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Cadmium in PDB 4az0: Crystal Structure of Cathepsin A, Complexed with 8A.

Enzymatic activity of Crystal Structure of Cathepsin A, Complexed with 8A.

All present enzymatic activity of Crystal Structure of Cathepsin A, Complexed with 8A.:
3.4.16.5;

Protein crystallography data

The structure of Crystal Structure of Cathepsin A, Complexed with 8A., PDB code: 4az0 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) 44.28 / 2.17
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.530, 101.638, 48.179, 90.00, 101.97, 90.00
R / Rfree (%) n/a / n/a

Other elements in 4az0:

The structure of Crystal Structure of Cathepsin A, Complexed with 8A. also contains other interesting chemical elements:

Fluorine (F) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Cathepsin A, Complexed with 8A. (pdb code 4az0). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Crystal Structure of Cathepsin A, Complexed with 8A., PDB code: 4az0:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 4az0

Go back to Cadmium Binding Sites List in 4az0
Cadmium binding site 1 out of 6 in the Crystal Structure of Cathepsin A, Complexed with 8A.


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 8A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1263

b:75.5
occ:0.56
 O A:HOH2134 2.3 41.3 1.0
CD A:CD1265 2.6 48.2 0.5
O A:HOH2183 2.7 53.2 1.0
OE1 A:GLU184 2.8 62.6 1.0
OE2 A:GLU184 3.1 62.3 1.0
CD A:GLU184 3.1 65.4 1.0
O A:HOH2135 4.1 41.0 1.0
CG A:GLU184 4.3 42.4 1.0
OD1 A:ASP222 4.7 52.0 1.0
OD2 A:ASP222 4.7 57.1 1.0

Cadmium binding site 2 out of 6 in 4az0

Go back to Cadmium Binding Sites List in 4az0
Cadmium binding site 2 out of 6 in the Crystal Structure of Cathepsin A, Complexed with 8A.


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 8A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1264

b:53.1
occ:0.96
 OD1 A:ASP225 2.6 69.3 1.0
OD2 A:ASP225 2.6 74.1 1.0
CD2 A:HIS211 2.7 58.2 1.0
CG A:ASP225 3.0 68.1 1.0
CG A:HIS211 3.4 56.3 1.0
CB A:HIS211 3.5 52.6 1.0
NE2 A:HIS211 3.8 58.1 1.0
CA A:HIS211 4.0 51.5 1.0
O A:HIS211 4.4 54.8 1.0
CB A:ASP225 4.5 56.3 1.0
CB A:GLU227 4.5 56.0 1.0
ND1 A:HIS211 4.6 58.2 1.0
N A:GLU227 4.7 55.0 1.0
C A:HIS211 4.8 54.9 1.0
CE1 A:HIS211 4.8 57.7 1.0

Cadmium binding site 3 out of 6 in 4az0

Go back to Cadmium Binding Sites List in 4az0
Cadmium binding site 3 out of 6 in the Crystal Structure of Cathepsin A, Complexed with 8A.


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 8A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1265

b:48.2
occ:0.53
 O A:HOH2134 2.0 41.3 1.0
OD1 A:ASP222 2.5 52.0 1.0
CD A:CD1263 2.6 75.5 0.6
O A:HOH2183 2.8 53.2 1.0
OD2 A:ASP222 2.8 57.1 1.0
CG A:ASP222 3.0 52.0 1.0
ND2 A:ASN219 4.2 50.5 1.0
OD1 A:ASN219 4.4 52.7 1.0
O A:HOH2135 4.5 41.0 1.0
CB A:ASP222 4.5 44.0 1.0
CG A:ASN219 4.6 60.4 1.0
OE1 A:GLU184 4.7 62.6 1.0
CD2 A:TYR221 4.8 45.5 1.0

Cadmium binding site 4 out of 6 in 4az0

Go back to Cadmium Binding Sites List in 4az0
Cadmium binding site 4 out of 6 in the Crystal Structure of Cathepsin A, Complexed with 8A.


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 8A. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1266

b:46.0
occ:0.40
 O A:HOH2184 2.1 31.9 1.0
O A:HOH2075 2.4 42.0 1.0
OE1 A:GLU83 3.4 73.6 1.0
O A:HOH2073 4.0 52.8 1.0
CE A:LYS15 4.2 53.9 1.0
O A:HOH2074 4.4 63.2 1.0
CD1 A:TYR84 4.5 32.5 1.0
CD A:LYS15 4.6 49.7 1.0
NZ A:LYS15 4.6 59.9 1.0
CD A:GLU83 4.7 73.8 1.0
N A:TYR84 4.8 28.6 1.0
CB A:TYR84 4.9 28.8 1.0

Cadmium binding site 5 out of 6 in 4az0

Go back to Cadmium Binding Sites List in 4az0
Cadmium binding site 5 out of 6 in the Crystal Structure of Cathepsin A, Complexed with 8A.


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 8A. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1456

b:70.2
occ:0.47
 O A:HOH2173 2.3 28.8 1.0
OD1 B:ASP434 2.5 30.9 1.0
OD2 B:ASP434 3.1 34.3 1.0
CG B:ASP434 3.2 31.0 1.0
ND2 A:ASN248 3.8 30.2 1.0
CB A:ASN248 4.1 23.4 1.0
CG A:ASN248 4.4 38.6 1.0
O B:HOH2107 4.6 59.5 1.0
CB B:ASP434 4.6 24.1 1.0
CE B:MET430 5.0 32.1 1.0

Cadmium binding site 6 out of 6 in 4az0

Go back to Cadmium Binding Sites List in 4az0
Cadmium binding site 6 out of 6 in the Crystal Structure of Cathepsin A, Complexed with 8A.


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Cathepsin A, Complexed with 8A. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1457

b:79.6
occ:0.66
 O B:HOH2032 2.6 61.3 1.0
O B:CYS334 3.3 36.6 1.0
CB B:ASP332 4.2 39.6 1.0
C B:CYS334 4.4 36.7 1.0
N B:CYS334 4.4 33.0 1.0
CG B:ASP332 4.6 54.9 1.0
OD1 B:ASP332 4.6 56.3 1.0
O B:HOH2021 4.7 54.9 1.0
CA B:CYS334 4.8 32.2 1.0
N B:MET333 4.9 37.6 1.0
CB B:CYS334 4.9 32.0 1.0

Reference:

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
Page generated: Sun Jan 24 09:56:32 2021

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