Cadmium in PDB 4cib: Crystal Structure of Cathepsin A, Complexed with Compound 2

All present enzymatic activity of Crystal Structure of Cathepsin A, Complexed with Compound 2:
3.4.16.5;

The structure of Crystal Structure of Cathepsin A, Complexed with Compound 2, PDB code: 4cib was solved by H.A.Schreuder, A.Liesum, K.Kroll, B.Boehnisch, C.Buning, S.Ruf, C.Buning, T.Sadowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.02 / 1.89
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.649, 102.527, 49.395, 90.00, 100.94, 90.00
R / Rfree (%)	14.141 / 21.073

The binding sites of Cadmium atom in the Crystal Structure of Cathepsin A, Complexed with Compound 2 (pdb code 4cib). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the Crystal Structure of Cathepsin A, Complexed with Compound 2, PDB code: 4cib:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5;

Cadmium binding site 1 out of 5 in the Crystal Structure of Cathepsin A, Complexed with Compound 2


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 Compound 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1455 b:13.6 occ:0.80 OD2 A:ASP222 2.3 19.0 1.0 OD1 A:ASP222 2.4 15.7 1.0 O A:HOH2575 2.4 18.1 1.0 O A:HOH2513 2.5 5.0 1.0 O A:HOH2583 2.6 7.5 1.0 CG A:ASP222 2.7 15.3 1.0 CD A:CD1457 3.7 19.7 0.8 O A:HOH2874 3.9 17.7 1.0 ND2 A:ASN219 4.1 12.2 1.0 CB A:ASP222 4.2 13.0 1.0 O A:HOH2581 4.4 30.0 1.0 O A:HOH2582 4.7 33.7 1.0 OE2 A:GLU184 4.8 10.3 1.0 CD2 A:TYR221 4.9 11.2 1.0 O A:ASP222 4.9 13.2 1.0 CG A:ASN219 4.9 12.6 1.0 OD1 A:ASN219 4.9 12.4 1.0

Cadmium binding site 2 out of 5 in the Crystal Structure of Cathepsin A, Complexed with Compound 2


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 Compound 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1456 b:18.2 occ:0.50 O A:GLY179 2.2 10.8 1.0 O A:HOH2502 2.3 20.4 1.0 O A:HOH2520 2.5 11.1 1.0 OD2 A:ASP380 2.7 13.8 1.0 CG A:ASP380 3.2 15.4 1.0 OD1 A:ASP380 3.2 19.2 1.0 C A:GLY179 3.3 11.5 1.0 CB A:CYS375 3.6 10.4 1.0 O A:HOH2504 3.7 23.7 1.0 CA A:LEU180 3.8 12.4 1.0 CD A:CD1459 3.9 14.9 0.6 N A:LEU180 4.0 11.7 1.0 N A:SER181 4.0 10.8 1.0 ND2 A:ASN186 4.1 9.2 1.0 SG A:CYS375 4.1 18.3 1.0 CA A:CYS375 4.1 9.1 1.0 C A:CYS375 4.3 8.2 1.0 O A:CYS375 4.4 8.0 1.0 O A:ASN376 4.4 7.3 1.0 O A:HOH2503 4.4 33.1 1.0 C A:LEU180 4.5 11.3 1.0 CB A:ASP380 4.5 10.0 1.0 CA A:GLY179 4.5 10.6 1.0 CB A:ASN186 4.5 10.1 1.0 N A:GLY179 4.5 9.6 1.0 CG A:ASN186 4.5 12.4 1.0 N A:ASP380 4.7 9.4 1.0 ND2 A:ASN368 4.7 5.9 1.0 C A:ASN178 4.8 9.0 1.0 N A:ASN376 4.9 7.0 1.0 O A:ASN178 4.9 8.8 1.0 CA A:ASP380 5.0 9.8 1.0 CB A:LEU180 5.0 12.5 1.0 CD1 A:LEU180 5.0 17.9 1.0

Cadmium binding site 3 out of 5 in the Crystal Structure of Cathepsin A, Complexed with Compound 2


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 Compound 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1457 b:19.7 occ:0.80 OE2 A:GLU184 2.3 10.3 1.0 O A:HOH2512 2.4 25.9 1.0 O A:HOH2874 2.5 17.7 1.0 O A:HOH2583 2.6 7.5 1.0 O A:HOH2513 2.7 5.0 1.0 CD A:GLU184 3.1 11.9 1.0 OE1 A:GLU184 3.2 13.0 1.0 CD A:CD1455 3.7 13.6 0.8 O A:HOH2511 4.1 13.9 1.0 O A:HOH2223 4.1 53.8 1.0 CG A:GLU184 4.5 9.6 1.0 O A:HOH2222 4.9 47.2 1.0 O A:HOH2571 4.9 27.8 1.0 OD1 A:ASP222 4.9 15.7 1.0

Cadmium binding site 4 out of 5 in the Crystal Structure of Cathepsin A, Complexed with Compound 2


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 Compound 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1458 b:11.6 occ:0.90 OD2 A:ASP3 2.3 9.9 1.0 OD1 A:ASP3 2.4 9.3 1.0 O A:HOH2875 2.6 9.9 1.0 CG A:ASP3 2.7 9.7 1.0 O A:HOH2018 3.1 24.4 1.0 CB A:ASP3 4.2 10.2 1.0 O A:HOH2031 4.3 31.2 1.0 O A:HOH2109 4.7 35.6 1.0 O A:ALA1 4.9 17.9 1.0

Cadmium binding site 5 out of 5 in the Crystal Structure of Cathepsin A, Complexed with Compound 2


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Cathepsin A, Complexed with Compound 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1459 b:14.9 occ:0.60 SG A:CYS375 2.5 18.3 1.0 OD1 A:ASN186 3.2 21.5 1.0 CD1 A:LEU180 3.3 17.9 1.0 O A:ALA374 3.3 7.7 1.0 O A:HOH2463 3.4 38.9 1.0 CG A:ASN186 3.4 12.4 1.0 CB A:CYS375 3.5 10.4 1.0 ND2 A:ASN186 3.6 9.2 1.0 O A:HOH2502 3.6 20.4 1.0 CA A:CYS375 3.7 9.1 1.0 CB A:LEU180 3.8 12.5 1.0 CD A:CD1456 3.9 18.2 0.5 CA A:LEU180 4.0 12.4 1.0 CG A:LEU180 4.0 14.6 1.0 C A:ALA374 4.2 8.1 1.0 CB A:ASN186 4.2 10.1 1.0 O A:HOH2518 4.2 23.9 1.0 N A:CYS375 4.3 7.8 1.0 CD2 A:LEU180 4.5 13.3 1.0 N A:LEU180 4.5 11.7 1.0 O A:HOH2517 4.7 24.7 1.0 O A:GLY179 4.7 10.8 1.0 O A:HOH2520 4.8 11.1 1.0 C A:GLY179 4.9 11.5 1.0

H.A.Schreuder, A.Liesum, K.Kroll, B.Boehnisch, C.Buning, S.Ruf, T.Sadowski. Crystal Structure of Cathepsin A, A Novel Target For the Treatment of Cardiovascular Diseases. Biochem.Biophys.Res.Commun. V. 445 451 2014.
ISSN: ISSN 0006-291X
PubMed: 24530914
DOI: 10.1016/J.BBRC.2014.02.014