cu CA A:Leu165 4.80 Cu O A:His166 3.07 Cu N A:His166 4.26 Cu C A:His166 3.87 Cu CA A:His166 3.92 Cu CD1 A:Tyr168 4.84 Cu CE1 A:Tyr168 4.50 Cu O F:Leu165 2.81 Cu CB F:Leu165 4.49 Cu CD2 F:Leu165 4.31 Cu C F:Leu165 3.65 Cu CG F:Leu165 4.03 Cu CA F:Leu165 4.73 Cu O F:His166 2.80 Cu N F:His166 4.12 Cu C F:His166 3.61 Cu CA F:His166 3.76 Cu N F:Asp167 4.82 Cu CD1 F:Tyr168 4.78 Cu CE1 F:Tyr168 4.59 Cu CU A:Cu208 4.48 Cu O A:Hoh217 3.30 Cu O F:Hoh220 3.13 interactive model: Copper binding site 5 out of 19 in 2fk3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Copper in the PDB 2fk3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: His137, D: His137, B: Hoh233, conact list: Atom Atom Distance (A) Cu NE2 B:His137 2.10 Cu ND1 B:His137 4.17 Cu CD2 B:His137 3.10 Cu CE1 B:His137 3.06 Cu CG B:His137 4.23 Cu NE2 D:His137 2.17 Cu ND1 D:His137 4.25 Cu CD2 D:His137 3.17 Cu CE1 D:His137 3.12 Cu CG D:His137 4.31 Cu O B:Hoh233 4.76 interactive model: Copper binding site 6 out of 19 in 2fk3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Copper in the PDB 2fk3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Tyr168, B: Gly169, C: Tyr168, C: Gly169, B: Hoh235, B: Hoh236, C: Hoh237, conact list: Atom Atom Distance (A) Cu O B:Tyr168 2.77 Cu N B:Tyr168 4.84 Cu C B:Tyr168 3.79 Cu CA B:Tyr168 4.95 Cu N B:Gly169 4.35 Cu CA B:Gly169 4.12 Cu O C:Tyr168 2.78 Cu N C:Tyr168 4.67 Cu C C:Tyr168 3.76 Cu CA C:Tyr168 4.84 Cu N C:Gly169 4.36 Cu CA C:Gly169 4.23 Cu O B:Hoh235 4.77 Cu O B:Hoh236 3.45 Cu O C:Hoh237 3.27 interactive model: Copper binding site 7 out of 19 in 2fk3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Copper in the PDB 2fk3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: His137, G: His137, C: Hoh215, C: Hoh244, G: Hoh190, G: Hoh195, G: Hoh196, conact list: Atom Atom Distance (A) Cu NE2 C:His137 1.99 Cu ND1 C:His137 4.11 Cu CD2 C:His137 2.92 Cu CE1 C:His137 3.04 Cu CG C:His137 4.09 Cu NE2 G:His137 1.86 Cu ND1 G:His137 3.95 Cu CD2 G:His137 2.87 Cu CE1 G:His137 2.84 Cu CG G:His137 3.99 Cu O C:Hoh215 4.27 Cu O C:Hoh244 3.21 Cu O G:Hoh190 2.78 Cu O G:Hoh195 4.40 Cu O G:Hoh196 3.48 interactive model: Copper binding site 8 out of 19 in 2fk3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Copper in the PDB 2fk3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Glu131, C: Ala132, H: His137, H: Glu139, H: Hoh217, conact list: Atom Atom Distance (A) Cu O C:Glu131 2.14 Cu N C:Glu131 2.05 Cu CB C:Glu131 4.00 Cu C C:Glu131 2.85 Cu CG C:Glu131 5.00 Cu CA C:Glu131 2.93 Cu N C:Ala132 4.14 Cu CB C:Ala132 4.99 Cu CA C:Ala132 4.88 Cu NE2 H:His137 2.12 Cu ND1 H:His137 4.22 Cu CD2 H:His137 3.09 Cu CE1 H:His137 3.11 Cu CG H:His137 4.24 Cu OE1 H:Glu139 2.51 Cu OE2 H:Glu139 4.61 Cu CD H:Glu139 3.54 Cu CG H:Glu139 3.98 Cu O H:Hoh217 4.13 interactive model: Copper binding site 9 out of 19 in 2fk3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Copper in the PDB 2fk3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Hoh244, G: Hoh214, conact list: Atom Atom Distance (A) Cu O C:Hoh244 1.88 Cu O G:Hoh214 4.68 interactive model: Copper binding site 10 out of 19 in 2fk3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Copper in the PDB 2fk3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Tyr168, D: Gly169, G: Tyr168, G: Gly169, G: Glu183, D: Hoh229, G: Hoh192, G: Hoh209, G: Hoh210, conact list: Atom Atom Distance (A) Cu O D:Tyr168 2.80 Cu N D:Tyr168 4.89 Cu C D:Tyr168 3.84 Cu CA D:Tyr168 5.00 Cu N D:Gly169 4.39 Cu CA D:Gly169 4.14 Cu O G:Tyr168 2.60 Cu N G:Tyr168 4.52 Cu C G:Tyr168 3.55 Cu CA G:Tyr168 4.66 Cu N G:Gly169 4.10 Cu CA G:Gly169 3.98 Cu OE1 G:Glu183 4.78 Cu O D:Hoh229 2.11 Cu O G:Hoh192 5.00 Cu O G:Hoh209 3.10 Cu O G:Hoh210 3.35 interactive model: Copper binding site 11 out of 19 in 2fk3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Copper in the PDB 2fk3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: E: Hoh221, E: Hoh238, conact list: Atom Atom Distance (A) Cu O E:Hoh221 2.39 Cu O E:Hoh238 3.29 interactive model: Copper binding site 12 out of 19 in 2fk3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Copper in the PDB 2fk3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Glu131, D: Ala132, E: His137, E: Glu139, E: Hoh219, E: Hoh221, E: Hoh238, conact list: Atom Atom Distance (A) Cu O D:Glu131 2.16 Cu N D:Glu131 2.38 Cu CB D:Glu131 4.40 Cu C D:Glu131 2.84 Cu CA D:Glu131 3.10 Cu N D:Ala132 4.00 Cu CB D:Ala132 4.52 Cu CA D:Ala132 4.63 Cu NE2 E:His137 2.05 Cu ND1 E:His137 4.11 Cu CD2 E:His137 2.88 Cu CE1 E:His137 3.09 Cu CG E:His137 4.04 Cu OE1 E:Glu139 3.96 Cu OE2 E:Glu139 2.09 Cu CD E:Glu139 3.30 Cu CG E:Glu139 4.40 Cu O E:Hoh219 4.87 Cu O E:Hoh221 4.46 Cu O E:Hoh238 1.97 interactive model: Copper binding site 13 out of 19 in 2fk3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Copper in the PDB 2fk3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: E: Leu165, E: His166, E: Asp167, E: Tyr168, H: Leu165, H: His166, H: Asp167, H: Tyr168, H: Cu207, E: Hoh223, E: Hoh224, H: Hoh213, H: Hoh214, conact list: Atom Atom Distance (A) Cu O E:Leu165 2.97 Cu CB E:Leu165 4.59 Cu CD2 E:Leu165 4.79 Cu C E:Leu165 3.79 Cu CG E:Leu165 4.24 Cu CA E:Leu165 4.86 Cu O E:His166 2.89 Cu N E:His166 4.24 Cu C E:His166 3.71 Cu CA E:His166 3.87 Cu N E:Asp167 4.90 Cu CD1 E:Tyr168 4.67 Cu CE1 E:Tyr168 4.34 Cu O H:Leu165 2.84 Cu CB H:Leu165 4.60 Cu CD2 H:Leu165 4.71 Cu C H:Leu165 3.70 Cu CG H:Leu165 4.20 Cu CA H:Leu165 4.79 Cu O H:His166 2.90 Cu N H:His166 4.20 Cu C H:His166 3.73 Cu CA H:His166 3.88 Cu N H:Asp167 4.94 Cu CD1 H:Tyr168 4.83 Cu CE1 H:Tyr168 4.57 Cu CU H:Cu207 4.32 Cu O E:Hoh223 4.94 Cu O E:Hoh224 3.12 Cu O H:Hoh213 3.08 Cu O H:Hoh214 4.98 interactive model: Copper binding site 14 out of 19 in 2fk3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 14 of Copper in the PDB 2fk3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: E: His147, E: Tyr168, E: Gly169, E: Met170, H: His166, E: Hoh228, E: Hoh235, conact list: Atom Atom Distance (A) Cu CE1 E:His147 4.61 Cu O E:Tyr168 4.47 Cu C E:Gly169 4.73 Cu CA E:Gly169 4.22 Cu N E:Met170 4.12 Cu CB E:Met170 4.88 Cu CE E:Met170 4.98 Cu CG E:Met170 4.44 Cu CE1 H:His166 4.43 Cu O E:Hoh228 3.76 Cu O E:Hoh235 4.84 interactive model: Copper binding site 15 out of 19 in 2fk3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 15 of Copper in the PDB 2fk3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Glu131, B: Ala132, F: His137, F: Glu139, conact list: Atom Atom Distance (A) Cu O B:Glu131 2.90 Cu N B:Glu131 2.05 Cu CB B:Glu131 4.24 Cu C B:Glu131 2.95 Cu CG B:Glu131 4.97 Cu CA B:Glu131 2.96 Cu N B:Ala132 3.79 Cu CB B:Ala132 4.96 Cu CA B:Ala132 4.63 Cu NE2 F:His137 2.07 Cu ND1 F:His137 4.14 Cu CD2 F:His137 2.94 Cu CE1 F:His137 3.11 Cu CG F:His137 4.10 Cu OE1 F:Glu139 3.37 Cu OE2 F:Glu139 1.75 Cu CD F:Glu139 2.86 Cu CG F:Glu139 4.11 interactive model: Copper binding site 16 out of 19 in 2fk3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 16 of Copper in the PDB 2fk3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: F: Lys155, F: Ser159, F: Thr163, F: Asn164, F: Leu165, F: Hoh221, F: Hoh222, F: Hoh225, conact list: Atom Atom Distance (A) Cu O F:Lys155 4.85 Cu N F:Ser159 4.54 Cu CB F:Ser159 4.15 Cu OG F:Ser159 3.00 Cu CA F:Ser159 4.32 Cu O F:Thr163 3.23 Cu C F:Thr163 4.24 Cu N F:Asn164 4.60 Cu CB F:Asn164 4.49 Cu ND2 F:Asn164 4.69 Cu C F:Asn164 4.97 Cu OD1 F:Asn164 3.37 Cu CG F:Asn164 3.96 Cu CA F:Asn164 4.00 Cu N F:Leu165 4.77 Cu O F:Hoh221 4.69 Cu O F:Hoh222 2.68 Cu O F:Hoh225 3.19 interactive model: Copper binding site 17 out of 19 in 2fk3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 17 of Copper in the PDB 2fk3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Lys178, F: Glu131, F: His166, F: Cys187, F: Leu189, A: Hoh224, A: Hoh227, conact list: Atom Atom Distance (A) Cu NZ D:Lys178 4.64 Cu N F:Glu131 4.74 Cu NE2 F:His166 4.89 Cu CE1 F:His166 4.35 Cu CB F:Cys187 4.73 Cu SG F:Cys187 4.90 Cu CD1 F:Leu189 4.16 Cu OXT F:Leu189 4.73 Cu O A:Hoh224 3.25 Cu O A:Hoh227 2.56 interactive model: Copper binding site 18 out of 19 in 2fk3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 18 of Copper in the PDB 2fk3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: E: Lys155, H: Lys155, E: Cu212, E: Hoh223, E: Hoh224, E: Hoh225, E: Hoh226, H: Hoh212, H: Hoh213, H: Hoh214, H: Hoh228, conact list: Atom Atom Distance (A) Cu CE E:Lys155 4.87 Cu CE H:Lys155 4.88 Cu CD H:Lys155 4.97 Cu NZ H:Lys155 4.78 Cu CU E:Cu212 4.32 Cu O E:Hoh223 4.90 Cu O E:Hoh224 2.63 Cu O E:Hoh225 2.62 Cu O E:Hoh226 2.74 Cu O H:Hoh212 2.61 Cu O H:Hoh213 2.61 Cu O H:Hoh214 2.66 Cu O H:Hoh228 4.77 interactive model: Copper binding site 19 out of 19 in 2fk3 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 19 of Copper in the PDB 2fk3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Copper atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: H: Lys134, H: Hoh223, H: Hoh224, H: Hoh230, H: Hoh231, H: Hoh232, conact list: Atom Atom Distance (A) Cu CE H:Lys134 4.85 Cu O H:Hoh223 2.27 Cu O H:Hoh224 2.20 Cu O H:Hoh230 4.93 Cu O H:Hoh231 2.42 Cu O H:Hoh232 2.13 interactive model: