Zinc in the structure of Crystal Structure of Xiap-BIR3 in Complex With A Bivalent Compound (pdb 3g76)

The binding sites of Zinc atom in the structure of Crystal Structure of Xiap-BIR3 in Complex With A Bivalent Compound (pdb code 3g76). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 3g76 structure was solved by F.COSSU, M.MILANI, E.MASTRANGELO, M.BOLOGNESI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 40.0-3.0 Space group P31 a (A) 119.077 b (A) 119.077 c (A) 105.590 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 23.1 Rfree (%) 31.1 Zinc Binding Sites: Zinc binding site 1 out of 8 in 3g76 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 3g76. 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: Cys300, A: His302, A: Cys303, A: His320, A: Tyr324, A: Cys327, conact list: Atom Atom Distance (A) Zn CB A:Cys300 2.94 Zn SG A:Cys300 2.26 Zn CA A:Cys300 4.43 Zn CB A:His302 4.92 Zn N A:Cys303 3.91 Zn CB A:Cys303 3.32 Zn SG A:Cys303 2.39 Zn C A:Cys303 4.74 Zn CA A:Cys303 4.16 Zn NE2 A:His320 2.07 Zn ND1 A:His320 3.97 Zn CD2 A:His320 3.29 Zn CE1 A:His320 2.73 Zn CG A:His320 4.26 Zn CB A:Tyr324 4.93 Zn CB A:Cys327 3.03 Zn SG A:Cys327 2.23 Zn CA A:Cys327 4.32 interactive model: Zinc binding site 2 out of 8 in 3g76 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 3g76. 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: Cys300, B: His302, B: Cys303, B: His320, B: Tyr324, B: Cys327, B: Leu330, conact list: Atom Atom Distance (A) Zn CB B:Cys300 3.19 Zn SG B:Cys300 2.21 Zn CA B:Cys300 4.65 Zn N B:His302 4.96 Zn CB B:His302 4.67 Zn C B:His302 4.93 Zn N B:Cys303 3.84 Zn CB B:Cys303 3.55 Zn SG B:Cys303 2.29 Zn CA B:Cys303 4.28 Zn NE2 B:His320 2.03 Zn ND1 B:His320 3.93 Zn CD2 B:His320 3.27 Zn CE1 B:His320 2.69 Zn CG B:His320 4.22 Zn CB B:Tyr324 4.98 Zn CB B:Cys327 3.24 Zn SG B:Cys327 2.40 Zn CA B:Cys327 4.56 Zn CB B:Leu330 4.98 interactive model: Zinc binding site 3 out of 8 in 3g76 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 3g76. 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: C: Cys300, C: His302, C: Cys303, C: His320, C: Cys327, conact list: Atom Atom Distance (A) Zn CB C:Cys300 3.13 Zn SG C:Cys300 2.31 Zn CA C:Cys300 4.61 Zn CB C:His302 4.85 Zn N C:Cys303 3.93 Zn CB C:Cys303 3.35 Zn SG C:Cys303 2.35 Zn C C:Cys303 4.85 Zn CA C:Cys303 4.20 Zn NE2 C:His320 2.00 Zn ND1 C:His320 3.83 Zn CD2 C:His320 3.28 Zn CE1 C:His320 2.57 Zn CG C:His320 4.19 Zn CB C:Cys327 2.97 Zn SG C:Cys327 2.17 Zn CA C:Cys327 4.31 interactive model: Zinc binding site 4 out of 8 in 3g76 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 3g76. 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: Cys300, D: His302, D: Cys303, D: His320, D: Cys327, D: Tyr329, D: Leu330, conact list: Atom Atom Distance (A) Zn CB D:Cys300 3.22 Zn SG D:Cys300 2.28 Zn CA D:Cys300 4.68 Zn N D:His302 4.99 Zn CB D:His302 4.78 Zn C D:His302 4.95 Zn N D:Cys303 3.87 Zn CB D:Cys303 3.40 Zn SG D:Cys303 2.29 Zn C D:Cys303 4.99 Zn CA D:Cys303 4.23 Zn NE2 D:His320 2.07 Zn ND1 D:His320 3.93 Zn CD2 D:His320 3.32 Zn CE1 D:His320 2.69 Zn CG D:His320 4.26 Zn CB D:Cys327 3.21 Zn SG D:Cys327 2.59 Zn CA D:Cys327 4.61 Zn CD2 D:Tyr329 4.88 Zn CB D:Leu330 4.95 interactive model: Zinc binding site 5 out of 8 in 3g76 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 3g76. 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: E: Cys300, E: His302, E: Cys303, E: Gly304, E: Gly305, E: His320, E: Tyr324, E: Cys327, conact list: Atom Atom Distance (A) Zn CB E:Cys300 3.21 Zn SG E:Cys300 2.33 Zn CA E:Cys300 4.68 Zn CB E:His302 4.83 Zn C E:His302 4.98 Zn N E:Cys303 3.82 Zn CB E:Cys303 3.21 Zn SG E:Cys303 2.47 Zn C E:Cys303 4.72 Zn CA E:Cys303 4.06 Zn N E:Gly304 4.91 Zn N E:Gly305 4.89 Zn NE2 E:His320 2.07 Zn ND1 E:His320 4.03 Zn CD2 E:His320 3.26 Zn CE1 E:His320 2.81 Zn CG E:His320 4.27 Zn CB E:Tyr324 4.77 Zn CB E:Cys327 2.79 Zn SG E:Cys327 2.47 Zn CA E:Cys327 4.14 interactive model: Zinc binding site 6 out of 8 in 3g76 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 3g76. 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: F: Cys300, F: His302, F: Cys303, F: Gly304, F: His320, F: Cys327, conact list: Atom Atom Distance (A) Zn CB F:Cys300 3.21 Zn SG F:Cys300 2.31 Zn CA F:Cys300 4.66 Zn N F:His302 4.72 Zn CB F:His302 4.33 Zn C F:His302 4.54 Zn CA F:His302 4.77 Zn N F:Cys303 3.42 Zn CB F:Cys303 3.18 Zn SG F:Cys303 2.14 Zn C F:Cys303 4.66 Zn CA F:Cys303 3.86 Zn N F:Gly304 4.69 Zn NE2 F:His320 2.23 Zn ND1 F:His320 3.91 Zn CD2 F:His320 3.52 Zn CE1 F:His320 2.64 Zn CG F:His320 4.36 Zn CB F:Cys327 3.24 Zn SG F:Cys327 2.75 Zn CA F:Cys327 4.44 interactive model: Zinc binding site 7 out of 8 in 3g76 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Zinc in the PDB 3g76. 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: G: Cys300, G: His302, G: Cys303, G: Gly304, G: Gly305, G: His320, G: Cys327, conact list: Atom Atom Distance (A) Zn CB G:Cys300 3.15 Zn SG G:Cys300 2.28 Zn CA G:Cys300 4.61 Zn CB G:His302 4.62 Zn C G:His302 4.87 Zn N G:Cys303 3.78 Zn CB G:Cys303 3.32 Zn SG G:Cys303 2.56 Zn C G:Cys303 4.82 Zn CA G:Cys303 4.13 Zn N G:Gly304 4.99 Zn N G:Gly305 4.87 Zn NE2 G:His320 2.10 Zn ND1 G:His320 3.97 Zn CD2 G:His320 3.35 Zn CE1 G:His320 2.73 Zn CG G:His320 4.29 Zn CB G:Cys327 2.98 Zn SG G:Cys327 2.25 Zn CA G:Cys327 4.26 interactive model: Zinc binding site 8 out of 8 in 3g76 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Zinc in the PDB 3g76. 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: H: Cys300, H: His302, H: Cys303, H: Gly304, H: His320, H: Tyr324, H: Cys327, conact list: Atom Atom Distance (A) Zn CB H:Cys300 3.28 Zn SG H:Cys300 2.56 Zn CA H:Cys300 4.75 Zn N H:His302 4.88 Zn CB H:His302 4.54 Zn C H:His302 4.66 Zn CA H:His302 4.94 Zn N H:Cys303 3.50 Zn CB H:Cys303 3.03 Zn SG H:Cys303 1.81 Zn C H:Cys303 4.54 Zn CA H:Cys303 3.82 Zn N H:Gly304 4.58 Zn NE2 H:His320 2.17 Zn ND1 H:His320 3.96 Zn CD2 H:His320 3.40 Zn CE1 H:His320 2.73 Zn CG H:His320 4.31 Zn CB H:Tyr324 4.89 Zn CB H:Cys327 3.25 Zn SG H:Cys327 2.92 Zn CA H:Cys327 4.48 interactive model: