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Zinc in PDB 4p4d: X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor MP1C

Enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor MP1C

All present enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor MP1C:
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 MP1C, PDB code: 4p4d was solved by C.Barinka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.63 / 1.65
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.902, 130.079, 159.667, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 17.4

Other elements in 4p4d:

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor MP1C 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 MP1C (pdb code 4p4d). 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 MP1C, PDB code: 4p4d:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4p4d

Go back to Zinc Binding Sites List in 4p4d
Zinc binding site 1 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor MP1C


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 MP1C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn816

b:19.1
occ:1.00
 OE2 A:GLU425 2.0 16.8 1.0
NE2 A:HIS553 2.0 16.9 1.0
OD2 A:ASP387 2.0 19.3 1.0
OAD A:2GR820 2.1 17.4 1.0
OE1 A:GLU425 2.5 16.9 1.0
CD A:GLU425 2.6 17.3 1.0
OAG A:2GR820 2.8 17.6 1.0
CE1 A:HIS553 2.9 16.4 1.0
PAY A:2GR820 2.9 18.5 1.0
CG A:ASP387 3.0 18.9 1.0
CD2 A:HIS553 3.1 18.6 1.0
OD1 A:ASP387 3.4 17.8 1.0
ZN A:ZN817 3.6 19.0 1.0
CE1 A:TYR552 3.7 19.9 1.0
O A:HOH1030 3.9 19.2 1.0
OH A:TYR552 4.0 18.2 1.0
CA A:2GR820 4.0 16.9 1.0
N A:2GR820 4.1 16.2 1.0
ND1 A:HIS553 4.1 17.1 1.0
CG A:GLU425 4.1 17.3 1.0
OAS A:2GR820 4.1 18.3 1.0
CG A:HIS553 4.2 16.9 1.0
CB A:ASP387 4.3 18.0 1.0
CZ A:TYR552 4.3 18.7 1.0
C A:2GR820 4.4 17.6 1.0
CD1 A:TRP381 4.4 17.1 1.0
OE1 A:GLU424 4.5 17.3 1.0
O A:2GR820 4.5 17.9 1.0
NE1 A:TRP381 4.6 18.1 1.0
O A:HOH1513 4.7 33.5 1.0
NE2 A:HIS377 4.7 16.1 1.0
CD1 A:TYR552 4.7 20.2 1.0
CE1 A:HIS377 4.8 16.2 1.0

Zinc binding site 2 out of 2 in 4p4d

Go back to Zinc Binding Sites List in 4p4d
Zinc binding site 2 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Phosphoramidate Inhibitor MP1C


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 MP1C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn817

b:19.0
occ:1.00
 OAG A:2GR820 1.9 17.6 1.0
OD2 A:ASP453 2.0 19.1 1.0
OD1 A:ASP387 2.0 17.8 1.0
NE2 A:HIS377 2.0 16.1 1.0
CG A:ASP453 2.7 19.7 1.0
OD1 A:ASP453 2.7 19.1 1.0
CG A:ASP387 3.0 18.9 1.0
CD2 A:HIS377 3.0 16.0 1.0
CE1 A:HIS377 3.0 16.2 1.0
O A:HOH1513 3.2 33.5 1.0
PAY A:2GR820 3.3 18.5 1.0
OD2 A:ASP387 3.4 19.3 1.0
OE2 A:GLU425 3.6 16.8 1.0
ZN A:ZN816 3.6 19.1 1.0
OE1 A:GLU424 3.8 17.3 1.0
OAS A:2GR820 3.8 18.3 1.0
OAD A:2GR820 4.1 17.4 1.0
ND1 A:HIS377 4.1 16.5 1.0
CG A:HIS377 4.2 15.9 1.0
CB A:ASP453 4.2 17.6 1.0
ND2 A:ASN519 4.2 18.1 1.0
CD A:GLU424 4.2 17.2 1.0
CB A:ASP387 4.2 18.0 1.0
OE2 A:GLU424 4.3 16.3 1.0
CB A:PRO388 4.3 16.6 1.0
CD A:GLU425 4.4 17.3 1.0
N A:2GR820 4.5 16.2 1.0
CA A:ASP387 4.6 17.6 1.0
OG A:SER454 4.6 17.1 0.8
CA A:PRO388 4.6 17.3 1.0
C A:ASP387 4.7 18.1 1.0
N A:PRO388 4.7 17.6 1.0
OE1 A:GLU425 4.9 16.9 1.0

Reference:

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

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