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Zinc in PDB 4mcp: A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Folyl-Gamma-L-Glutamic Acid (Pteroyldi-Gamma- L-Glutamic Acid)

Enzymatic activity of A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Folyl-Gamma-L-Glutamic Acid (Pteroyldi-Gamma- L-Glutamic Acid)

All present enzymatic activity of A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Folyl-Gamma-L-Glutamic Acid (Pteroyldi-Gamma- L-Glutamic Acid):
3.4.17.21;

Protein crystallography data

The structure of A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Folyl-Gamma-L-Glutamic Acid (Pteroyldi-Gamma- L-Glutamic Acid), PDB code: 4mcp was solved by M.Navratil, C.Barinka, J.Lubkowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.65
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.533, 130.176, 158.809, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 16.4

Other elements in 4mcp:

The structure of A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Folyl-Gamma-L-Glutamic Acid (Pteroyldi-Gamma- L-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) in Complex with Folyl-Gamma-L-Glutamic Acid (Pteroyldi-Gamma- L-Glutamic Acid) (pdb code 4mcp). 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) in Complex with Folyl-Gamma-L-Glutamic Acid (Pteroyldi-Gamma- L-Glutamic Acid), PDB code: 4mcp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4mcp

Go back to Zinc Binding Sites List in 4mcp
Zinc binding site 1 out of 2 in the A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Folyl-Gamma-L-Glutamic Acid (Pteroyldi-Gamma- L-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) in Complex with Folyl-Gamma-L-Glutamic Acid (Pteroyldi-Gamma- L-Glutamic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:19.8
occ:1.00
 O A:HOH1345 2.0 18.7 1.0
NE2 A:HIS553 2.0 17.6 1.0
OD2 A:ASP387 2.1 21.1 1.0
OE2 A:GLU425 2.2 17.9 1.0
OE1 A:GLU425 2.4 18.6 1.0
OAE A:28Z818 2.5 23.1 1.0
CD A:GLU425 2.6 18.4 1.0
CE1 A:HIS553 2.9 18.3 1.0
CG A:ASP387 3.0 21.0 1.0
CD2 A:HIS553 3.1 19.8 1.0
CBE A:28Z818 3.2 25.3 1.0
ZN A:ZN802 3.3 21.0 1.0
OD1 A:ASP387 3.3 18.8 1.0
N A:28Z818 3.9 23.4 1.0
CA A:28Z818 4.0 23.4 1.0
CE1 A:TYR552 4.0 19.7 1.0
ND1 A:HIS553 4.1 17.2 1.0
CAQ A:28Z818 4.1 24.6 1.0
O A:HOH916 4.2 18.9 1.0
CG A:GLU425 4.2 17.6 1.0
CG A:HIS553 4.2 18.8 1.0
CB A:ASP387 4.3 19.7 1.0
OH A:TYR552 4.4 19.7 1.0
NE2 A:HIS377 4.5 18.0 1.0
C A:28Z818 4.6 24.4 1.0
CD1 A:TRP381 4.6 19.1 1.0
CZ A:TYR552 4.7 18.5 1.0
CE1 A:HIS377 4.7 17.9 1.0
NE1 A:TRP381 4.8 18.2 1.0
O A:28Z818 4.8 24.8 1.0
OD2 A:ASP453 4.9 22.4 1.0
O A:HOH1340 4.9 48.1 1.0
CD1 A:TYR552 5.0 21.5 1.0

Zinc binding site 2 out of 2 in 4mcp

Go back to Zinc Binding Sites List in 4mcp
Zinc binding site 2 out of 2 in the A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Folyl-Gamma-L-Glutamic Acid (Pteroyldi-Gamma- L-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) in Complex with Folyl-Gamma-L-Glutamic Acid (Pteroyldi-Gamma- L-Glutamic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:21.0
occ:1.00
 O A:HOH1345 1.9 18.7 1.0
OD2 A:ASP453 2.0 22.4 1.0
OD1 A:ASP387 2.0 18.8 1.0
NE2 A:HIS377 2.0 18.0 1.0
CG A:ASP453 2.7 22.5 1.0
OD1 A:ASP453 2.8 25.4 1.0
CG A:ASP387 2.9 21.0 1.0
CE1 A:HIS377 3.0 17.9 1.0
CD2 A:HIS377 3.0 16.7 1.0
OD2 A:ASP387 3.2 21.1 1.0
ZN A:ZN801 3.3 19.8 1.0
OE2 A:GLU425 3.7 17.9 1.0
ND1 A:HIS377 4.1 17.8 1.0
CG A:HIS377 4.2 17.6 1.0
CB A:ASP453 4.2 19.2 1.0
CB A:ASP387 4.2 19.7 1.0
CB A:PRO388 4.3 19.2 1.0
ND2 A:ASN519 4.3 19.1 1.0
CD A:GLU425 4.4 18.4 1.0
CAQ A:28Z818 4.4 24.6 1.0
CBE A:28Z818 4.4 25.3 1.0
OAE A:28Z818 4.5 23.1 1.0
CA A:PRO388 4.6 18.9 1.0
CA A:ASP387 4.6 19.5 1.0
O A:HOH1340 4.6 48.1 1.0
OE1 A:GLU425 4.6 18.6 1.0
C A:ASP387 4.6 19.6 1.0
O A:HOH1512 4.7 43.0 1.0
N A:PRO388 4.7 19.3 1.0
OG A:SER454 4.8 16.8 0.7
N A:28Z818 4.9 23.4 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: Sun Oct 27 02:20:27 2024

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