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Calcium 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:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Ligand-Free N-Acetylated-Alpha-Linked-Acidic-Dipeptidase Like Protein (Naaladasel), PDB code: 4twe:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 4twe

Go back to Calcium Binding Sites List in 4twe
Calcium binding site 1 out of 2 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 Calcium with other atoms in the Ca 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:Ca803

b:17.9
occ:1.00
O A:LEU261 2.3 19.8 1.0
OE1 A:GLU428 2.4 25.6 1.0
O A:THR258 2.4 18.3 1.0
OG1 A:THR258 2.4 17.8 1.0
OE1 A:GLU425 2.4 21.1 1.0
O A:HOH1012 2.5 20.5 1.0
OE2 A:GLU425 2.5 21.8 1.0
OE2 A:GLU428 2.8 21.8 1.0
CD A:GLU425 2.9 20.1 1.0
CD A:GLU428 2.9 23.0 1.0
CB A:THR258 3.3 18.6 1.0
C A:THR258 3.4 19.8 1.0
C A:LEU261 3.5 19.1 1.0
OH A:TYR677 3.9 19.0 1.0
CA A:THR258 4.0 18.0 1.0
N A:LEU261 4.1 19.3 1.0
CA A:PRO262 4.2 18.6 1.0
CB A:ASP255 4.3 18.2 1.0
N A:ALA263 4.3 19.5 1.0
N A:PRO262 4.3 17.9 1.0
CG A:GLU425 4.4 17.6 1.0
CG A:GLU428 4.4 16.8 1.0
CA A:LEU261 4.5 19.0 1.0
N A:PRO259 4.5 20.6 1.0
C A:PRO262 4.5 19.8 1.0
N A:TYR260 4.6 18.3 1.0
N A:ASP255 4.7 17.4 1.0
N A:THR258 4.7 19.0 1.0
O A:ASP255 4.7 18.6 1.0
CG2 A:THR258 4.7 19.4 1.0
CA A:PRO259 4.8 20.7 1.0
OD2 A:ASP255 4.8 21.0 1.0
C A:PRO259 4.9 21.1 1.0
CB A:ALA263 4.9 20.0 1.0
CA A:GLU425 4.9 15.5 1.0
CB A:GLU428 5.0 16.8 1.0

Calcium binding site 2 out of 2 in 4twe

Go back to Calcium Binding Sites List in 4twe
Calcium binding site 2 out of 2 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 Calcium with other atoms in the Ca 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
B:Ca803

b:18.4
occ:1.00
OE1 B:GLU428 2.4 26.5 1.0
O B:LEU261 2.4 19.6 1.0
OE1 B:GLU425 2.4 19.9 1.0
OG1 B:THR258 2.4 17.6 1.0
O B:THR258 2.4 18.5 1.0
OE2 B:GLU425 2.5 21.7 1.0
O B:HOH992 2.5 20.2 1.0
OE2 B:GLU428 2.8 22.0 1.0
CD B:GLU425 2.8 20.4 1.0
CD B:GLU428 2.9 21.8 1.0
CB B:THR258 3.3 19.5 1.0
C B:THR258 3.4 20.5 1.0
C B:LEU261 3.5 18.9 1.0
OH B:TYR677 3.9 19.0 1.0
CA B:THR258 4.0 19.8 1.0
N B:LEU261 4.1 19.6 1.0
CA B:PRO262 4.2 19.6 1.0
N B:ALA263 4.3 20.6 1.0
CG B:GLU425 4.3 17.9 1.0
N B:PRO262 4.3 18.7 1.0
CB B:ASP255 4.3 17.9 1.0
CG B:GLU428 4.4 19.0 1.0
CA B:LEU261 4.4 18.6 1.0
C B:PRO262 4.5 20.0 1.0
N B:PRO259 4.5 20.2 1.0
O B:ASP255 4.6 19.3 1.0
CG2 B:THR258 4.6 21.9 1.0
N B:TYR260 4.7 19.4 1.0
N B:ASP255 4.7 18.0 1.0
N B:THR258 4.7 20.5 1.0
OD2 B:ASP255 4.8 22.3 1.0
CA B:PRO259 4.8 20.2 1.0
CB B:ALA263 4.9 19.8 1.0
C B:PRO259 4.9 20.7 1.0
CA B:GLU425 4.9 17.2 1.0
CB B:GLU428 5.0 17.3 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: Sat Dec 12 05:08:27 2020

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