Cadmium in PDB 4az3: Crystal Structure of Cathepsin A, Complexed with 15A

All present enzymatic activity of Crystal Structure of Cathepsin A, Complexed with 15A:
3.4.16.5;

The structure of Crystal Structure of Cathepsin A, Complexed with 15A, PDB code: 4az3 was solved by S.Ruf, C.Buning, H.Schreuder, G.Horstick, W.Linz, T.Olpp, J.Pernerstorfer, K.Hiss, K.Kroll, A.Kannt, M.Kohlmann, D.Linz, T.Huebschle, H.Ruetten, K.Wirth, T.Schmidt, T.Sadowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.36 / 2.04
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.590, 102.800, 48.390, 90.00, 101.87, 90.00
R / Rfree (%)	18.8 / 21.5

The structure of Crystal Structure of Cathepsin A, Complexed with 15A also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Cadmium atom in the Crystal Structure of Cathepsin A, Complexed with 15A (pdb code 4az3). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Crystal Structure of Cathepsin A, Complexed with 15A, PDB code: 4az3:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Crystal Structure of Cathepsin A, Complexed with 15A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Cathepsin A, Complexed with 15A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1260 b:58.8 occ:0.62 OE2 A:GLU184 2.8 42.0 1.0 CD A:CD1262 3.0 38.6 0.5 OE1 A:GLU184 3.0 38.5 1.0 CD A:GLU184 3.2 47.0 1.0 O A:HOH2194 4.1 25.8 1.0 CG A:GLU184 4.5 31.1 1.0 OD1 A:ASP222 4.7 38.5 1.0 OD2 A:ASP222 4.8 44.9 1.0

Cadmium binding site 2 out of 4 in the Crystal Structure of Cathepsin A, Complexed with 15A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Cathepsin A, Complexed with 15A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1261 b:28.2 occ:0.64 ND1 A:HIS211 2.2 45.8 1.0 OD2 A:ASP225 2.3 58.7 1.0 O A:HOH2220 2.4 28.8 1.0 OD1 A:ASP225 2.7 53.6 1.0 CG A:ASP225 2.8 52.8 1.0 CE1 A:HIS211 3.2 45.1 1.0 CG A:HIS211 3.2 43.9 1.0 CB A:HIS211 3.5 40.4 1.0 CA A:HIS211 4.1 39.6 1.0 O A:HOH2232 4.2 47.2 1.0 CB A:GLU227 4.3 41.9 1.0 CB A:ASP225 4.3 41.7 1.0 NE2 A:HIS211 4.3 45.4 1.0 CD2 A:HIS211 4.4 45.6 1.0 N A:GLU227 4.5 40.6 1.0 O A:HIS211 4.6 43.2 1.0 C A:HIS211 4.8 43.5 1.0 N A:LEU226 5.0 40.2 1.0 CA A:GLU227 5.0 40.5 1.0

Cadmium binding site 3 out of 4 in the Crystal Structure of Cathepsin A, Complexed with 15A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Cathepsin A, Complexed with 15A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1262 b:38.6 occ:0.45 OD1 A:ASP222 2.4 38.5 1.0 OD2 A:ASP222 2.8 44.9 1.0 CG A:ASP222 2.9 38.9 1.0 CD A:CD1260 3.0 58.8 0.6 ND2 A:ASN219 4.0 41.5 1.0 OD1 A:ASN219 4.4 45.0 1.0 CB A:ASP222 4.4 32.2 1.0 CG A:ASN219 4.5 50.9 1.0 O A:HOH2194 4.7 25.8 1.0 CD2 A:TYR221 5.0 31.9 1.0

Cadmium binding site 4 out of 4 in the Crystal Structure of Cathepsin A, Complexed with 15A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Cathepsin A, Complexed with 15A within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd1454 b:33.4 occ:0.22 SG B:CYS375 2.0 24.3 1.0 O B:HOH2091 2.4 56.6 1.0 O B:ALA374 2.8 22.9 1.0 CB B:CYS375 3.3 20.0 1.0 C B:ALA374 3.5 23.1 1.0 OD1 A:ASN186 3.5 32.7 1.0 CD1 A:LEU180 3.6 25.8 1.0 CA B:CYS375 3.6 19.1 1.0 N B:CYS375 3.9 19.4 1.0 CG A:ASN186 4.0 36.8 1.0 CB A:LEU180 4.0 20.1 1.0 ND2 A:ASN186 4.1 24.3 1.0 CG A:LEU180 4.3 25.4 1.0 CA A:LEU180 4.4 19.7 1.0 O A:HOH2197 4.7 35.7 1.0 CD2 A:LEU180 4.7 28.4 1.0 CA B:ALA374 4.7 18.6 1.0 N A:LEU180 4.8 19.4 1.0 O A:HOH2087 4.9 54.5 1.0 CB B:ALA374 5.0 19.3 1.0

S.Ruf, C.Buning, H.Schreuder, G.Horstick, W.Linz, T.Olpp, J.Pernerstorfer, K.Hiss, K.Kroll, A.Kannt, M.Kohlmann, D.Linz, T.Hubschle, H.Rutten, K.Wirth, T.Schmidt, T.Sadowski. Novel Beta-Amino Acid Derivatives As Inhibitors of Cathepsin A. J.Med.Chem. V. 55 7636 2012.
ISSN: ISSN 0022-2623
PubMed: 22861813
DOI: 10.1021/JM300663N