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Zinc in PDB 4twe: Structure of Ligand-Free N-Acetylated-Alpha-Linked-Acidic-Dipeptidase Like Protein (Naaladasel)

Enzymatic activity of Structure of Ligand-Free N-Acetylated-Alpha-Linked-Acidic-Dipeptidase Like Protein (Naaladasel)

All present enzymatic activity of Structure of Ligand-Free N-Acetylated-Alpha-Linked-Acidic-Dipeptidase Like Protein (Naaladasel):
3.4.17.21;

Protein crystallography data

The structure of Structure of Ligand-Free N-Acetylated-Alpha-Linked-Acidic-Dipeptidase Like Protein (Naaladasel), PDB code: 4twe was solved by J.Tykvart, C.Barinka, J.Lubkowski, P.Sacha, J.Konvalinka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.14 / 1.75
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 98.512, 174.844, 208.034, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 18.8

Other elements in 4twe:

The structure of Structure of Ligand-Free N-Acetylated-Alpha-Linked-Acidic-Dipeptidase Like Protein (Naaladasel) also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Ligand-Free N-Acetylated-Alpha-Linked-Acidic-Dipeptidase Like Protein (Naaladasel) (pdb code 4twe). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Ligand-Free N-Acetylated-Alpha-Linked-Acidic-Dipeptidase Like Protein (Naaladasel), PDB code: 4twe:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4twe

Go back to Zinc Binding Sites List in 4twe
Zinc binding site 1 out of 4 in the Structure of Ligand-Free N-Acetylated-Alpha-Linked-Acidic-Dipeptidase Like Protein (Naaladasel)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Ligand-Free N-Acetylated-Alpha-Linked-Acidic-Dipeptidase Like Protein (Naaladasel) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:19.8
occ:1.00
 OE2 A:GLU417 1.9 20.7 1.0
NE2 A:HIS545 2.0 18.1 1.0
OD2 A:ASP378 2.0 20.7 1.0
OE1 A:GLU417 2.3 19.2 1.0
CD A:GLU417 2.5 19.0 1.0
CE1 A:HIS545 2.9 18.4 1.0
CG A:ASP378 3.0 19.4 1.0
CD2 A:HIS545 3.0 19.8 1.0
OD1 A:ASP378 3.4 15.6 1.0
ZN A:ZN802 3.5 19.8 1.0
O A:HOH1006 3.9 21.3 1.0
CE1 A:TYR544 4.0 17.2 1.0
O A:HOH1721 4.0 33.2 1.0
CG A:GLU417 4.0 17.1 1.0
ND1 A:HIS545 4.1 19.2 1.0
CG A:HIS545 4.1 17.3 1.0
OE1 A:GLU416 4.2 19.6 1.0
OH A:TYR544 4.2 22.0 1.0
CB A:ASP378 4.3 18.6 1.0
CZ A:TYR544 4.4 21.0 1.0
CD1 A:TRP372 4.4 18.3 1.0
NE2 A:HIS368 4.4 18.1 1.0
CE1 A:HIS368 4.5 18.0 1.0
NE1 A:TRP372 4.7 17.6 1.0
CD1 A:TYR544 4.9 19.5 1.0
CB A:GLU417 5.0 18.0 1.0
O A:HOH1041 5.0 19.0 1.0

Zinc binding site 2 out of 4 in 4twe

Go back to Zinc Binding Sites List in 4twe
Zinc binding site 2 out of 4 in the Structure of Ligand-Free N-Acetylated-Alpha-Linked-Acidic-Dipeptidase Like Protein (Naaladasel)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Ligand-Free N-Acetylated-Alpha-Linked-Acidic-Dipeptidase Like Protein (Naaladasel) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:19.8
occ:1.00
 OD1 A:ASP445 1.9 20.0 1.0
OD1 A:ASP378 2.0 15.6 1.0
NE2 A:HIS368 2.0 18.1 1.0
CG A:ASP445 2.6 19.4 1.0
OD2 A:ASP445 2.6 22.1 1.0
CG A:ASP378 2.9 19.4 1.0
CE1 A:HIS368 3.0 18.0 1.0
CD2 A:HIS368 3.0 16.5 1.0
OD2 A:ASP378 3.3 20.7 1.0
ZN A:ZN801 3.5 19.8 1.0
OE1 A:GLU416 3.8 19.6 1.0
OE2 A:GLU417 3.9 20.7 1.0
CB A:ASP445 4.1 18.6 1.0
ND1 A:HIS368 4.1 16.9 1.0
CG A:HIS368 4.2 17.2 1.0
CB A:PRO379 4.2 17.3 1.0
CD A:GLU416 4.3 23.3 1.0
CB A:ASP378 4.3 18.6 1.0
O A:HOH1429 4.3 41.8 1.0
OE2 A:GLU416 4.3 22.6 1.0
CA A:PRO379 4.5 17.7 1.0
CG1 A:ILE446 4.6 18.3 1.0
CA A:ASP378 4.6 18.1 1.0
CD A:GLU417 4.7 19.0 1.0
CD1 A:ILE446 4.7 18.2 1.0
N A:PRO379 4.7 17.9 1.0
C A:ASP378 4.7 18.7 1.0
CA A:ASP445 4.8 18.5 1.0
C A:ASP445 4.8 19.1 1.0
OE1 A:GLU417 4.9 19.2 1.0
N A:ILE446 5.0 18.8 1.0

Zinc binding site 3 out of 4 in 4twe

Go back to Zinc Binding Sites List in 4twe
Zinc binding site 3 out of 4 in the Structure of Ligand-Free N-Acetylated-Alpha-Linked-Acidic-Dipeptidase Like Protein (Naaladasel)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Ligand-Free N-Acetylated-Alpha-Linked-Acidic-Dipeptidase Like Protein (Naaladasel) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:20.2
occ:1.00
 OD2 B:ASP378 2.0 21.3 1.0
OE2 B:GLU417 2.0 21.1 1.0
NE2 B:HIS545 2.0 18.8 1.0
OE1 B:GLU417 2.3 19.9 1.0
CD B:GLU417 2.5 20.9 1.0
CG B:ASP378 3.0 19.4 1.0
CE1 B:HIS545 3.0 22.1 1.0
CD2 B:HIS545 3.0 19.8 1.0
OD1 B:ASP378 3.3 16.1 1.0
ZN B:ZN802 3.5 20.2 1.0
O B:HOH1024 3.8 21.6 1.0
O B:HOH1267 3.9 33.1 1.0
CE1 B:TYR544 4.0 18.8 1.0
CG B:GLU417 4.0 18.6 1.0
ND1 B:HIS545 4.1 19.3 1.0
OH B:TYR544 4.1 22.1 1.0
CG B:HIS545 4.2 18.5 1.0
OE1 B:GLU416 4.2 19.7 1.0
CB B:ASP378 4.3 18.5 1.0
CZ B:TYR544 4.4 20.1 1.0
NE2 B:HIS368 4.4 18.3 1.0
CE1 B:HIS368 4.4 17.3 1.0
CD1 B:TRP372 4.5 18.0 1.0
NE1 B:TRP372 4.7 17.6 1.0
CD1 B:TYR544 4.9 17.4 1.0

Zinc binding site 4 out of 4 in 4twe

Go back to Zinc Binding Sites List in 4twe
Zinc binding site 4 out of 4 in the Structure of Ligand-Free N-Acetylated-Alpha-Linked-Acidic-Dipeptidase Like Protein (Naaladasel)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Ligand-Free N-Acetylated-Alpha-Linked-Acidic-Dipeptidase Like Protein (Naaladasel) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn802

b:20.2
occ:1.00
 OD1 B:ASP445 1.9 23.1 1.0
NE2 B:HIS368 2.0 18.3 1.0
OD1 B:ASP378 2.0 16.1 1.0
OD2 B:ASP445 2.6 22.1 1.0
CG B:ASP445 2.6 22.9 1.0
CG B:ASP378 3.0 19.4 1.0
CE1 B:HIS368 3.0 17.3 1.0
CD2 B:HIS368 3.0 17.5 1.0
OD2 B:ASP378 3.3 21.3 1.0
ZN B:ZN801 3.5 20.2 1.0
OE1 B:GLU416 3.8 19.7 1.0
OE2 B:GLU417 3.9 21.1 1.0
ND1 B:HIS368 4.1 18.7 1.0
CB B:ASP445 4.1 21.9 1.0
CG B:HIS368 4.1 17.6 1.0
CD B:GLU416 4.2 22.7 1.0
CB B:PRO379 4.2 18.5 1.0
CB B:ASP378 4.3 18.5 1.0
OE2 B:GLU416 4.3 21.9 1.0
CA B:PRO379 4.5 17.8 1.0
CG1 B:ILE446 4.6 19.1 1.0
CA B:ASP378 4.6 19.0 1.0
CD B:GLU417 4.7 20.9 1.0
N B:PRO379 4.7 18.4 1.0
CD1 B:ILE446 4.7 19.7 1.0
C B:ASP378 4.8 18.8 1.0
CA B:ASP445 4.8 18.9 1.0
C B:ASP445 4.8 20.6 1.0
OE1 B:GLU417 4.9 19.9 1.0

Reference:

J.Tykvart, C.Barinka, M.Svoboda, V.Navratil, R.Soucek, M.Hubalek, M.Hradilek, P.Sacha, J.Lubkowski, J.Konvalinka. Structural and Biochemical Characterization of A Novel Aminopeptidase From Human Intestine J.Biol.Chem. 2015.
ISSN: ESSN 1083-351X
DOI: 10.1074/JBC.M114.628149
Page generated: Wed Dec 16 05:47:23 2020

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