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Zinc in PDB 4mcs: A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) HIS475TYR Variant in Complex with Glutamic Acid

Enzymatic activity of A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) HIS475TYR Variant in Complex with Glutamic Acid

All present enzymatic activity of A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) HIS475TYR Variant in Complex with Glutamic Acid:
3.4.17.21;

Protein crystallography data

The structure of A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) HIS475TYR Variant in Complex with Glutamic Acid, PDB code: 4mcs was solved by J.Ptacek, C.Barinka, P.Sacha, M.Navratil, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.53 / 1.83
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.547, 130.395, 158.980, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 19.1

Other elements in 4mcs:

The structure of A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) HIS475TYR Variant in Complex with Glutamic Acid also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) HIS475TYR Variant in Complex with Glutamic Acid (pdb code 4mcs). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) HIS475TYR Variant in Complex with Glutamic Acid, PDB code: 4mcs:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4mcs

Go back to Zinc Binding Sites List in 4mcs
Zinc binding site 1 out of 2 in the A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) HIS475TYR Variant in Complex with Glutamic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) HIS475TYR Variant in Complex with Glutamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn814

b:23.4
occ:1.00
 NE2 A:HIS553 2.0 18.7 1.0
OE2 A:GLU425 2.1 17.9 1.0
OD2 A:ASP387 2.1 23.1 1.0
O A:HOH1454 2.1 20.5 1.0
OE1 A:GLU425 2.4 20.1 1.0
CD A:GLU425 2.6 18.8 1.0
OD1 A:ASP819 2.7 38.8 1.0
CE1 A:HIS553 2.9 21.0 1.0
CG A:ASP387 3.0 22.6 1.0
CD2 A:HIS553 3.1 20.6 1.0
ZN A:ZN815 3.3 20.2 1.0
OD1 A:ASP387 3.3 23.0 1.0
CG A:ASP819 3.6 39.2 1.0
OD2 A:ASP819 3.7 37.2 1.0
CE1 A:TYR552 4.0 22.7 1.0
OE1 A:GLU424 4.1 19.9 1.0
O A:HOH916 4.1 21.0 1.0
ND1 A:HIS553 4.1 18.9 1.0
CG A:GLU425 4.1 18.6 1.0
CA A:GLU818 4.1 21.4 1.0
N A:GLU818 4.2 20.9 1.0
CG A:HIS553 4.2 21.3 1.0
OH A:TYR552 4.2 21.0 1.0
CB A:ASP387 4.3 20.6 1.0
NE2 A:HIS377 4.5 16.9 1.0
C A:GLU818 4.5 22.9 1.0
CZ A:TYR552 4.5 21.1 1.0
CD1 A:TRP381 4.6 22.3 1.0
CE1 A:HIS377 4.6 14.8 1.0
OXT A:GLU818 4.7 22.6 1.0
NE1 A:TRP381 4.8 22.2 1.0
OD2 A:ASP453 4.9 20.2 1.0
CB A:ASP819 4.9 42.2 1.0

Zinc binding site 2 out of 2 in 4mcs

Go back to Zinc Binding Sites List in 4mcs
Zinc binding site 2 out of 2 in the A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) HIS475TYR Variant in Complex with Glutamic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) HIS475TYR Variant in Complex with Glutamic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn815

b:20.2
occ:1.00
 O A:HOH1454 1.8 20.5 1.0
NE2 A:HIS377 2.0 16.9 1.0
OD1 A:ASP387 2.0 23.0 1.0
OD2 A:ASP453 2.0 20.2 1.0
CG A:ASP453 2.7 21.3 1.0
OD1 A:ASP453 2.7 22.5 1.0
CE1 A:HIS377 2.9 14.8 1.0
CG A:ASP387 2.9 22.6 1.0
CD2 A:HIS377 3.0 16.1 1.0
ZN A:ZN814 3.3 23.4 1.0
OD2 A:ASP387 3.3 23.1 1.0
OE1 A:GLU424 3.5 19.9 1.0
OD2 A:ASP819 3.5 37.2 1.0
OE2 A:GLU425 3.5 17.9 1.0
O A:HOH1437 3.9 35.5 1.0
CD A:GLU424 4.0 17.9 1.0
ND1 A:HIS377 4.1 17.7 1.0
CG A:HIS377 4.1 15.4 1.0
CB A:ASP453 4.2 18.9 1.0
CB A:PRO388 4.3 19.5 1.0
CB A:ASP387 4.3 20.6 1.0
CD A:GLU425 4.3 18.8 1.0
ND2 A:ASN519 4.3 19.4 1.0
OE2 A:GLU424 4.3 17.9 1.0
CG A:ASP819 4.4 39.2 1.0
OD1 A:ASP819 4.4 38.8 1.0
CA A:PRO388 4.5 19.7 1.0
N A:PRO388 4.6 20.1 1.0
C A:ASP387 4.6 20.1 1.0
CA A:ASP387 4.6 21.5 1.0
OE1 A:GLU425 4.6 20.1 1.0
OG A:SER454 4.7 23.7 1.0
N A:GLU818 4.8 20.9 1.0

Reference:

M.Navratil, J.Ptacek, P.Sacha, J.Starkova, J.Lubkowski, C.Barinka, J.Konvalinka. Structural and Biochemical Characterization of the Folyl-Poly-Gamma-L-Glutamate Hydrolyzing Activity of Human Glutamate Carboxypeptidase II. Febs J. V. 281 3228 2014.
ISSN: ISSN 1742-464X
PubMed: 24863754
DOI: 10.1111/FEBS.12857
Page generated: Wed Aug 20 20:18:54 2025

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