Zinc in PDB 3a9l: Structure of Bacteriophage Poly-Gamma-Glutamate Hydrolase

The structure of Structure of Bacteriophage Poly-Gamma-Glutamate Hydrolase, PDB code: 3a9l was solved by Z.Fujimoto, K.Kimura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.04 / 1.90
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	86.809, 86.809, 85.116, 90.00, 90.00, 120.00
R / Rfree (%)	28.1 / 31.5

The binding sites of Zinc atom in the Structure of Bacteriophage Poly-Gamma-Glutamate Hydrolase (pdb code 3a9l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Bacteriophage Poly-Gamma-Glutamate Hydrolase, PDB code: 3a9l:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Bacteriophage Poly-Gamma-Glutamate Hydrolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Bacteriophage Poly-Gamma-Glutamate Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn251 b:32.1 occ:1.00 ND1 A:HIS103 2.1 16.5 1.0 ND1 A:HIS40 2.2 21.7 1.0 O A:HOH294 2.3 34.5 1.0 OE1 A:GLU45 2.3 22.1 1.0 O4 A:PO4261 2.4 34.4 1.0 OE2 A:GLU45 2.5 22.2 1.0 CD A:GLU45 2.7 20.7 1.0 CE1 A:HIS103 3.0 19.9 1.0 CE1 A:HIS40 3.1 18.7 1.0 CG A:HIS103 3.2 17.1 1.0 CG A:HIS40 3.3 21.0 1.0 P A:PO4261 3.5 36.3 1.0 CB A:HIS103 3.6 18.6 1.0 CB A:HIS40 3.7 20.2 1.0 O3 A:PO4261 3.8 37.4 1.0 NE2 A:HIS78 4.0 28.6 1.0 O2 A:PO4261 4.1 36.5 1.0 NE2 A:HIS103 4.1 16.9 1.0 CA A:HIS103 4.2 19.1 1.0 CG A:GLU45 4.2 21.3 1.0 NE2 A:HIS40 4.2 22.4 1.0 CD2 A:HIS103 4.3 14.1 1.0 N A:GLY104 4.3 19.7 1.0 CD2 A:HIS78 4.3 27.4 1.0 CD2 A:HIS40 4.3 22.9 1.0 OE2 A:GLU165 4.4 22.9 1.0 O A:GLY104 4.4 20.3 1.0 O A:HOH302 4.5 33.4 1.0 OE1 A:GLU165 4.8 21.8 1.0 O1 A:PO4261 4.8 37.4 1.0 C A:HIS103 4.8 18.7 1.0 O A:HOH292 4.8 27.8 1.0 CD A:GLU165 4.9 18.9 1.0

Zinc binding site 2 out of 2 in the Structure of Bacteriophage Poly-Gamma-Glutamate Hydrolase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Bacteriophage Poly-Gamma-Glutamate Hydrolase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn251 b:29.4 occ:1.00 OE1 B:GLU45 2.0 15.9 1.0 ND1 B:HIS40 2.1 17.1 1.0 ND1 B:HIS103 2.2 17.6 1.0 OE2 B:GLU45 2.2 16.1 1.0 O B:HOH259 2.3 22.9 1.0 CD B:GLU45 2.4 17.5 1.0 O4 B:PO4261 2.6 28.3 1.0 CE1 B:HIS40 2.9 15.4 1.0 CE1 B:HIS103 3.1 21.9 1.0 CG B:HIS40 3.2 16.5 1.0 CG B:HIS103 3.3 19.0 1.0 P B:PO4261 3.6 28.1 1.0 CB B:HIS103 3.6 18.5 1.0 CB B:HIS40 3.6 18.4 1.0 NE2 B:HIS78 3.8 22.4 1.0 O2 B:PO4261 3.9 29.7 1.0 O3 B:PO4261 3.9 29.1 1.0 CG B:GLU45 3.9 18.7 1.0 NE2 B:HIS40 4.1 7.8 1.0 CA B:HIS103 4.1 17.6 1.0 CD2 B:HIS78 4.1 22.7 1.0 CD2 B:HIS40 4.2 16.0 1.0 NE2 B:HIS103 4.3 22.7 1.0 O B:GLY104 4.3 17.3 1.0 OE2 B:GLU165 4.3 31.0 1.0 N B:GLY104 4.4 17.1 1.0 CD2 B:HIS103 4.4 20.8 1.0 CB B:GLU45 4.8 19.4 1.0 C B:HIS103 4.8 18.6 1.0

Z.Fujimoto, K.Kimura. Crystal Structure of Bacteriophage PHINIT1 Zinc Peptidase Pghp That Hydrolyzes Gamma-Glutamyl Linkage of Bacterial Poly-Gamma-Glutamate Proteins V. 80 722 2012.
ISSN: ISSN 0887-3585
PubMed: 22105902
DOI: 10.1002/PROT.23229