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

Protein crystallography data

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

Other elements in 3ij6:

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

Sodium (Na) 4 atoms

Zinc Binding Sites:

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 3ij6

Go back to Zinc Binding Sites List in 3ij6
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 3ij6

Go back to Zinc Binding Sites List in 3ij6
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 3ij6

Go back to Zinc Binding Sites List in 3ij6
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 3ij6

Go back to Zinc Binding Sites List in 3ij6
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

Reference:

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.
Page generated: Wed Dec 16 04:26:26 2020

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