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Zinc in PDB 4p44: X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor Jrb-4-81

Enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor Jrb-4-81

All present enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor Jrb-4-81:
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-4-81, PDB code: 4p44 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) 29.51 / 1.75
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.505, 130.487, 158.939, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 18.7

Other elements in 4p44:

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor Jrb-4-81 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-4-81 (pdb code 4p44). 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-4-81, PDB code: 4p44:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4p44

Go back to Zinc Binding Sites List in 4p44
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-4-81


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-4-81 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn814

b:16.0
occ:1.00
 OAL A:2F7818 1.9 15.5 1.0
NE2 A:HIS553 2.0 18.1 1.0
OD2 A:ASP387 2.0 16.4 1.0
OE2 A:GLU425 2.0 15.2 1.0
OE1 A:GLU425 2.5 15.0 1.0
CD A:GLU425 2.6 16.2 1.0
CE1 A:HIS553 2.9 14.9 1.0
CG A:ASP387 3.0 18.2 1.0
PBK A:2F7818 3.0 15.6 1.0
CD2 A:HIS553 3.0 17.0 1.0
OAH A:2F7818 3.1 16.7 1.0
OD1 A:ASP387 3.4 16.1 1.0
ZN A:ZN815 3.7 17.3 1.0
CE1 A:TYR552 3.7 15.1 1.0
O A:HOH1023 3.9 16.5 1.0
OH A:TYR552 3.9 16.9 1.0
ND1 A:HIS553 4.0 15.4 1.0
N A:2F7818 4.0 14.9 1.0
CA A:2F7818 4.1 15.7 1.0
CG A:HIS553 4.1 15.6 1.0
CG A:GLU425 4.1 13.3 1.0
CZ A:TYR552 4.2 17.1 1.0
OAY A:2F7818 4.2 18.9 1.0
CB A:ASP387 4.3 16.6 1.0
C A:2F7818 4.4 15.7 1.0
CD1 A:TRP381 4.4 18.2 1.0
OE1 A:GLU424 4.5 13.9 1.0
OXT A:2F7818 4.5 15.9 1.0
NE1 A:TRP381 4.6 15.7 1.0
CD1 A:TYR552 4.7 17.1 1.0
NE2 A:HIS377 4.7 15.2 1.0
CE1 A:HIS377 4.8 14.9 1.0
O A:2F7818 5.0 15.2 1.0

Zinc binding site 2 out of 2 in 4p44

Go back to Zinc Binding Sites List in 4p44
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-4-81


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-4-81 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn815

b:17.3
occ:1.00
 OD2 A:ASP453 1.9 18.4 1.0
OAH A:2F7818 2.0 16.7 1.0
OD1 A:ASP387 2.0 16.1 1.0
NE2 A:HIS377 2.0 15.2 1.0
CG A:ASP453 2.7 18.9 1.0
OD1 A:ASP453 2.8 19.4 1.0
CG A:ASP387 2.9 18.2 1.0
CD2 A:HIS377 3.0 12.5 1.0
CE1 A:HIS377 3.0 14.9 1.0
OD2 A:ASP387 3.4 16.4 1.0
PBK A:2F7818 3.4 15.6 1.0
O A:HOH1501 3.5 36.2 1.0
OE2 A:GLU425 3.6 15.2 1.0
ZN A:ZN814 3.7 16.0 1.0
OE1 A:GLU424 3.9 13.9 1.0
OAL A:2F7818 4.0 15.5 1.0
OAY A:2F7818 4.0 18.9 1.0
ND2 A:ASN519 4.1 17.1 1.0
ND1 A:HIS377 4.1 15.9 1.0
CG A:HIS377 4.1 15.0 1.0
CB A:ASP453 4.2 16.1 1.0
CD A:GLU424 4.2 14.2 1.0
CB A:ASP387 4.2 16.6 1.0
OE2 A:GLU424 4.3 14.6 1.0
CB A:PRO388 4.4 15.6 1.0
CD A:GLU425 4.5 16.2 1.0
N A:2F7818 4.5 14.9 1.0
CA A:ASP387 4.6 16.1 1.0
OG A:SER454 4.6 20.8 1.0
CA A:PRO388 4.6 15.7 1.0
C A:ASP387 4.7 16.2 1.0
N A:PRO388 4.7 15.9 1.0
OE1 A:GLU425 5.0 15.0 1.0
CG A:ASN519 5.0 17.1 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 04:13:27 2024

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