Zinc in PDB 5dfa: 3D Structure of the E323A Catalytic Mutant of GAN42B, A GH42 Beta- Galactosidase From G. Stearothermophilus

All present enzymatic activity of 3D Structure of the E323A Catalytic Mutant of GAN42B, A GH42 Beta- Galactosidase From G. Stearothermophilus:
3.2.1.23;

The structure of 3D Structure of the E323A Catalytic Mutant of GAN42B, A GH42 Beta- Galactosidase From G. Stearothermophilus, PDB code: 5dfa was solved by H.V.Solomon, O.Tabachnikov, S.Lansky, H.Feinberg, L.Govada, N.E.Chayen, Y.Shoham, G.Shoham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.81 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.730, 181.310, 197.660, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 22

The binding sites of Zinc atom in the 3D Structure of the E323A Catalytic Mutant of GAN42B, A GH42 Beta- Galactosidase From G. Stearothermophilus (pdb code 5dfa). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the 3D Structure of the E323A Catalytic Mutant of GAN42B, A GH42 Beta- Galactosidase From G. Stearothermophilus, PDB code: 5dfa:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the 3D Structure of the E323A Catalytic Mutant of GAN42B, A GH42 Beta- Galactosidase From G. Stearothermophilus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 3D Structure of the E323A Catalytic Mutant of GAN42B, A GH42 Beta- Galactosidase From G. Stearothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:27.0 occ:1.00 SG A:CYS166 2.4 25.7 1.0 SG A:CYS164 2.4 17.5 1.0 SG A:CYS169 2.4 24.3 1.0 SG A:CYS124 2.4 27.2 1.0 CB A:CYS164 3.1 19.7 1.0 CB A:CYS166 3.4 19.9 1.0 CB A:CYS124 3.5 27.4 1.0 CB A:CYS169 3.5 23.3 1.0 N A:CYS166 3.8 21.1 1.0 O A:HOH931 3.9 20.8 1.0 CA A:CYS166 4.1 19.8 1.0 N A:CYS169 4.1 19.6 1.0 CA A:CYS124 4.2 27.3 1.0 C A:CYS164 4.3 22.2 1.0 CA A:CYS164 4.4 27.2 1.0 CA A:CYS169 4.4 19.3 1.0 CB A:THR126 4.5 27.1 1.0 N A:HIS165 4.6 19.7 1.0 OG1 A:THR126 4.6 24.6 1.0 C A:CYS166 4.7 20.6 1.0 O A:CYS166 4.7 24.6 1.0 O A:CYS164 4.7 25.8 1.0 C A:CYS124 4.8 34.0 1.0 N A:THR126 4.8 22.3 1.0 N A:PHE125 4.8 27.1 1.0 CB A:LEU168 4.9 18.8 1.0 C A:HIS165 4.9 19.4 1.0

Zinc binding site 2 out of 3 in the 3D Structure of the E323A Catalytic Mutant of GAN42B, A GH42 Beta- Galactosidase From G. Stearothermophilus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 3D Structure of the E323A Catalytic Mutant of GAN42B, A GH42 Beta- Galactosidase From G. Stearothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:22.9 occ:1.00 SG B:CYS164 2.3 20.0 1.0 SG B:CYS169 2.3 18.9 1.0 SG B:CYS166 2.4 17.0 1.0 SG B:CYS124 2.4 17.3 1.0 CB B:CYS164 3.2 16.9 1.0 CB B:CYS166 3.3 13.7 1.0 CB B:CYS124 3.4 18.1 1.0 CB B:CYS169 3.6 16.5 1.0 N B:CYS166 3.9 21.0 1.0 CA B:CYS166 4.1 15.0 1.0 N B:CYS169 4.1 17.2 1.0 CA B:CYS124 4.1 17.6 1.0 O B:HOH916 4.1 18.4 1.0 OG1 B:THR126 4.4 21.6 1.0 C B:CYS164 4.4 21.8 1.0 CA B:CYS164 4.4 22.4 1.0 CA B:CYS169 4.5 24.3 1.0 CB B:THR126 4.5 23.8 1.0 N B:HIS165 4.6 20.1 1.0 C B:CYS166 4.7 22.6 1.0 C B:CYS124 4.7 22.7 1.0 O B:CYS166 4.7 23.2 1.0 O B:CYS164 4.7 23.4 1.0 N B:PHE125 4.7 21.8 1.0 N B:THR126 4.7 16.1 1.0 CB B:LEU168 4.8 26.7 1.0 C B:HIS165 5.0 22.1 1.0

Zinc binding site 3 out of 3 in the 3D Structure of the E323A Catalytic Mutant of GAN42B, A GH42 Beta- Galactosidase From G. Stearothermophilus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 3D Structure of the E323A Catalytic Mutant of GAN42B, A GH42 Beta- Galactosidase From G. Stearothermophilus within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn701 b:25.2 occ:1.00 SG C:CYS164 2.3 20.9 1.0 SG C:CYS166 2.4 24.2 1.0 SG C:CYS169 2.4 23.5 1.0 SG C:CYS124 2.4 23.7 1.0 CB C:CYS164 3.3 25.6 1.0 CB C:CYS124 3.3 21.8 1.0 CB C:CYS166 3.4 20.6 1.0 CB C:CYS169 3.6 21.4 1.0 N C:CYS166 3.9 22.3 1.0 N C:CYS169 4.1 17.3 1.0 CA C:CYS124 4.1 21.6 1.0 CA C:CYS166 4.2 17.7 1.0 O C:HOH868 4.2 14.6 1.0 CA C:CYS169 4.4 24.2 1.0 C C:CYS164 4.4 24.3 1.0 CA C:CYS164 4.5 25.2 1.0 CB C:THR126 4.5 22.1 1.0 OG1 C:THR126 4.6 27.1 1.0 N C:HIS165 4.7 25.8 1.0 C C:CYS166 4.7 20.3 1.0 CB C:LEU168 4.7 24.7 1.0 O C:CYS166 4.7 22.4 1.0 C C:CYS124 4.7 24.3 1.0 O C:CYS164 4.8 19.0 1.0 N C:THR126 4.9 19.6 1.0 N C:PHE125 4.9 20.9 1.0

H.V.Solomon, O.Tabachnikov, S.Lansky, R.Salama, H.Feinberg, Y.Shoham, G.Shoham. Structure-Function Relationships in GAN42B, An Intracellular GH42 Beta-Galactosidase From Geobacillus Stearothermophilus. Acta Crystallogr.,Sect.D V. 71 2433 2015.
ISSN: ESSN 1399-0047
PubMed: 26627651
DOI: 10.1107/S1399004715018672