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Zinc in PDB 4p45: X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor Jrb-4-73

Enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor Jrb-4-73

All present enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor Jrb-4-73:
3.4.17.21;

Protein crystallography data

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor Jrb-4-73, PDB code: 4p45 was solved by Z.Novakova, C.Barinka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.18 / 1.87
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.436, 130.310, 158.752, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 19.3

Other elements in 4p45:

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor Jrb-4-73 also contains other interesting chemical elements:

Fluorine (F) 1 atom
Calcium (Ca) 1 atom
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor Jrb-4-73 (pdb code 4p45). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor Jrb-4-73, PDB code: 4p45:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4p45

Go back to Zinc Binding Sites List in 4p45
Zinc binding site 1 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor Jrb-4-73


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor Jrb-4-73 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn818

b:15.1
occ:1.00
 OAL A:2F9822 1.9 8.2 1.0
NE2 A:HIS553 1.9 16.1 1.0
OD2 A:ASP387 2.0 14.5 1.0
OE2 A:GLU425 2.0 11.8 1.0
OE1 A:GLU425 2.5 10.9 1.0
CD A:GLU425 2.6 13.2 1.0
CE1 A:HIS553 2.9 15.9 1.0
CG A:ASP387 3.0 16.0 1.0
PBJ A:2F9822 3.0 7.8 1.0
CD2 A:HIS553 3.0 14.4 1.0
OAH A:2F9822 3.1 8.2 1.0
OD1 A:ASP387 3.4 15.7 1.0
ZN A:ZN819 3.7 16.5 1.0
CE1 A:TYR552 3.8 14.6 1.0
O A:HOH1019 3.8 14.9 1.0
OH A:TYR552 3.9 15.1 1.0
N A:2F9822 4.0 8.7 1.0
ND1 A:HIS553 4.0 15.3 1.0
CA A:2F9822 4.0 8.1 1.0
CG A:HIS553 4.1 16.3 1.0
CG A:GLU425 4.1 10.9 1.0
OAX A:2F9822 4.1 8.5 1.0
CZ A:TYR552 4.2 16.1 1.0
CB A:ASP387 4.3 16.4 1.0
C A:2F9822 4.4 8.5 1.0
CD1 A:TRP381 4.5 14.7 1.0
O A:2F9822 4.5 8.7 1.0
OE1 A:GLU424 4.5 10.8 1.0
NE1 A:TRP381 4.7 15.2 1.0
NE2 A:HIS377 4.7 14.6 1.0
CD1 A:TYR552 4.8 17.9 1.0
CE1 A:HIS377 4.9 13.5 1.0
CAT A:2F9822 4.9 17.3 1.0

Zinc binding site 2 out of 2 in 4p45

Go back to Zinc Binding Sites List in 4p45
Zinc binding site 2 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor Jrb-4-73


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor Jrb-4-73 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn819

b:16.5
occ:1.00
 OD2 A:ASP453 1.9 18.9 1.0
OAH A:2F9822 1.9 8.2 1.0
OD1 A:ASP387 2.0 15.7 1.0
NE2 A:HIS377 2.0 14.6 1.0
CG A:ASP453 2.7 16.9 1.0
OD1 A:ASP453 2.8 21.3 1.0
CD2 A:HIS377 3.0 10.6 1.0
CG A:ASP387 3.0 16.0 1.0
CE1 A:HIS377 3.0 13.5 1.0
PBJ A:2F9822 3.3 7.8 1.0
OD2 A:ASP387 3.4 14.5 1.0
OE2 A:GLU425 3.5 11.8 1.0
ZN A:ZN818 3.7 15.1 1.0
O A:HOH1484 3.7 28.8 1.0
OE1 A:GLU424 3.8 10.8 1.0
OAX A:2F9822 3.9 8.5 1.0
OAL A:2F9822 4.0 8.2 1.0
ND2 A:ASN519 4.1 13.7 1.0
ND1 A:HIS377 4.1 13.4 1.0
CG A:HIS377 4.1 11.4 1.0
CD A:GLU424 4.1 12.7 1.0
CB A:ASP453 4.1 16.6 1.0
OE2 A:GLU424 4.3 12.0 1.0
CB A:ASP387 4.3 16.4 1.0
CB A:PRO388 4.4 15.3 1.0
N A:2F9822 4.4 8.7 1.0
CD A:GLU425 4.4 13.2 1.0
CA A:PRO388 4.6 15.7 1.0
OG A:SER454 4.6 17.6 1.0
CA A:ASP387 4.6 16.4 1.0
C A:ASP387 4.7 15.0 1.0
N A:PRO388 4.7 15.0 1.0
OE1 A:GLU425 4.8 10.9 1.0
OD1 A:ASN519 5.0 16.3 1.0
CG A:ASN519 5.0 16.9 1.0

Reference:

Z.Novakova, C.Barinka. The Importance of the Non-Pharmacophore Pocket of Glutamate Carboxypeptidase II For the Design of Small-Molecule Inhibitors To Be Published.
Page generated: Sun Oct 27 04:14:22 2024

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