Zinc in the structure of Crystal Structure Of The Binding Domain of the Ampa Subunit GLUR2 Bound to UBP277 (pdb 3h03)

The binding sites of Zinc atom in the structure of Crystal Structure Of The Binding Domain of the Ampa Subunit GLUR2 Bound to UBP277 (pdb code 3h03). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 3h03 structure was solved by A.H.AHMED, R.E.OSWALD, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 28.1-1.9 Space group P1211 a (A) 98.953 b (A) 57.719 c (A) 105.461 alpha (°) 90.00 beta (°) 114.88 gamma (°) 90.00 Rfactor (%) 22.1 Rfree (%) 25.8 Zinc Binding Sites: Zinc binding site 1 out of 8 in 3h03 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 3h03. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Glu42, A: His46, A: Leu241, A: Gln244, A: Leu246, conact list: Atom Atom Distance (A) Zn O A:Glu42 4.95 Zn OE1 A:Glu42 2.19 Zn CB A:Glu42 4.82 Zn OE2 A:Glu42 3.21 Zn CD A:Glu42 3.04 Zn CG A:Glu42 4.45 Zn CA A:Glu42 4.98 Zn NE2 A:His46 2.16 Zn ND1 A:His46 4.14 Zn CD2 A:His46 3.16 Zn CE1 A:His46 3.04 Zn CG A:His46 4.23 Zn CD2 A:Leu241 4.22 Zn OE1 A:Gln244 4.28 Zn CD2 A:Leu246 4.12 interactive model: Zinc binding site 2 out of 8 in 3h03 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 3h03. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: His23, A: Glu24, conact list: Atom Atom Distance (A) Zn NE2 A:His23 2.34 Zn ND1 A:His23 4.47 Zn CD2 A:His23 3.19 Zn CE1 A:His23 3.41 Zn CG A:His23 4.40 Zn OE1 A:Glu24 4.88 interactive model: Zinc binding site 3 out of 8 in 3h03 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 3h03. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Glu42, B: Lys45, B: His46, B: Leu241, B: Gln244, conact list: Atom Atom Distance (A) Zn OE1 B:Glu42 2.36 Zn CB B:Glu42 4.67 Zn OE2 B:Glu42 3.15 Zn CD B:Glu42 3.03 Zn CG B:Glu42 4.38 Zn CE B:Lys45 4.19 Zn CD B:Lys45 3.98 Zn NE2 B:His46 2.13 Zn ND1 B:His46 4.22 Zn CD2 B:His46 3.04 Zn CE1 B:His46 3.15 Zn CG B:His46 4.20 Zn CD2 B:Leu241 4.03 Zn OE1 B:Gln244 4.02 Zn CD B:Gln244 4.94 interactive model: Zinc binding site 4 out of 8 in 3h03 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 3h03. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: His23, B: Glu24, B: Hoh281, conact list: Atom Atom Distance (A) Zn NE2 B:His23 2.16 Zn ND1 B:His23 4.26 Zn CD2 B:His23 3.02 Zn CE1 B:His23 3.22 Zn CG B:His23 4.20 Zn OE1 B:Glu24 4.17 Zn CB B:Glu24 4.73 Zn OE2 B:Glu24 2.10 Zn CD B:Glu24 3.01 Zn CG B:Glu24 3.26 Zn O B:Hoh281 4.87 interactive model: Zinc binding site 5 out of 8 in 3h03 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 3h03. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: His23, D: Glu24, G: Asp139, G: Arg172, conact list: Atom Atom Distance (A) Zn NE2 D:His23 2.40 Zn ND1 D:His23 4.54 Zn CD2 D:His23 3.17 Zn CE1 D:His23 3.51 Zn CG D:His23 4.41 Zn OE1 D:Glu24 3.86 Zn OE2 D:Glu24 4.63 Zn CD D:Glu24 4.62 Zn OD2 G:Asp139 4.27 Zn OD1 G:Asp139 4.28 Zn CG G:Asp139 4.69 Zn NH1 G:Arg172 4.86 interactive model: Zinc binding site 6 out of 8 in 3h03 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 3h03. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Glu42, D: His46, D: Leu241, D: Gln244, D: Leu246, D: Hoh489, conact list: Atom Atom Distance (A) Zn O D:Glu42 4.95 Zn OE1 D:Glu42 3.12 Zn CB D:Glu42 4.80 Zn OE2 D:Glu42 2.15 Zn CD D:Glu42 2.98 Zn CG D:Glu42 4.40 Zn CA D:Glu42 4.99 Zn NE2 D:His46 2.20 Zn ND1 D:His46 4.26 Zn CD2 D:His46 3.07 Zn CE1 D:His46 3.21 Zn CG D:His46 4.23 Zn CD2 D:Leu241 4.18 Zn OE1 D:Gln244 4.26 Zn CD1 D:Leu246 4.17 Zn O D:Hoh489 3.66 interactive model: Zinc binding site 7 out of 8 in 3h03 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Zinc in the PDB 3h03. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Glu166, G: Glu42, G: Lys45, G: His46, G: Leu241, G: Gln244, G: Leu246, conact list: Atom Atom Distance (A) Zn CG A:Glu166 4.77 Zn OE1 G:Glu42 2.14 Zn CB G:Glu42 4.80 Zn OE2 G:Glu42 3.30 Zn CD G:Glu42 3.06 Zn CG G:Glu42 4.45 Zn CE G:Lys45 4.32 Zn CD G:Lys45 4.02 Zn NE2 G:His46 2.08 Zn ND1 G:His46 4.19 Zn CD2 G:His46 3.03 Zn CE1 G:His46 3.10 Zn CG G:His46 4.19 Zn CD2 G:Leu241 4.11 Zn OE1 G:Gln244 3.98 Zn CD G:Gln244 4.90 Zn CD2 G:Leu246 4.80 interactive model: Zinc binding site 8 out of 8 in 3h03 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Zinc in the PDB 3h03. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Zinc atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Asp139, D: Ser140, D: Arg172, G: His23, G: Glu24, D: Hoh306, G: Hoh414, conact list: Atom Atom Distance (A) Zn O D:Asp139 5.00 Zn CB D:Asp139 4.34 Zn OD2 D:Asp139 2.23 Zn C D:Asp139 4.75 Zn OD1 D:Asp139 2.84 Zn CG D:Asp139 2.87 Zn N D:Ser140 4.77 Zn CB D:Ser140 4.10 Zn CD D:Arg172 4.90 Zn CG D:Arg172 4.32 Zn NE2 G:His23 2.15 Zn ND1 G:His23 4.25 Zn CD2 G:His23 3.06 Zn CE1 G:His23 3.18 Zn CG G:His23 4.23 Zn OE1 G:Glu24 2.21 Zn CB G:Glu24 4.73 Zn OE2 G:Glu24 4.16 Zn CD G:Glu24 3.44 Zn CG G:Glu24 4.46 Zn O D:Hoh306 3.84 Zn O G:Hoh414 4.91 interactive model: