Cadmium in PDB 6wia: Crystal Structure of Human Protective Protein/Cathepsin A, Dfp- Inhibited (Aged)

Enzymatic activity of Crystal Structure of Human Protective Protein/Cathepsin A, Dfp- Inhibited (Aged)

All present enzymatic activity of Crystal Structure of Human Protective Protein/Cathepsin A, Dfp- Inhibited (Aged):
3.4.16.5;

Protein crystallography data

The structure of Crystal Structure of Human Protective Protein/Cathepsin A, Dfp- Inhibited (Aged), PDB code: 6wia was solved by J.R.Compton, P.M.Legler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.70 / 2.21
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 91.273, 101.999, 48.114, 90.00, 101.61, 90.00
R / Rfree (%) 19.5 / 22.4

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Human Protective Protein/Cathepsin A, Dfp- Inhibited (Aged) (pdb code 6wia). 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 Human Protective Protein/Cathepsin A, Dfp- Inhibited (Aged), PDB code: 6wia:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 6wia

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Cadmium binding site 1 out of 6 in the Crystal Structure of Human Protective Protein/Cathepsin A, Dfp- Inhibited (Aged)


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 Human Protective Protein/Cathepsin A, Dfp- Inhibited (Aged) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd510

b:0.5
occ:0.70
OD2 A:ASP110 2.2 78.4 1.0
OD1 A:ASP110 2.3 60.0 1.0
NE2 A:HIS33 2.3 58.7 1.0
CG A:ASP110 2.5 56.2 1.0
O A:HOH732 3.1 41.7 1.0
CE1 A:HIS33 3.3 51.4 1.0
CD2 A:HIS33 3.3 47.3 1.0
CB A:ASP110 4.0 54.2 1.0
O A:SER31 4.4 31.1 1.0
ND1 A:HIS33 4.4 48.2 1.0
CG A:HIS33 4.5 44.9 1.0
CB A:SER31 4.8 36.5 1.0
CA A:SER31 4.8 33.3 1.0
N A:ASP110 4.8 47.9 1.0
C A:SER31 4.9 34.0 1.0
CA A:ASP110 5.0 52.4 1.0

Cadmium binding site 2 out of 6 in 6wia

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Cadmium binding site 2 out of 6 in the Crystal Structure of Human Protective Protein/Cathepsin A, Dfp- Inhibited (Aged)


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 Human Protective Protein/Cathepsin A, Dfp- Inhibited (Aged) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd511

b:64.7
occ:0.70
OD2 A:ASP166 2.3 47.6 1.0
O A:HOH741 2.3 53.5 1.0
OG A:SER168 2.3 52.3 1.0
OD1 A:ASP166 2.4 42.7 1.0
O A:HOH751 2.6 59.7 1.0
CG A:ASP166 2.7 41.4 1.0
CB A:SER168 3.4 44.6 1.0
O A:HOH710 3.8 40.5 1.0
NE2 A:GLN130 3.9 34.8 1.0
CB A:ASP166 4.2 41.8 1.0
CA A:SER168 4.6 41.2 1.0
N A:SER168 4.7 41.7 1.0
CG A:GLN130 4.8 33.5 1.0
CD A:GLN130 4.9 33.7 1.0
O A:HOH655 4.9 27.8 1.0

Cadmium binding site 3 out of 6 in 6wia

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Cadmium binding site 3 out of 6 in the Crystal Structure of Human Protective Protein/Cathepsin A, Dfp- Inhibited (Aged)


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 Human Protective Protein/Cathepsin A, Dfp- Inhibited (Aged) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd512

b:34.3
occ:0.65
OD1 A:ASP225 2.2 69.4 1.0
OD2 A:ASP225 2.2 59.1 1.0
ND1 A:HIS211 2.3 58.5 1.0
CG A:ASP225 2.4 70.5 1.0
CE1 A:HIS211 3.2 66.6 1.0
CG A:HIS211 3.2 57.8 1.0
CB A:HIS211 3.5 45.4 1.0
CB A:ASP225 3.7 61.9 1.0
CA A:HIS211 3.9 46.7 1.0
NE2 A:HIS211 4.2 63.1 1.0
CD2 A:HIS211 4.2 60.7 1.0
CB A:GLU227 4.3 55.7 1.0
O A:HIS211 4.4 56.2 1.0
C A:HIS211 4.7 48.5 1.0
CA A:ASP225 4.7 57.5 1.0
N A:GLU227 4.8 49.4 1.0
N A:LEU226 5.0 58.9 1.0

Cadmium binding site 4 out of 6 in 6wia

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Cadmium binding site 4 out of 6 in the Crystal Structure of Human Protective Protein/Cathepsin A, Dfp- Inhibited (Aged)


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 Human Protective Protein/Cathepsin A, Dfp- Inhibited (Aged) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd513

b:46.0
occ:0.70
O A:HOH648 2.0 31.7 1.0
O A:HOH733 2.1 4.7 1.0
OE2 A:GLU184 2.3 45.2 1.0
CD A:GLU184 3.1 39.9 1.0
CD A:CD514 3.2 41.6 0.7
OE1 A:GLU184 3.3 42.3 1.0
CG A:GLU184 4.5 36.8 1.0
OD1 A:ASP222 5.0 35.8 1.0

Cadmium binding site 5 out of 6 in 6wia

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Cadmium binding site 5 out of 6 in the Crystal Structure of Human Protective Protein/Cathepsin A, Dfp- Inhibited (Aged)


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 Human Protective Protein/Cathepsin A, Dfp- Inhibited (Aged) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd514

b:41.6
occ:0.70
O A:HOH733 2.2 4.7 1.0
OD1 A:ASP222 2.3 35.8 1.0
OD2 A:ASP222 2.4 45.6 1.0
CG A:ASP222 2.7 36.4 1.0
CD A:CD513 3.2 46.0 0.7
ND2 A:ASN219 4.1 42.2 1.0
CB A:ASP222 4.3 36.8 1.0
O A:HOH648 4.6 31.7 1.0
OE2 A:GLU184 4.6 45.2 1.0
CG A:ASN219 4.7 37.6 1.0
CD2 A:TYR221 4.8 42.3 1.0
OD1 A:ASN219 4.9 40.1 1.0

Cadmium binding site 6 out of 6 in 6wia

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Cadmium binding site 6 out of 6 in the Crystal Structure of Human Protective Protein/Cathepsin A, Dfp- Inhibited (Aged)


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 Human Protective Protein/Cathepsin A, Dfp- Inhibited (Aged) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd515

b:85.7
occ:0.80
OE2 A:GLU415 2.2 64.0 1.0
OE1 A:GLU415 2.3 55.4 1.0
CD A:GLU415 2.6 51.4 1.0
CG A:GLU415 4.1 45.0 1.0
NH2 A:ARG396 4.4 58.4 1.0
C A:GLN450 4.8 94.6 1.0
CB A:GLU415 4.8 40.9 1.0
NH1 A:ARG396 4.9 55.6 1.0

Reference:

K.D.Bouknight, K.M.Jurkouich, J.R.Compton, I.V.Khavrutskii, M.A.Guelta, S.P.Harvey, P.M.Legler. Structural and Kinetic Evidence of Aging After Organophosphate Inhibition of Human Cathepsin A. Biochem. Pharmacol. 13980 2020.
ISSN: ISSN 1873-2968
PubMed: 32305437
DOI: 10.1016/J.BCP.2020.113980
Page generated: Sat Dec 12 08:29:24 2020

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