Zinc in PDB 4uf4: Crystal Structure of the Human Carboxypeptidase A1 in Complex with A Thiirane Mechanism-Based Inhibitor

Enzymatic activity of Crystal Structure of the Human Carboxypeptidase A1 in Complex with A Thiirane Mechanism-Based Inhibitor

All present enzymatic activity of Crystal Structure of the Human Carboxypeptidase A1 in Complex with A Thiirane Mechanism-Based Inhibitor:
3.4.17.1;

Protein crystallography data

The structure of Crystal Structure of the Human Carboxypeptidase A1 in Complex with A Thiirane Mechanism-Based Inhibitor, PDB code: 4uf4 was solved by P.Gallego, C.Granados, I.Pallares, G.Covaleda, F.X.Aviles, J.Vendrell, D.Reverter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 133.51 / 1.77
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.901, 52.544, 133.984, 90.00, 94.84, 90.00
R / Rfree (%) 14.742 / 20.89

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Human Carboxypeptidase A1 in Complex with A Thiirane Mechanism-Based Inhibitor (pdb code 4uf4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Human Carboxypeptidase A1 in Complex with A Thiirane Mechanism-Based Inhibitor, PDB code: 4uf4:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4uf4

Go back to Zinc Binding Sites List in 4uf4
Zinc binding site 1 out of 3 in the Crystal Structure of the Human Carboxypeptidase A1 in Complex with A Thiirane Mechanism-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Human Carboxypeptidase A1 in Complex with A Thiirane Mechanism-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1420

b:10.4
occ:1.00
ND1 A:HIS306 2.0 6.8 1.0
ND1 A:HIS179 2.1 6.6 1.0
OE1 A:GLU182 2.2 7.6 1.0
OE2 A:GLU182 2.3 9.8 1.0
CD A:GLU182 2.5 4.5 1.0
S10 A:O2V1419 2.8 27.6 1.0
CE1 A:HIS306 3.0 7.9 1.0
CG A:HIS306 3.0 6.3 1.0
CE1 A:HIS179 3.0 7.8 1.0
CG A:HIS179 3.1 6.7 1.0
CB A:HIS306 3.4 6.4 1.0
CB A:HIS179 3.4 5.5 1.0
O A:SER307 3.8 6.5 1.0
O A:HOH2113 3.9 10.5 1.0
CG A:GLU182 4.0 7.3 1.0
NE2 A:HIS306 4.1 9.7 1.0
CD2 A:HIS306 4.2 7.0 1.0
CA A:HIS306 4.2 6.2 1.0
NE2 A:HIS179 4.2 9.9 1.0
C09 A:O2V1419 4.2 24.9 1.0
CD2 A:HIS179 4.2 7.3 1.0
O A:HOH2115 4.4 15.9 1.0
O A:HOH2116 4.4 65.4 1.0
N A:SER307 4.5 7.5 1.0
NH1 A:ARG237 4.5 13.1 1.0
CA A:HIS179 4.7 5.7 1.0
C11 A:O2V1419 4.7 20.4 1.0
O03 A:O2V1419 4.7 13.9 1.0
N A:HIS179 4.8 6.1 1.0
C04 A:O2V1419 4.8 22.0 1.0
C A:HIS306 4.9 7.0 1.0
CB A:GLU182 4.9 6.6 1.0
C A:SER307 4.9 8.0 1.0

Zinc binding site 2 out of 3 in 4uf4

Go back to Zinc Binding Sites List in 4uf4
Zinc binding site 2 out of 3 in the Crystal Structure of the Human Carboxypeptidase A1 in Complex with A Thiirane Mechanism-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Human Carboxypeptidase A1 in Complex with A Thiirane Mechanism-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1420

b:11.7
occ:1.00
ND1 B:HIS306 2.0 10.4 1.0
OE2 B:GLU182 2.1 11.8 1.0
ND1 B:HIS179 2.1 7.8 1.0
OE1 B:GLU182 2.3 9.4 1.0
CD B:GLU182 2.5 6.7 1.0
S10 B:O2V1419 2.6 26.6 1.0
CE1 B:HIS306 3.0 10.7 1.0
CE1 B:HIS179 3.0 8.2 1.0
CG B:HIS306 3.1 7.4 1.0
CG B:HIS179 3.1 5.6 1.0
CB B:HIS179 3.4 4.8 1.0
CB B:HIS306 3.5 7.0 1.0
C09 B:O2V1419 4.0 26.1 1.0
CG B:GLU182 4.0 6.9 1.0
O B:SER307 4.1 10.8 1.0
NE2 B:HIS306 4.1 9.3 1.0
O B:HOH2091 4.2 11.6 1.0
O B:HOH2093 4.2 14.0 1.0
NE2 B:HIS179 4.2 9.9 1.0
CD2 B:HIS306 4.2 10.2 1.0
CD2 B:HIS179 4.2 8.6 1.0
CA B:HIS306 4.3 5.6 1.0
NH1 B:ARG237 4.3 12.9 1.0
O B:HOH2010 4.4 40.8 1.0
C04 B:O2V1419 4.5 24.3 1.0
C11 B:O2V1419 4.5 25.1 1.0
O03 B:O2V1419 4.6 15.8 1.0
N B:SER307 4.6 6.5 1.0
CA B:HIS179 4.8 5.9 1.0
N B:HIS179 4.8 7.9 1.0
OE1 B:GLU380 4.9 23.8 1.0
CB B:GLU182 5.0 6.5 1.0
C B:HIS306 5.0 6.4 1.0

Zinc binding site 3 out of 3 in 4uf4

Go back to Zinc Binding Sites List in 4uf4
Zinc binding site 3 out of 3 in the Crystal Structure of the Human Carboxypeptidase A1 in Complex with A Thiirane Mechanism-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Human Carboxypeptidase A1 in Complex with A Thiirane Mechanism-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1421

b:13.3
occ:1.00
OE2 B:GLU412 1.9 13.5 0.5
NE2 B:HIS417 2.0 12.3 1.0
O B:HOH2196 2.5 14.3 0.5
CD B:GLU412 2.7 9.1 0.5
OE1 B:GLU412 2.8 8.4 0.5
CE1 B:HIS417 2.9 15.4 1.0
CD2 B:HIS417 3.1 14.0 1.0
CB B:ASN416 4.0 13.8 1.0
ND1 B:HIS417 4.1 17.3 1.0
ND2 B:ASN416 4.1 14.0 1.0
CG B:HIS417 4.2 15.0 1.0
CG B:GLU412 4.2 8.3 0.5
CG B:ASN416 4.5 15.2 1.0
O B:GLU412 4.9 10.4 0.5

Reference:

P.Gallego, C.Granados, I.Pallares, G.Covaleda, F.X.Aviles, D.Reverter. Design and Functional-Structural Characterization of Mechanism-Based Inactivators of Human Pancreatic Carboxypeptidase A. To Be Published.
Page generated: Wed Dec 16 05:48:33 2020

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