Zinc in PDB 3ij6: Crystal Structure of An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidophilus

The structure of Crystal Structure of An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidophilus, PDB code: 3ij6 was solved by Y.Patskovsky, R.Toro, M.Dickey, S.Chang, J.M.Sauder, F.M.Raushel, S.K.Burley, S.C.Almo, New York Sgx Research Center For Structuralgenomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	170.717, 96.433, 96.033, 90.00, 90.40, 90.00
R / Rfree (%)	22.1 / 26.8

The structure of Crystal Structure of An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidophilus also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidophilus (pdb code 3ij6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidophilus, PDB code: 3ij6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidophilus


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 An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn312 b:34.4 occ:0.50 OD1 A:ASP262 2.1 46.3 1.0 O A:HOH357 2.3 63.2 1.0 NE2 A:HIS10 2.4 32.1 1.0 NE2 A:HIS160 2.4 42.9 1.0 NE2 A:HIS204 2.5 33.6 1.0 O A:HOH358 2.7 40.1 1.0 CD2 A:HIS160 3.0 30.0 1.0 CD2 A:HIS204 3.1 30.0 1.0 CE1 A:HIS10 3.1 34.8 1.0 CG A:ASP262 3.2 39.3 1.0 CD2 A:HIS10 3.3 27.3 1.0 CE1 A:HIS160 3.5 37.7 1.0 OD2 A:ASP262 3.6 56.3 1.0 CE1 A:HIS204 3.7 31.4 1.0 ND1 A:HIS10 4.2 34.1 1.0 CG A:HIS160 4.3 32.6 1.0 CG A:HIS10 4.3 24.2 1.0 CG A:HIS204 4.3 25.6 1.0 O A:HOH329 4.4 32.6 1.0 CB A:ASP262 4.4 31.4 1.0 ND1 A:HIS160 4.5 35.2 1.0 ND1 A:HIS204 4.6 26.5 1.0 CA A:ASP262 4.8 30.8 1.0 CE1 A:HIS205 4.8 40.6 1.0 NE2 A:HIS205 4.8 27.1 1.0 CD2 A:PHE265 4.9 43.0 1.0 CE2 A:PHE265 5.0 41.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidophilus


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 An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn312 b:38.0 occ:0.50 OD1 B:ASP262 2.1 42.2 1.0 NE2 B:HIS160 2.3 34.7 1.0 NE2 B:HIS204 2.5 33.8 1.0 NE2 B:HIS10 2.6 48.5 1.0 O B:HOH394 2.6 37.6 1.0 CG B:ASP262 3.0 38.2 1.0 CD2 B:HIS204 3.1 34.6 1.0 CD2 B:HIS160 3.2 38.3 1.0 CE1 B:HIS160 3.3 43.5 1.0 OD2 B:ASP262 3.4 50.4 1.0 CD2 B:HIS10 3.4 33.9 1.0 CE1 B:HIS10 3.4 47.5 1.0 CE1 B:HIS204 3.7 32.4 1.0 CG B:HIS160 4.4 24.4 1.0 CB B:ASP262 4.4 32.2 1.0 ND1 B:HIS10 4.4 48.2 1.0 CG B:HIS204 4.4 27.5 1.0 CG B:HIS10 4.4 37.7 1.0 ND1 B:HIS160 4.4 32.8 1.0 CD2 B:PHE265 4.6 53.2 1.0 ND1 B:HIS204 4.6 30.4 1.0 CE2 B:PHE265 4.6 38.9 1.0 CA B:ASP262 4.7 29.9 1.0 O B:HOH417 4.7 44.0 1.0 CE1 B:HIS205 4.8 34.0 1.0 NE2 B:HIS205 4.8 27.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidophilus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidophilus within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn312 b:50.6 occ:0.50 OD1 C:ASP262 2.1 44.8 1.0 NE2 C:HIS160 2.1 53.3 1.0 NE2 C:HIS10 2.4 45.1 1.0 O C:HOH329 2.4 37.6 1.0 NE2 C:HIS204 2.7 35.8 1.0 CG C:ASP262 3.0 43.5 1.0 CD2 C:HIS204 3.1 31.3 1.0 CE1 C:HIS160 3.1 49.7 1.0 CD2 C:HIS160 3.1 35.8 1.0 CE1 C:HIS10 3.2 61.5 1.0 CD2 C:HIS10 3.4 53.0 1.0 OD2 C:ASP262 3.4 50.7 1.0 CE1 C:HIS204 3.9 31.6 1.0 ND1 C:HIS160 4.2 46.9 1.0 CG C:HIS160 4.3 43.5 1.0 CB C:ASP262 4.3 31.7 1.0 ND1 C:HIS10 4.3 54.4 1.0 CG C:HIS204 4.3 35.2 1.0 CG C:HIS10 4.4 57.1 1.0 CE1 C:HIS205 4.6 34.4 1.0 CA C:ASP262 4.7 37.7 1.0 ND1 C:HIS204 4.7 42.9 1.0 NE2 C:HIS205 4.9 44.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidophilus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidophilus within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn312 b:51.4 occ:0.50 NE2 D:HIS160 2.2 51.0 1.0 OD1 D:ASP262 2.2 58.7 1.0 NE2 D:HIS10 2.6 64.5 1.0 NE2 D:HIS204 2.6 41.7 1.0 CD2 D:HIS204 3.0 35.3 1.0 CD2 D:HIS160 3.0 46.5 1.0 CG D:ASP262 3.1 48.8 1.0 CE1 D:HIS10 3.3 68.3 1.0 OD2 D:ASP262 3.3 62.5 1.0 CE1 D:HIS160 3.3 59.6 1.0 CD2 D:HIS10 3.5 62.1 1.0 CE1 D:HIS204 3.8 43.2 1.0 CG D:HIS160 4.2 47.5 1.0 CG D:HIS204 4.3 37.4 1.0 ND1 D:HIS160 4.4 41.3 1.0 CB D:ASP262 4.4 38.4 1.0 ND1 D:HIS10 4.4 65.3 1.0 CG D:HIS10 4.5 61.3 1.0 ND1 D:HIS204 4.7 43.3 1.0 O D:HOH338 4.7 35.1 1.0 CE1 D:HIS205 4.7 45.3 1.0 CA D:ASP262 4.8 44.0 1.0 NE2 D:HIS205 4.9 39.4 1.0

Y.Patskovsky, R.Toro, M.Dickey, S.Chang, J.M.Sauder, F.M.Raushel, S.K.Burley, S.C.Almo. Crystal Structure of An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidopphilus To Be Published.