Zinc in the structure of Crystal Structure of Beta-Galactosidase From Bacillus Circulans Sp. Alkalophilus in Complex With Galactose (pdb 3tty)

The binding sites of Zinc atom in the structure of Crystal Structure of Beta-Galactosidase From Bacillus Circulans Sp. Alkalophilus in Complex With Galactose (pdb code 3tty). This binding sites where shown with 5.0 Angstroms radius around Zinc atom. The 3tty structure was solved by M.MAKSIMAINEN, N.HAKULINEN, J.ROUVINEN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 47.6-2.2 Space group H3 a (A) 228.200 b (A) 228.200 c (A) 246.800 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 16 Rfree (%) 21 Zinc Binding Sites: Zinc binding site 1 out of 6 in 3tty Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Zinc in the PDB 3tty. 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: Cys115, A: Pro116, A: Asn117, A: Cys155, A: Tyr156, A: Cys157, A: Asn159, A: Cys160, A: Hoh1003, conact list: Atom Atom Distance (A) Zn CB A:Cys115 3.40 Zn SG A:Cys115 2.45 Zn C A:Cys115 4.79 Zn CA A:Cys115 4.22 Zn N A:Pro116 4.84 Zn CD A:Pro116 4.33 Zn N A:Asn117 4.79 Zn CB A:Asn117 4.73 Zn O A:Cys155 4.84 Zn CB A:Cys155 3.29 Zn SG A:Cys155 2.38 Zn C A:Cys155 4.50 Zn CA A:Cys155 4.51 Zn N A:Tyr156 4.71 Zn O A:Cys157 4.83 Zn N A:Cys157 3.99 Zn CB A:Cys157 3.65 Zn SG A:Cys157 2.52 Zn C A:Cys157 4.79 Zn CA A:Cys157 4.32 Zn CB A:Asn159 4.99 Zn C A:Asn159 4.86 Zn N A:Cys160 3.82 Zn CB A:Cys160 3.31 Zn SG A:Cys160 2.31 Zn CA A:Cys160 4.09 Zn O A:Hoh1003 4.54 interactive model: Zinc binding site 2 out of 6 in 3tty Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Zinc in the PDB 3tty. 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: Cys115, B: Pro116, B: Asn117, B: Cys155, B: Tyr156, B: Cys157, B: Asn159, B: Cys160, B: Hoh744, conact list: Atom Atom Distance (A) Zn CB B:Cys115 3.43 Zn SG B:Cys115 2.44 Zn C B:Cys115 4.78 Zn CA B:Cys115 4.23 Zn N B:Pro116 4.85 Zn CD B:Pro116 4.39 Zn N B:Asn117 4.81 Zn CB B:Asn117 4.86 Zn O B:Cys155 4.74 Zn CB B:Cys155 3.25 Zn SG B:Cys155 2.31 Zn C B:Cys155 4.44 Zn CA B:Cys155 4.47 Zn N B:Tyr156 4.65 Zn O B:Cys157 4.68 Zn N B:Cys157 3.92 Zn CB B:Cys157 3.68 Zn SG B:Cys157 2.58 Zn C B:Cys157 4.70 Zn CA B:Cys157 4.29 Zn C B:Asn159 4.89 Zn N B:Cys160 3.83 Zn CB B:Cys160 3.21 Zn SG B:Cys160 2.39 Zn CA B:Cys160 4.07 Zn O B:Hoh744 4.44 interactive model: Zinc binding site 3 out of 6 in 3tty Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Zinc in the PDB 3tty. 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: Cys115, C: Pro116, C: Asn117, C: Cys155, C: Tyr156, C: Cys157, C: Asn159, C: Cys160, C: Hoh700, conact list: Atom Atom Distance (A) Zn CB C:Cys115 3.37 Zn SG C:Cys115 2.36 Zn C C:Cys115 4.70 Zn CA C:Cys115 4.12 Zn N C:Pro116 4.78 Zn CD C:Pro116 4.30 Zn N C:Asn117 4.77 Zn CB C:Asn117 4.86 Zn O C:Cys155 4.81 Zn CB C:Cys155 3.23 Zn SG C:Cys155 2.28 Zn C C:Cys155 4.48 Zn CA C:Cys155 4.47 Zn N C:Tyr156 4.67 Zn O C:Cys157 4.62 Zn N C:Cys157 4.03 Zn CB C:Cys157 3.74 Zn SG C:Cys157 2.73 Zn C C:Cys157 4.73 Zn CA C:Cys157 4.37 Zn CB C:Asn159 4.99 Zn C C:Asn159 4.91 Zn N C:Cys160 3.87 Zn CB C:Cys160 3.32 Zn SG C:Cys160 2.32 Zn CA C:Cys160 4.12 Zn O C:Hoh700 4.55 interactive model: Zinc binding site 4 out of 6 in 3tty Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Zinc in the PDB 3tty. 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: Cys115, D: Pro116, D: Asn117, D: Cys155, D: Tyr156, D: Cys157, D: Asn159, D: Cys160, D: Hoh716, conact list: Atom Atom Distance (A) Zn CB D:Cys115 3.38 Zn SG D:Cys115 2.36 Zn C D:Cys115 4.73 Zn CA D:Cys115 4.17 Zn N D:Pro116 4.74 Zn CD D:Pro116 4.29 Zn N D:Asn117 4.75 Zn CB D:Asn117 4.87 Zn O D:Cys155 4.71 Zn CB D:Cys155 3.26 Zn SG D:Cys155 2.34 Zn C D:Cys155 4.42 Zn CA D:Cys155 4.46 Zn N D:Tyr156 4.63 Zn O D:Cys157 4.79 Zn N D:Cys157 3.94 Zn CB D:Cys157 3.72 Zn SG D:Cys157 2.69 Zn C D:Cys157 4.76 Zn CA D:Cys157 4.31 Zn C D:Asn159 4.86 Zn N D:Cys160 3.80 Zn CB D:Cys160 3.21 Zn SG D:Cys160 2.30 Zn CA D:Cys160 4.02 Zn O D:Hoh716 4.32 interactive model: Zinc binding site 5 out of 6 in 3tty Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Zinc in the PDB 3tty. 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: Cys115, E: Pro116, E: Asn117, E: Cys155, E: Tyr156, E: Cys157, E: Asn159, E: Cys160, E: Hoh731, conact list: Atom Atom Distance (A) Zn CB E:Cys115 3.52 Zn SG E:Cys115 2.48 Zn C E:Cys115 4.81 Zn CA E:Cys115 4.22 Zn N E:Pro116 4.87 Zn CD E:Pro116 4.38 Zn N E:Asn117 4.83 Zn CB E:Asn117 5.00 Zn O E:Cys155 4.68 Zn CB E:Cys155 3.16 Zn SG E:Cys155 2.33 Zn C E:Cys155 4.38 Zn CA E:Cys155 4.39 Zn N E:Tyr156 4.63 Zn O E:Cys157 4.73 Zn N E:Cys157 3.96 Zn CB E:Cys157 3.65 Zn SG E:Cys157 2.57 Zn C E:Cys157 4.71 Zn CA E:Cys157 4.28 Zn CB E:Asn159 4.99 Zn C E:Asn159 4.87 Zn N E:Cys160 3.81 Zn CB E:Cys160 3.20 Zn SG E:Cys160 2.37 Zn CA E:Cys160 4.04 Zn O E:Hoh731 4.46 interactive model: Zinc binding site 6 out of 6 in 3tty Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Zinc in the PDB 3tty. 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: Cys115, F: Pro116, F: Asn117, F: Cys155, F: Tyr156, F: Cys157, F: Asn159, F: Cys160, F: Hoh706, conact list: Atom Atom Distance (A) Zn CB F:Cys115 3.48 Zn SG F:Cys115 2.42 Zn C F:Cys115 4.80 Zn CA F:Cys115 4.25 Zn N F:Pro116 4.85 Zn CD F:Pro116 4.33 Zn N F:Asn117 4.78 Zn CB F:Asn117 4.83 Zn O F:Cys155 4.73 Zn CB F:Cys155 3.32 Zn SG F:Cys155 2.34 Zn C F:Cys155 4.48 Zn CA F:Cys155 4.53 Zn N F:Tyr156 4.71 Zn O F:Cys157 4.83 Zn N F:Cys157 4.03 Zn CB F:Cys157 3.76 Zn SG F:Cys157 2.69 Zn C F:Cys157 4.81 Zn CA F:Cys157 4.37 Zn C F:Asn159 4.86 Zn N F:Cys160 3.82 Zn CB F:Cys160 3.22 Zn SG F:Cys160 2.35 Zn CA F:Cys160 4.05 Zn O F:Hoh706 4.66 interactive model: