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Cadmium in PDB 4cia: Crystal Structure of Cathepsin A, Complexed with Compound 1

Enzymatic activity of Crystal Structure of Cathepsin A, Complexed with Compound 1

All present enzymatic activity of Crystal Structure of Cathepsin A, Complexed with Compound 1:
3.4.16.5;

Protein crystallography data

The structure of Crystal Structure of Cathepsin A, Complexed with Compound 1, PDB code: 4cia 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) 36.11 / 1.98
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.106, 101.295, 48.077, 90.00, 101.91, 90.00
R / Rfree (%) 16.991 / 23.2

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Cathepsin A, Complexed with Compound 1 (pdb code 4cia). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the Crystal Structure of Cathepsin A, Complexed with Compound 1, PDB code: 4cia:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in 4cia

Go back to Cadmium Binding Sites List in 4cia
Cadmium binding site 1 out of 7 in the Crystal Structure of Cathepsin A, Complexed with Compound 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1455

b:67.0
occ:1.00
 O A:HOH2224 2.4 28.3 1.0
OD1 A:ASP434 2.4 13.9 1.0
O A:HOH2220 2.5 18.6 1.0
OD2 A:ASP434 2.9 13.5 1.0
CG A:ASP434 3.0 13.4 1.0
O A:HOH2351 3.2 34.0 1.0
ND2 A:ASN248 3.8 11.2 1.0
O A:HOH2217 3.9 29.8 1.0
O A:HOH2339 4.3 39.7 1.0
CB A:ASN248 4.5 11.8 1.0
CB A:ASP434 4.5 12.3 1.0
CG A:ASN248 4.7 11.9 1.0
CB A:MET430 4.7 15.4 1.0
O A:MET430 4.7 12.6 1.0
CG2 A:THR433 4.7 12.6 1.0
CB A:THR433 4.8 11.4 1.0
N A:MET430 5.0 12.3 1.0

Cadmium binding site 2 out of 7 in 4cia

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Cadmium binding site 2 out of 7 in the Crystal Structure of Cathepsin A, Complexed with Compound 1


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

b:53.8
occ:1.00
 O A:HOH2162 1.8 7.3 1.0
O A:HOH2163 2.1 20.0 1.0
CD A:CD1458 2.5 49.3 1.0
OE2 A:GLU184 2.6 24.5 1.0
CD A:GLU184 3.3 21.6 1.0
OE1 A:GLU184 3.4 22.8 1.0
O A:HOH2165 4.0 16.4 1.0
OD1 A:ASP222 4.3 24.2 1.0
OD2 A:ASP222 4.5 27.0 1.0
CD2 A:TYR221 4.6 22.5 1.0
CG A:GLU184 4.6 18.2 1.0
CG A:ASP222 4.8 24.8 1.0
CE2 A:TYR221 4.9 26.0 1.0
O A:HOH2195 5.0 28.3 1.0

Cadmium binding site 3 out of 7 in 4cia

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Cadmium binding site 3 out of 7 in the Crystal Structure of Cathepsin A, Complexed with Compound 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1457

b:68.9
occ:1.00
 O A:HOH2352 2.3 35.0 1.0
ND1 A:HIS211 2.8 42.3 1.0
OD2 A:ASP225 3.1 27.6 1.0
CA A:HIS211 3.4 29.8 1.0
CG A:HIS211 3.5 39.6 1.0
O A:THR210 3.6 29.4 1.0
CB A:HIS211 3.6 31.9 1.0
CE1 A:HIS211 3.7 47.8 1.0
CG A:ASP225 3.9 27.7 1.0
O A:HOH2203 4.0 34.4 1.0
N A:HIS211 4.1 27.6 1.0
C A:THR210 4.1 29.3 1.0
OD1 A:ASP225 4.2 27.1 1.0
CG2 A:THR210 4.3 33.3 1.0
C A:HIS211 4.4 29.2 1.0
O A:HIS211 4.4 30.3 1.0
CD2 A:HIS211 4.5 42.9 1.0
NE2 A:HIS211 4.6 47.9 1.0

Cadmium binding site 4 out of 7 in 4cia

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Cadmium binding site 4 out of 7 in the Crystal Structure of Cathepsin A, Complexed with Compound 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1458

b:49.3
occ:1.00
 OD1 A:ASP222 2.4 24.2 1.0
CD A:CD1456 2.5 53.8 1.0
OD2 A:ASP222 2.8 27.0 1.0
CG A:ASP222 3.0 24.8 1.0
O A:HOH2162 3.9 7.3 1.0
ND2 A:ASN219 3.9 21.2 1.0
OE2 A:GLU184 4.4 24.5 1.0
CG A:ASN219 4.5 22.8 1.0
CB A:ASP222 4.5 24.6 1.0
O A:HOH2165 4.6 16.4 1.0
OD1 A:ASN219 4.6 22.6 1.0
O A:HOH2163 4.6 20.0 1.0
CD2 A:TYR221 4.7 22.5 1.0

Cadmium binding site 5 out of 7 in 4cia

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Cadmium binding site 5 out of 7 in the Crystal Structure of Cathepsin A, Complexed with Compound 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1459

b:50.0
occ:0.60
 SG A:CYS375 2.5 17.3 1.0
O A:ALA374 2.7 11.9 1.0
OD1 A:ASN186 3.0 18.2 1.0
CD1 A:LEU180 3.1 19.8 1.0
CG A:ASN186 3.4 16.2 1.0
CB A:CYS375 3.4 12.9 1.0
CA A:CYS375 3.6 11.2 1.0
ND2 A:ASN186 3.6 14.0 1.0
C A:ALA374 3.7 12.1 1.0
C14 A:6KZ1454 3.8 20.2 1.0
CB A:LEU180 3.8 15.8 1.0
CG A:LEU180 3.9 18.2 1.0
N A:CYS375 4.0 11.8 1.0
CA A:LEU180 4.1 14.2 1.0
CD A:CD1460 4.2 83.0 0.6
CD2 A:LEU180 4.3 19.5 1.0
O A:HOH2167 4.3 34.8 1.0
C13 A:6KZ1454 4.3 21.1 1.0
CB A:ASN186 4.4 14.4 1.0
N A:LEU180 4.5 12.4 1.0
O A:GLY179 4.9 11.3 1.0
C A:CYS375 4.9 10.7 1.0
O A:HOH2168 4.9 10.0 1.0
CA A:ALA374 5.0 12.3 1.0

Cadmium binding site 6 out of 7 in 4cia

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Cadmium binding site 6 out of 7 in the Crystal Structure of Cathepsin A, Complexed with Compound 1


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 Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1460

b:83.0
occ:0.60
 O A:GLY179 2.6 11.3 1.0
O A:HOH2169 2.7 15.0 1.0
O A:HOH2158 2.8 55.6 1.0
OD2 A:ASP380 3.3 11.2 1.0
OD1 A:ASP380 3.4 12.4 1.0
CG A:ASP380 3.5 12.1 1.0
N A:SER181 3.6 13.6 1.0
C A:GLY179 3.6 12.3 1.0
CA A:LEU180 3.7 14.2 1.0
ND2 A:ASN186 3.8 14.0 1.0
CB A:ASN186 4.0 14.4 1.0
CB A:CYS375 4.0 12.9 1.0
N A:LEU180 4.1 12.4 1.0
CG A:ASN186 4.1 16.2 1.0
C A:LEU180 4.2 14.2 1.0
CD A:CD1459 4.2 50.0 0.6
CD1 A:LEU180 4.4 19.8 1.0
CA A:CYS375 4.4 11.2 1.0
SG A:CYS375 4.6 17.3 1.0
N A:ASP380 4.6 11.5 1.0
CA A:ASN186 4.6 14.1 1.0
O A:SER182 4.7 13.8 1.0
C A:CYS375 4.7 10.7 1.0
N A:SER182 4.7 13.5 1.0
CB A:ASP380 4.7 11.7 1.0
CA A:SER181 4.7 13.6 1.0
O A:ASN376 4.7 9.6 1.0
CB A:SER181 4.8 13.6 1.0
CB A:LEU180 4.8 15.8 1.0
C A:GLY379 4.8 11.2 1.0
CA A:ASP380 4.9 12.4 1.0
OG A:SER181 4.9 15.1 1.0
O A:CYS375 4.9 10.2 1.0
OD1 A:ASN186 5.0 18.2 1.0
CA A:GLY179 5.0 11.8 1.0

Cadmium binding site 7 out of 7 in 4cia

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Cadmium binding site 7 out of 7 in the Crystal Structure of Cathepsin A, Complexed with Compound 1


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of Cathepsin A, Complexed with Compound 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1461

b:27.0
occ:1.00
 OD2 A:ASP3 2.2 28.5 1.0
O A:HOH2002 2.9 23.3 1.0
CG A:ASP3 3.2 35.4 1.0
O A:HOH2033 3.4 39.4 1.0
CB A:ASP3 3.6 31.8 1.0
OD1 A:ASP3 4.4 39.1 1.0
O A:ALA1 4.7 25.1 1.0
O A:HOH2004 4.9 30.1 1.0
CA A:ASP3 5.0 27.7 1.0

Reference:

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
Page generated: Fri Jul 19 17:06:35 2024

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