Calcium in PDB 3ee6: Crystal Structure Analysis of Tripeptidyl Peptidase -I

All present enzymatic activity of Crystal Structure Analysis of Tripeptidyl Peptidase -I:
3.4.14.9;

The structure of Crystal Structure Analysis of Tripeptidyl Peptidase -I, PDB code: 3ee6 was solved by A.Pal, R.Kraetzner, M.Grapp, T.Gruene, K.Schreiber, M.Granborg, H.Urlaub, A.R.Asif, S.Becker, J.Gartner, G.M.Sheldrick, R.Steinfeld, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.21 / 2.35
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	113.450, 128.930, 100.500, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 26.2

The structure of Crystal Structure Analysis of Tripeptidyl Peptidase -I also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Zinc	(Zn)	8 atoms

The binding sites of Calcium atom in the Crystal Structure Analysis of Tripeptidyl Peptidase -I (pdb code 3ee6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure Analysis of Tripeptidyl Peptidase -I, PDB code: 3ee6:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure Analysis of Tripeptidyl Peptidase -I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure Analysis of Tripeptidyl Peptidase -I within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca581 b:66.3 occ:1.00 O A:VAL518 2.2 68.6 1.0 O A:HOH609 2.3 69.3 1.0 O A:GLY541 2.3 68.3 1.0 O A:GLY539 2.5 67.8 1.0 OD1 A:ASP517 2.5 67.5 1.0 OD1 A:ASP543 2.5 67.8 1.0 C A:VAL518 3.4 68.6 1.0 C A:GLY541 3.5 67.9 1.0 CG A:ASP543 3.6 66.1 1.0 CG A:ASP517 3.7 68.9 1.0 C A:GLY539 3.7 67.9 1.0 N A:VAL518 3.7 68.5 1.0 OG1 A:THR546 4.0 65.5 1.0 CA A:VAL518 4.1 68.5 1.0 N A:GLY541 4.1 68.2 1.0 N A:GLY539 4.2 67.6 1.0 O A:GLY547 4.2 63.4 1.0 C A:PRO540 4.2 68.6 1.0 OD2 A:ASP543 4.3 66.5 1.0 CA A:GLY541 4.3 68.1 1.0 OD2 A:ASP517 4.3 68.3 1.0 OG1 A:THR519 4.4 69.2 1.0 O A:PRO540 4.4 69.3 1.0 C A:ASP517 4.4 68.6 1.0 N A:THR519 4.4 68.9 1.0 CB A:ASP543 4.5 66.2 1.0 CA A:GLY539 4.5 67.7 1.0 N A:TRP542 4.6 67.5 1.0 CB A:VAL518 4.6 68.5 1.0 N A:ASP543 4.6 66.5 1.0 C A:TRP542 4.7 66.8 1.0 N A:PRO540 4.7 68.1 1.0 CA A:THR519 4.7 69.0 1.0 CA A:PRO540 4.8 68.5 1.0 CA A:ASP517 4.8 68.6 1.0 CA A:TRP542 4.8 66.9 1.0 CB A:ASP517 4.8 68.5 1.0 CB A:SER538 5.0 67.0 1.0

Calcium binding site 2 out of 2 in the Crystal Structure Analysis of Tripeptidyl Peptidase -I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure Analysis of Tripeptidyl Peptidase -I within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca581 b:62.0 occ:1.00 O B:GLY539 2.3 63.9 1.0 O B:HOH634 2.3 58.0 1.0 O B:VAL518 2.4 64.3 1.0 O B:GLY541 2.4 63.8 1.0 OD1 B:ASP517 2.4 67.0 1.0 OD1 B:ASP543 2.6 64.8 1.0 O B:PRO540 3.5 64.6 1.0 CG B:ASP517 3.5 65.9 1.0 C B:VAL518 3.5 64.8 1.0 C B:GLY539 3.5 64.5 1.0 CG B:ASP543 3.6 66.5 1.0 C B:GLY541 3.6 64.3 1.0 C B:PRO540 3.9 64.2 1.0 OD2 B:ASP517 4.0 65.7 1.0 N B:VAL518 4.0 65.0 1.0 N B:GLY539 4.1 65.5 1.0 O B:GLY547 4.1 64.2 1.0 OG1 B:THR546 4.2 66.0 1.0 CA B:VAL518 4.3 64.8 1.0 OD2 B:ASP543 4.3 66.8 1.0 CB B:ASP543 4.4 66.7 1.0 N B:ASP543 4.4 66.1 1.0 N B:GLY541 4.4 63.9 1.0 N B:PRO540 4.4 64.2 1.0 CA B:GLY539 4.5 65.0 1.0 C B:TRP542 4.5 65.6 1.0 N B:THR519 4.5 65.5 1.0 N B:TRP542 4.5 64.7 1.0 CA B:PRO540 4.5 64.4 1.0 C B:ASP517 4.5 65.4 1.0 CA B:GLY541 4.6 64.2 1.0 CA B:TRP542 4.6 65.2 1.0 CA B:THR519 4.6 66.2 1.0 CB B:ASP517 4.7 65.8 1.0 CA B:ASP517 4.8 65.7 1.0 CB B:SER538 4.9 65.7 1.0 CB B:VAL518 4.9 65.0 1.0 O B:TRP542 4.9 66.0 1.0 OG1 B:THR519 5.0 66.9 1.0

A.Pal, R.Kraetzner, T.Gruene, M.Grapp, K.Schreiber, M.Gronborg, H.Urlaub, S.Becker, A.R.Asif, J.Gartner, G.M.Sheldrick, R.Steinfeld. Structure of Tripeptidyl-Peptidase I Provides Insight Into the Molecular Basis of Late Infantile Neuronal Ceroid Lipofuscinosis J.Biol.Chem. V. 284 3976 2009.
ISSN: ISSN 0021-9258
PubMed: 19038966
DOI: 10.1074/JBC.M806947200