Calcium in PDB 3edy: Crystal Structure of the Precursor Form of Human Tripeptidyl-Peptidase 1

All present enzymatic activity of Crystal Structure of the Precursor Form of Human Tripeptidyl-Peptidase 1:
3.4.14.9;

The structure of Crystal Structure of the Precursor Form of Human Tripeptidyl-Peptidase 1, PDB code: 3edy was solved by J.Guhaniyogi, I.Sohar, K.Das, P.Lobel, A.M.Stock, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.72 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.807, 93.173, 102.479, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 20.5

The binding sites of Calcium atom in the Crystal Structure of the Precursor Form of Human Tripeptidyl-Peptidase 1 (pdb code 3edy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of the Precursor Form of Human Tripeptidyl-Peptidase 1, PDB code: 3edy:

Calcium binding site 1 out of 1 in the Crystal Structure of the Precursor Form of Human Tripeptidyl-Peptidase 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Precursor Form of Human Tripeptidyl-Peptidase 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1 b:30.2 occ:1.00 O A:VAL518 2.2 20.7 1.0 O A:GLY539 2.3 23.7 1.0 O A:GLY541 2.3 23.2 1.0 OD1 A:ASP517 2.4 24.5 1.0 OD2 A:ASP543 2.4 22.1 1.0 O A:HOH738 2.4 26.1 1.0 C A:VAL518 3.4 20.5 1.0 C A:GLY539 3.5 25.6 1.0 C A:GLY541 3.5 21.5 1.0 CG A:ASP543 3.6 20.9 1.0 CG A:ASP517 3.6 24.9 1.0 N A:VAL518 3.8 21.5 1.0 N A:GLY541 3.8 22.3 1.0 N A:GLY539 4.0 24.8 1.0 O A:GLY547 4.1 17.6 1.0 C A:PRO540 4.1 22.3 1.0 CA A:VAL518 4.1 21.0 1.0 CA A:GLY541 4.2 23.0 1.0 OG1 A:THR546 4.2 20.1 1.0 OD2 A:ASP517 4.2 23.1 1.0 CA A:GLY539 4.3 25.3 1.0 N A:THR519 4.4 21.7 1.0 CG2 A:THR519 4.4 23.8 1.0 OD1 A:ASP543 4.4 19.5 1.0 C A:ASP517 4.4 23.7 1.0 N A:PRO540 4.4 24.6 1.0 N A:ASP543 4.5 20.1 1.0 CA A:PRO540 4.5 24.8 1.0 CA A:THR519 4.5 21.6 1.0 CB A:ASP543 4.5 19.4 1.0 N A:TRP542 4.6 21.1 1.0 O A:PRO540 4.6 25.5 1.0 C A:TRP542 4.7 21.1 1.0 CA A:ASP517 4.7 22.2 1.0 CB A:ASP517 4.8 22.4 1.0 CB A:VAL518 4.8 19.5 1.0 CA A:TRP542 4.8 21.4 1.0 CB A:SER538 4.9 23.3 1.0 O A:HOH796 4.9 34.2 1.0 C A:SER538 5.0 24.1 1.0

J.Guhaniyogi, I.Sohar, K.Das, A.M.Stock, P.Lobel. Crystal Structure and Autoactivation Pathway of the Precursor Form of Human Tripeptidyl-Peptidase 1, the Enzyme Deficient in Late Infantile Ceroid Lipofuscinosis J.Biol.Chem. V. 284 3985 2009.
ISSN: ISSN 0021-9258
PubMed: 19038967
DOI: 10.1074/JBC.M806943200