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Zinc in PDB 5o5t: X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Urea Based Inhibitor Psma 1007

Enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Urea Based Inhibitor Psma 1007

All present enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Urea Based Inhibitor Psma 1007:
3.4.17.21;

Protein crystallography data

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Urea Based Inhibitor Psma 1007, PDB code: 5o5t was solved by C.Barinka, Z.Novakova, L.Motlova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.38 / 1.43
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.657, 130.159, 159.160, 90.00, 90.00, 90.00
R / Rfree (%) 13.8 / 17.3

Other elements in 5o5t:

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Urea Based Inhibitor Psma 1007 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 Urea Based Inhibitor Psma 1007 (pdb code 5o5t). 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 Urea Based Inhibitor Psma 1007, PDB code: 5o5t:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5o5t

Go back to Zinc Binding Sites List in 5o5t
Zinc binding site 1 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Urea Based Inhibitor Psma 1007


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 Urea Based Inhibitor Psma 1007 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn815

b:20.8
occ:1.00
 O A:HOH1233 1.9 19.8 1.0
NE2 A:HIS553 2.1 17.9 1.0
OE2 A:GLU425 2.1 20.4 1.0
OD2 A:ASP387 2.1 22.9 1.0
OE1 A:GLU425 2.4 21.6 1.0
OAH A:9OT819 2.5 22.6 1.0
CD A:GLU425 2.6 21.2 1.0
CG A:ASP387 3.0 24.0 1.0
CE1 A:HIS553 3.1 20.4 1.0
CD2 A:HIS553 3.1 22.2 1.0
ZN A:ZN816 3.3 21.1 1.0
OD1 A:ASP387 3.3 20.7 1.0
CAD A:9OT819 3.4 22.8 1.0
NAE A:9OT819 3.9 22.4 1.0
CAF A:9OT819 4.0 22.4 1.0
CE1 A:TYR552 4.0 21.5 1.0
OE1 A:GLU424 4.1 21.3 1.0
CG A:GLU425 4.1 19.3 1.0
ND1 A:HIS553 4.2 22.6 1.0
O A:HOH987 4.2 21.9 1.0
CG A:HIS553 4.2 20.9 1.0
N A:9OT819 4.3 22.1 1.0
CB A:ASP387 4.3 21.8 1.0
OH A:TYR552 4.3 20.0 1.0
CA A:9OT819 4.4 22.9 1.0
CAG A:9OT819 4.6 23.6 1.0
NE2 A:HIS377 4.6 19.5 1.0
CZ A:TYR552 4.6 21.7 1.0
CD1 A:TRP381 4.7 23.3 1.0
OAM A:9OT819 4.8 24.5 1.0
CE1 A:HIS377 4.8 18.7 1.0
NE1 A:TRP381 4.8 21.2 1.0
OD2 A:ASP453 4.9 21.7 1.0
CD1 A:TYR552 5.0 22.6 1.0
CD A:GLU424 5.0 18.6 1.0

Zinc binding site 2 out of 2 in 5o5t

Go back to Zinc Binding Sites List in 5o5t
Zinc binding site 2 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Urea Based Inhibitor Psma 1007


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 Urea Based Inhibitor Psma 1007 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn816

b:21.1
occ:1.00
 O A:HOH1233 1.9 19.8 1.0
OD1 A:ASP387 2.0 20.7 1.0
OD2 A:ASP453 2.0 21.7 1.0
NE2 A:HIS377 2.0 19.5 1.0
CG A:ASP453 2.8 26.2 1.0
OD1 A:ASP453 2.8 25.2 1.0
CG A:ASP387 2.9 24.0 1.0
CE1 A:HIS377 3.0 18.7 1.0
CD2 A:HIS377 3.1 20.0 1.0
OD2 A:ASP387 3.2 22.9 1.0
ZN A:ZN815 3.3 20.8 1.0
OE2 A:GLU425 3.6 20.4 1.0
OE1 A:GLU424 3.7 21.3 1.0
CD A:GLU424 4.0 18.6 1.0
ND1 A:HIS377 4.1 20.1 1.0
OE2 A:GLU424 4.2 20.9 1.0
CB A:ASP453 4.2 23.3 1.0
ND2 A:ASN519 4.2 20.0 1.0
CG A:HIS377 4.2 19.5 1.0
CB A:ASP387 4.2 21.8 1.0
CD A:GLU425 4.3 21.2 1.0
CB A:PRO388 4.3 20.4 1.0
OAH A:9OT819 4.5 22.6 1.0
CAD A:9OT819 4.5 22.8 1.0
CA A:PRO388 4.5 19.8 1.0
CA A:ASP387 4.6 19.9 1.0
OE1 A:GLU425 4.6 21.6 1.0
C A:ASP387 4.6 23.2 1.0
N A:PRO388 4.7 20.7 1.0
N A:9OT819 4.7 22.1 1.0
CA A:9OT819 4.8 22.9 1.0
OG A:SER454 4.8 24.8 1.0
O A:HOH1044 4.8 26.3 1.0
C A:9OT819 4.9 22.9 1.0
NAE A:9OT819 4.9 22.4 1.0
CG A:GLU424 5.0 17.3 1.0

Reference:

C.Barinka, Z.Novakova, L.Motlova. X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Urea Based Inhibitor Psma 1007 To Be Published.
Page generated: Sun Oct 27 23:15:18 2024

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