Zinc in PDB 3x17: Crystal Structure of Metagenome-Derived Glycoside Hydrolase Family 9 Endoglucanase

All present enzymatic activity of Crystal Structure of Metagenome-Derived Glycoside Hydrolase Family 9 Endoglucanase:
3.2.1.4;

The structure of Crystal Structure of Metagenome-Derived Glycoside Hydrolase Family 9 Endoglucanase, PDB code: 3x17 was solved by H.Okano, C.Angkawidjaja, S.Kanaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.96 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	84.631, 89.913, 151.157, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 24.6

The structure of Crystal Structure of Metagenome-Derived Glycoside Hydrolase Family 9 Endoglucanase also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of Metagenome-Derived Glycoside Hydrolase Family 9 Endoglucanase (pdb code 3x17). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Metagenome-Derived Glycoside Hydrolase Family 9 Endoglucanase, PDB code: 3x17:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Metagenome-Derived Glycoside Hydrolase Family 9 Endoglucanase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Metagenome-Derived Glycoside Hydrolase Family 9 Endoglucanase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:34.3 occ:1.00 OD2 B:ASP166 1.9 38.9 1.0 NE2 B:HIS193 2.1 38.4 1.0 ND1 B:HIS167 2.1 33.6 1.0 SG B:CYS150 2.2 31.1 1.0 CD2 B:HIS193 3.0 34.0 1.0 CG B:ASP166 3.0 39.2 1.0 CE1 B:HIS167 3.0 29.9 1.0 CE1 B:HIS193 3.1 34.7 1.0 CG B:HIS167 3.1 36.5 1.0 CB B:CYS150 3.1 33.2 1.0 CB B:HIS167 3.4 37.3 1.0 CA B:CYS150 3.5 31.7 1.0 CB B:ASP166 3.7 37.8 1.0 N B:GLY151 3.9 31.1 1.0 OD1 B:ASP166 4.0 31.1 1.0 ND1 B:HIS193 4.2 36.7 1.0 NE2 B:HIS167 4.2 38.2 1.0 CG B:HIS193 4.2 34.2 1.0 C B:CYS150 4.2 33.2 1.0 O B:ASP166 4.2 38.0 1.0 CD2 B:HIS167 4.2 33.6 1.0 NH2 B:ARG283 4.3 33.0 1.0 C B:ASP166 4.3 37.2 1.0 CB B:PRO276 4.4 37.0 1.0 N B:HIS167 4.6 35.7 1.0 CA B:HIS167 4.7 37.2 1.0 CA B:ASP166 4.7 38.2 1.0 CB B:TYR198 4.7 36.9 1.0 N B:CYS150 4.8 31.3 1.0 O B:HOH734 4.8 35.0 1.0 O B:TYR198 4.9 32.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Metagenome-Derived Glycoside Hydrolase Family 9 Endoglucanase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Metagenome-Derived Glycoside Hydrolase Family 9 Endoglucanase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:40.6 occ:1.00 ND1 A:HIS167 1.9 31.6 1.0 OD2 A:ASP166 2.0 42.8 1.0 NE2 A:HIS193 2.1 39.4 1.0 SG A:CYS150 2.2 36.3 1.0 CE1 A:HIS167 2.9 35.3 1.0 CG A:HIS167 2.9 36.7 1.0 CG A:ASP166 3.1 43.4 1.0 CD2 A:HIS193 3.1 35.6 1.0 CE1 A:HIS193 3.1 33.9 1.0 CB A:CYS150 3.2 39.9 1.0 CB A:HIS167 3.3 33.7 1.0 CA A:CYS150 3.6 39.5 1.0 CB A:ASP166 3.8 43.5 1.0 N A:GLY151 3.9 44.4 1.0 OD1 A:ASP166 3.9 45.6 1.0 NE2 A:HIS167 4.0 33.3 1.0 CD2 A:HIS167 4.1 37.2 1.0 ND1 A:HIS193 4.2 34.4 1.0 C A:CYS150 4.2 42.1 1.0 CG A:HIS193 4.2 32.7 1.0 O A:ASP166 4.3 39.4 1.0 C A:ASP166 4.3 40.4 1.0 NH2 A:ARG283 4.4 34.1 1.0 CB A:PRO276 4.5 39.3 1.0 CA A:HIS167 4.6 37.9 1.0 N A:HIS167 4.6 38.0 1.0 O A:HOH716 4.7 31.9 1.0 CA A:ASP166 4.7 42.1 1.0 CB A:TYR198 4.8 33.0 1.0 N A:CYS150 4.9 38.2 1.0 O A:TYR198 4.9 32.9 1.0 CA A:GLY151 4.9 47.1 1.0

H.Okano, E.Kanaya, M.Ozaki, C.Angkawidjaja, S.Kanaya. Structure, Activity and Stability of Metagenome-Derived Glycoside Hydrolase Family 9 Endoglucanase with An N-Terminal Ig-Like Domain Protein Sci. 2014.
ISSN: ESSN 1469-896X
PubMed: 25545469
DOI: 10.1002/PRO.2632