Sodium 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:

Zinc

(Zn)

4 atoms

The binding sites of Sodium 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 Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidophilus, PDB code: 3ij6:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium 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 Sodium with other atoms in the Na 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:Na313 b:58.1 occ:1.00 O A:LEU124 2.5 44.5 1.0 O A:ILE118 2.5 34.0 1.0 O A:ASP121 2.6 49.0 1.0 OE2 A:GLU304 3.6 96.5 1.0 C A:ASP121 3.6 43.9 1.0 C A:ILE118 3.7 42.1 1.0 C A:LEU124 3.7 41.0 1.0 CG2 A:ILE118 4.1 34.0 1.0 CA A:GLU122 4.1 48.0 1.0 O A:GLU122 4.2 45.8 1.0 C A:GLU122 4.2 46.3 1.0 N A:GLU122 4.3 43.3 1.0 N A:LYS119 4.6 50.6 1.0 N A:LEU124 4.6 42.1 1.0 CA A:VAL125 4.6 38.5 1.0 N A:VAL125 4.6 32.3 1.0 CA A:LYS119 4.6 60.9 1.0 CA A:LEU124 4.6 40.0 1.0 CA A:ILE118 4.6 44.5 1.0 CD A:GLU304 4.7 92.7 1.0 O A:LYS119 4.7 62.2 1.0 N A:ASP121 4.8 46.6 1.0 CA A:ASP121 4.8 45.7 1.0 C A:LYS119 4.8 59.0 1.0 CB A:ILE118 5.0 45.2 1.0 N A:ASN123 5.0 44.7 1.0 CB A:LEU124 5.0 28.7 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na313 b:49.0 occ:1.00 O B:ILE118 2.4 33.5 1.0 O B:HOH354 2.5 46.2 1.0 O B:ASP121 2.6 50.4 1.0 O B:LEU124 2.6 35.7 1.0 C B:ILE118 3.6 37.9 1.0 C B:ASP121 3.6 39.6 1.0 C B:LEU124 3.8 39.2 1.0 OE2 B:GLU304 4.0 65.4 1.0 CG2 B:ILE118 4.1 36.3 1.0 CA B:GLU122 4.1 48.7 1.0 O B:GLU122 4.2 35.5 1.0 N B:GLU122 4.3 42.5 1.0 C B:GLU122 4.3 43.5 1.0 N B:LYS119 4.4 31.0 1.0 CA B:LYS119 4.4 46.7 1.0 OE1 B:GLU304 4.4 85.5 1.0 O B:HOH395 4.5 26.1 1.0 N B:ASP121 4.6 34.0 1.0 CA B:ILE118 4.6 34.4 1.0 C B:LYS119 4.6 45.6 1.0 N B:LEU124 4.7 35.0 1.0 CD B:GLU304 4.7 78.8 1.0 CA B:ASP121 4.7 35.6 1.0 N B:VAL125 4.7 43.6 1.0 CA B:LEU124 4.7 35.6 1.0 O B:LYS119 4.7 49.1 1.0 CA B:VAL125 4.7 38.8 1.0 CB B:ILE118 5.0 37.3 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na313 b:61.1 occ:1.00 O C:ILE118 2.5 41.8 1.0 O C:ASP121 2.8 46.8 1.0 O C:LEU124 2.8 41.5 1.0 C C:ASP121 3.5 46.8 1.0 CA C:GLU122 3.7 48.9 1.0 C C:ILE118 3.7 43.9 1.0 N C:GLU122 4.0 48.6 1.0 C C:GLU122 4.0 49.4 1.0 C C:LEU124 4.0 43.5 1.0 CA C:LYS119 4.0 53.4 0.5 CA C:LYS119 4.0 51.3 0.5 O C:GLU122 4.1 43.8 1.0 N C:LYS119 4.3 49.7 1.0 C C:LYS119 4.3 52.9 1.0 O C:LYS119 4.4 51.6 1.0 CG2 C:ILE118 4.4 35.8 0.5 CG2 C:ILE118 4.4 37.9 0.5 N C:ASP121 4.6 45.7 1.0 N C:LEU124 4.7 47.8 1.0 CA C:ASP121 4.7 42.4 1.0 N C:ASN123 4.8 42.6 1.0 CA C:ILE118 4.8 43.5 0.5 CA C:ILE118 4.8 42.7 0.5 CA C:LEU124 4.9 42.5 1.0 CB C:GLU122 4.9 56.5 1.0 CA C:VAL125 4.9 32.3 1.0 N C:VAL125 4.9 38.3 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na313 b:43.5 occ:1.00 O D:HOH394 2.4 41.5 1.0 O D:LEU124 2.5 38.3 1.0 O D:ASP121 2.5 59.5 1.0 O D:ILE118 2.6 45.5 1.0 C D:ASP121 3.7 57.3 1.0 C D:LEU124 3.7 40.7 1.0 C D:ILE118 3.8 48.9 1.0 CG2 D:ILE118 4.1 35.5 1.0 O D:GLU122 4.1 49.1 1.0 CA D:GLU122 4.3 52.6 1.0 C D:GLU122 4.3 51.9 1.0 O D:HOH346 4.3 27.9 1.0 N D:GLU122 4.4 51.4 1.0 CA D:VAL125 4.5 33.5 1.0 N D:VAL125 4.6 33.8 1.0 O D:LYS119 4.6 56.8 1.0 N D:LEU124 4.7 42.0 1.0 CA D:LEU124 4.7 40.0 1.0 CA D:ILE118 4.7 45.6 1.0 N D:LYS119 4.7 49.3 1.0 CA D:LYS119 4.8 57.7 1.0 C D:LYS119 4.8 57.6 1.0 CA D:ASP121 4.8 54.9 1.0 N D:ASP121 4.8 57.7 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.