Calcium in PDB 4u6d: ZG3615, A Family 117 Glycoside Hydrolase in Complex with Beta-3,6- Anhydro-L-Galactose

The structure of ZG3615, A Family 117 Glycoside Hydrolase in Complex with Beta-3,6- Anhydro-L-Galactose, PDB code: 4u6d was solved by E.Ficko-Blean, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.109, 226.132, 67.124, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 21.9

The binding sites of Calcium atom in the ZG3615, A Family 117 Glycoside Hydrolase in Complex with Beta-3,6- Anhydro-L-Galactose (pdb code 4u6d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the ZG3615, A Family 117 Glycoside Hydrolase in Complex with Beta-3,6- Anhydro-L-Galactose, PDB code: 4u6d:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the ZG3615, A Family 117 Glycoside Hydrolase in Complex with Beta-3,6- Anhydro-L-Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of ZG3615, A Family 117 Glycoside Hydrolase in Complex with Beta-3,6- Anhydro-L-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:13.7 occ:1.00 O A:VAL379 2.4 17.0 1.0 O A:SER376 2.4 13.5 1.0 O2 A:EDO509 2.4 16.6 1.0 OE1 A:GLU63 2.4 13.9 1.0 O A:HOH953 2.5 19.0 1.0 O A:HOH684 2.5 11.5 1.0 OD1 A:ASP374 2.6 14.1 1.0 OD2 A:ASP374 2.7 15.4 1.0 CG A:ASP374 3.0 13.2 1.0 C2 A:EDO509 3.5 20.5 1.0 CD A:GLU63 3.5 15.9 1.0 C A:SER376 3.6 13.6 1.0 C A:VAL379 3.6 18.0 1.0 OE2 A:GLU63 4.0 16.6 1.0 N A:SER376 4.0 10.9 1.0 C1 A:EDO509 4.2 20.1 1.0 CA A:SER376 4.4 12.6 1.0 N A:VAL379 4.4 15.6 1.0 NZ A:LYS385 4.4 14.1 1.0 CB A:ASP374 4.4 12.7 1.0 CA A:VAL379 4.5 16.7 1.0 N A:ASP380 4.5 19.3 1.0 CA A:ASP380 4.5 22.3 1.0 N A:LEU377 4.5 13.6 1.0 O A:HOH828 4.6 26.9 1.0 O A:ASP374 4.6 12.2 1.0 CE A:LYS385 4.6 16.0 1.0 CA A:LEU377 4.7 15.4 1.0 CB A:VAL379 4.7 15.9 1.0 O A:HOH904 4.7 28.9 1.0 C A:ASP374 4.8 12.2 1.0 CG A:GLU63 4.9 14.1 1.0 O1 A:EDO509 4.9 19.8 1.0 C A:LEU377 4.9 16.1 1.0 CB A:SER376 4.9 13.9 1.0 O A:GLU63 4.9 12.9 1.0 CA A:GLU63 5.0 11.9 1.0

Calcium binding site 2 out of 4 in the ZG3615, A Family 117 Glycoside Hydrolase in Complex with Beta-3,6- Anhydro-L-Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of ZG3615, A Family 117 Glycoside Hydrolase in Complex with Beta-3,6- Anhydro-L-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:10.9 occ:1.00 O A:HOH950 2.3 10.8 1.0 O A:HOH680 2.4 11.0 1.0 O A:HOH949 2.4 10.3 1.0 O A:HOH952 2.4 11.1 1.0 O A:HOH678 2.4 11.5 1.0 O A:HOH951 2.5 12.8 1.0 O A:HOH948 2.6 10.3 1.0 O A:PRO90 4.0 10.6 1.0 O A:THR286 4.3 12.2 1.0 O A:THR167 4.4 10.7 1.0 CG2 A:THR166 4.4 11.5 1.0 OD1 A:ASP231 4.6 13.1 1.0 O A:ASP89 4.6 10.4 1.0 O A:ALA330 4.6 10.4 1.0 CA A:ASP231 4.7 10.8 1.0 CD2 A:TYR233 4.7 9.6 1.0 OD1 A:ASP89 4.8 11.0 1.0 CB A:ASP231 4.8 11.1 1.0 O A:PRO232 4.8 10.0 1.0 C A:ASP89 4.8 10.1 1.0 CB A:ASP89 4.8 11.1 1.0 O A:THR166 4.8 10.2 1.0 C A:PRO90 4.9 10.3 1.0 O A:ALA331 4.9 11.3 1.0 CB A:ALA330 4.9 10.0 1.0 O A:ASP231 4.9 10.6 1.0 C A:ASP231 5.0 10.1 1.0 CA A:ASP89 5.0 10.1 1.0

Calcium binding site 3 out of 4 in the ZG3615, A Family 117 Glycoside Hydrolase in Complex with Beta-3,6- Anhydro-L-Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of ZG3615, A Family 117 Glycoside Hydrolase in Complex with Beta-3,6- Anhydro-L-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:20.1 occ:1.00 O B:HOH796 2.4 21.4 1.0 O B:HOH660 2.4 19.6 1.0 O B:HOH797 2.4 21.0 1.0 O B:HOH798 2.4 19.2 1.0 O B:HOH648 2.5 19.7 1.0 O B:HOH795 2.5 19.8 1.0 O B:HOH794 2.5 24.1 1.0 O B:PRO90 4.0 23.1 1.0 O B:THR167 4.3 24.2 1.0 O B:THR286 4.3 18.0 1.0 CG2 B:THR166 4.6 20.0 1.0 CA B:ASP231 4.7 17.2 1.0 CB B:ASP231 4.7 17.8 1.0 O B:ASP89 4.7 21.9 1.0 O B:PRO232 4.7 20.6 1.0 OD1 B:ASP89 4.7 22.6 1.0 O B:ASP231 4.7 17.5 1.0 CB B:ASP89 4.8 23.2 1.0 OD1 B:ASP231 4.8 18.0 1.0 O B:ALA330 4.8 20.5 1.0 C B:ASP231 4.8 17.0 1.0 C B:ASP89 4.8 22.6 1.0 O B:THR166 4.8 20.5 1.0 CD2 B:TYR233 4.8 19.4 1.0 C B:PRO90 4.9 26.2 1.0 CA B:ASP89 5.0 23.4 1.0

Calcium binding site 4 out of 4 in the ZG3615, A Family 117 Glycoside Hydrolase in Complex with Beta-3,6- Anhydro-L-Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of ZG3615, A Family 117 Glycoside Hydrolase in Complex with Beta-3,6- Anhydro-L-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:24.4 occ:1.00 O B:VAL379 2.3 25.6 1.0 O B:SER376 2.4 25.1 1.0 OE1 B:GLU63 2.4 25.2 1.0 O B:HOH609 2.4 35.3 1.0 O B:HOH674 2.4 22.8 1.0 O B:HOH691 2.4 27.8 1.0 OD1 B:ASP374 2.5 26.4 1.0 OD2 B:ASP374 2.7 26.5 1.0 CG B:ASP374 3.0 25.9 1.0 CD B:GLU63 3.5 25.1 1.0 C B:VAL379 3.5 31.3 1.0 C B:SER376 3.6 25.4 1.0 OE2 B:GLU63 3.9 32.2 1.0 N B:SER376 4.0 22.4 1.0 NZ B:LYS385 4.3 24.8 1.0 CA B:SER376 4.3 23.9 1.0 CA B:ASP380 4.3 32.7 1.0 N B:ASP380 4.4 30.9 1.0 N B:VAL379 4.5 30.4 1.0 CB B:ASP374 4.5 24.7 1.0 CA B:VAL379 4.5 31.5 1.0 CE B:LYS385 4.5 24.9 1.0 N B:LEU377 4.6 25.3 1.0 O B:ASP374 4.6 23.0 1.0 O B:HOH676 4.7 27.8 1.0 O B:HOH629 4.7 36.0 1.0 CB B:VAL379 4.8 29.5 1.0 C B:ASP374 4.8 23.4 1.0 CG B:GLU63 4.8 24.0 1.0 CA B:LEU377 4.8 26.2 1.0 O B:GLU63 4.8 22.6 1.0 CA B:GLU63 4.9 21.1 1.0 CB B:SER376 4.9 24.7 1.0 CB B:ASP380 5.0 37.5 1.0

E.Ficko-Blean, D.Duffieux, E.Rebuffet, R.Larocque, A.Groisillier, G.Michel, M.Czjzek. Biochemical and Structural Investigation of Two Paralogous Glycoside Hydrolases From Zobellia Galactanivorans: Novel Insights Into the Evolution, Dimerization Plasticity and Catalytic Mechanism of the GH117 Family Acta Crystallogr.,Sect.D 2015.
ISSN: ESSN 1399-0047
DOI: 10.1107/S1399004714025024