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Zinc in PDB 4p4e: X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor MP1D

Enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor MP1D

All present enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor MP1D:
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 MP1D, PDB code: 4p4e was solved by C.Barinka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.29 / 1.67
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.749, 130.680, 159.522, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 18.3

Other elements in 4p4e:

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor MP1D 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 MP1D (pdb code 4p4e). 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 MP1D, PDB code: 4p4e:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4p4e

Go back to Zinc Binding Sites List in 4p4e
Zinc binding site 1 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor MP1D


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 MP1D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn818

b:20.6
occ:1.00
 OAC A:2G4822 2.0 21.3 1.0
OD2 A:ASP387 2.0 23.2 1.0
OE2 A:GLU425 2.0 18.1 1.0
NE2 A:HIS553 2.0 17.9 1.0
OE1 A:GLU425 2.5 20.1 1.0
CD A:GLU425 2.6 19.8 1.0
CE1 A:HIS553 2.9 18.5 1.0
CG A:ASP387 3.0 21.9 1.0
PAX A:2G4822 3.0 21.0 1.0
OAF A:2G4822 3.0 20.9 1.0
CD2 A:HIS553 3.1 19.9 1.0
OD1 A:ASP387 3.4 19.7 1.0
ZN A:ZN819 3.7 21.2 1.0
CE1 A:TYR552 3.8 21.2 1.0
O A:HOH1079 3.9 22.5 1.0
OH A:TYR552 4.0 19.8 1.0
CA A:2G4822 4.1 21.4 1.0
ND1 A:HIS553 4.1 18.9 1.0
N A:2G4822 4.1 20.3 1.0
CG A:GLU425 4.1 18.6 1.0
CG A:HIS553 4.2 18.6 1.0
OAS A:2G4822 4.2 20.5 1.0
CB A:ASP387 4.3 21.8 1.0
CZ A:TYR552 4.3 19.4 1.0
C A:2G4822 4.4 22.4 1.0
OE1 A:GLU424 4.5 18.5 1.0
CD1 A:TRP381 4.5 20.1 1.0
O A:2G4822 4.5 21.7 1.0
NE1 A:TRP381 4.7 20.0 1.0
NE2 A:HIS377 4.8 19.3 1.0
CD1 A:TYR552 4.8 21.3 1.0
CE1 A:HIS377 4.8 18.5 1.0

Zinc binding site 2 out of 2 in 4p4e

Go back to Zinc Binding Sites List in 4p4e
Zinc binding site 2 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor MP1D


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 MP1D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn819

b:21.2
occ:1.00
 OD2 A:ASP453 1.9 23.9 1.0
OAF A:2G4822 2.0 20.9 1.0
OD1 A:ASP387 2.0 19.7 1.0
NE2 A:HIS377 2.0 19.3 1.0
CG A:ASP453 2.7 23.6 1.0
OD1 A:ASP453 2.8 26.0 1.0
CG A:ASP387 3.0 21.9 1.0
CE1 A:HIS377 3.0 18.5 1.0
CD2 A:HIS377 3.0 18.5 1.0
PAX A:2G4822 3.4 21.0 1.0
OD2 A:ASP387 3.4 23.2 1.0
OE2 A:GLU425 3.7 18.1 1.0
ZN A:ZN818 3.7 20.6 1.0
OE1 A:GLU424 3.8 18.5 1.0
OAS A:2G4822 3.9 20.5 1.0
OAC A:2G4822 4.0 21.3 1.0
ND2 A:ASN519 4.1 24.4 1.0
ND1 A:HIS377 4.1 19.2 1.0
CB A:ASP453 4.1 22.1 1.0
CD A:GLU424 4.2 19.3 1.0
O A:HOH1334 4.2 53.1 1.0
CG A:HIS377 4.2 18.1 1.0
OE2 A:GLU424 4.2 21.0 1.0
CB A:ASP387 4.2 21.8 1.0
CB A:PRO388 4.4 19.3 1.0
CD A:GLU425 4.5 19.8 1.0
N A:2G4822 4.5 20.3 1.0
CA A:ASP387 4.6 20.4 1.0
CA A:PRO388 4.6 19.6 1.0
OG A:SER454 4.6 22.6 0.8
C A:ASP387 4.7 20.8 1.0
N A:PRO388 4.8 19.7 1.0
OD1 A:ASN519 4.9 25.6 1.0
O A:HOH1263 4.9 43.1 1.0
CG A:ASN519 5.0 25.3 1.0

Reference:

C.Barinka, C.Barinka. N/A N/A.
Page generated: Sun Oct 27 04:14:22 2024

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