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Zinc in PDB 4p4f: X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor Nc-2-40

Enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor Nc-2-40

All present enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor Nc-2-40:
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 Nc-2-40, PDB code: 4p4f was solved by C.Barinka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.86
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.766, 130.612, 159.118, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 17.6

Other elements in 4p4f:

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor Nc-2-40 also contains other interesting chemical elements:

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 Nc-2-40 (pdb code 4p4f). 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 Nc-2-40, PDB code: 4p4f:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4p4f

Go back to Zinc Binding Sites List in 4p4f
Zinc binding site 1 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor Nc-2-40


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 Nc-2-40 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn816

b:20.6
occ:1.00
 OAU A:2GB820 2.0 20.8 1.0
OE2 A:GLU425 2.0 19.7 1.0
OD2 A:ASP387 2.0 23.0 1.0
NE2 A:HIS553 2.0 17.5 1.0
OE1 A:GLU425 2.6 17.6 1.0
CD A:GLU425 2.6 19.5 1.0
OAV A:2GB820 2.7 21.1 1.0
PBA A:2GB820 2.8 21.5 1.0
CE1 A:HIS553 3.0 17.8 1.0
CG A:ASP387 3.0 22.5 1.0
CD2 A:HIS553 3.1 18.1 1.0
OD1 A:ASP387 3.4 20.2 1.0
ZN A:ZN817 3.5 20.0 1.0
CE1 A:TYR552 3.8 20.9 1.0
CA A:2GB820 3.9 18.5 1.0
N A:2GB820 3.9 19.6 1.0
O A:HOH1022 4.0 18.1 1.0
OH A:TYR552 4.0 19.0 1.0
OAT A:2GB820 4.1 21.0 1.0
ND1 A:HIS553 4.1 18.8 1.0
CG A:GLU425 4.2 18.2 1.0
CG A:HIS553 4.2 20.3 1.0
CZ A:TYR552 4.3 19.7 1.0
C A:2GB820 4.3 19.9 1.0
CB A:ASP387 4.3 19.6 1.0
OE1 A:GLU424 4.4 16.7 1.0
OXT A:2GB820 4.5 19.6 1.0
CD1 A:TRP381 4.6 21.6 1.0
NE1 A:TRP381 4.7 21.1 1.0
NE2 A:HIS377 4.8 17.7 1.0
CD1 A:TYR552 4.8 18.9 1.0
CE1 A:HIS377 4.9 18.5 1.0
CAB A:2GB820 5.0 34.5 1.0

Zinc binding site 2 out of 2 in 4p4f

Go back to Zinc Binding Sites List in 4p4f
Zinc binding site 2 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor Nc-2-40


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 Nc-2-40 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn817

b:20.0
occ:1.00
 OAV A:2GB820 1.8 21.1 1.0
OD2 A:ASP453 1.9 20.5 1.0
OD1 A:ASP387 2.0 20.2 1.0
NE2 A:HIS377 2.1 17.7 1.0
CG A:ASP453 2.7 19.1 1.0
OD1 A:ASP453 2.8 19.5 1.0
CG A:ASP387 3.0 22.5 1.0
CE1 A:HIS377 3.0 18.5 1.0
CD2 A:HIS377 3.0 15.0 1.0
PBA A:2GB820 3.2 21.5 1.0
OD2 A:ASP387 3.4 23.0 1.0
OE2 A:GLU425 3.5 19.7 1.0
ZN A:ZN816 3.5 20.6 1.0
O A:HOH1461 3.6 39.2 1.0
OE1 A:GLU424 3.7 16.7 1.0
OAT A:2GB820 3.9 21.0 1.0
OAU A:2GB820 4.0 20.8 1.0
CD A:GLU424 4.1 16.4 1.0
ND2 A:ASN519 4.1 18.1 1.0
ND1 A:HIS377 4.1 18.7 1.0
OE2 A:GLU424 4.2 16.7 1.0
CG A:HIS377 4.2 17.6 1.0
CB A:ASP453 4.2 18.8 1.0
CB A:ASP387 4.3 19.6 1.0
CD A:GLU425 4.3 19.5 1.0
CB A:PRO388 4.3 18.2 1.0
N A:2GB820 4.4 19.6 1.0
CA A:ASP387 4.6 20.6 1.0
CA A:PRO388 4.6 18.5 1.0
C A:ASP387 4.7 20.0 1.0
OG A:SER454 4.7 18.0 0.8
N A:PRO388 4.7 19.3 1.0
OE1 A:GLU425 4.8 17.6 1.0

Reference:

C.Barinka, C.Barinka. N/A N/A.
Page generated: Sun Oct 27 04:15:07 2024

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