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

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

All present enzymatic activity of A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Folyltri-Gamma-L-Glutamic Acid (Pteroyltetra- 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 Folyltri-Gamma-L-Glutamic Acid (Pteroyltetra- Gamma-L-Glutamic Acid), PDB code: 4mcr 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) 29.48 / 1.65
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.491, 129.830, 158.811, 90.00, 90.00, 90.00
R / Rfree (%) 13.3 / 16.7

Other elements in 4mcr:

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

Zinc binding site 1 out of 2 in 4mcr

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

b:17.1
occ:1.00
 O A:HOH1339 2.0 17.6 1.0
OD2 A:ASP387 2.0 18.5 1.0
NE2 A:HIS553 2.0 15.5 1.0
OE2 A:GLU425 2.1 16.5 1.0
OAG A:29D818 2.2 19.1 1.0
OE1 A:GLU425 2.2 17.1 1.0
CD A:GLU425 2.5 14.2 1.0
CE1 A:HIS553 2.9 15.4 1.0
CG A:ASP387 3.0 17.0 1.0
CBS A:29D818 3.1 16.9 1.0
CD2 A:HIS553 3.1 16.0 1.0
ZN A:ZN802 3.3 18.9 1.0
OD1 A:ASP387 3.3 17.5 1.0
N A:29D818 3.9 16.9 1.0
CA A:29D818 4.0 16.4 1.0
CE1 A:TYR552 4.1 16.3 1.0
CAW A:29D818 4.1 20.2 1.0
CG A:GLU425 4.1 13.9 1.0
ND1 A:HIS553 4.1 15.3 1.0
O A:HOH916 4.2 16.1 1.0
CG A:HIS553 4.2 15.2 1.0
CB A:ASP387 4.3 16.0 1.0
OH A:TYR552 4.4 17.7 1.0
C A:29D818 4.5 17.1 1.0
NE2 A:HIS377 4.5 14.2 1.0
CZ A:TYR552 4.6 17.0 1.0
CD1 A:TRP381 4.6 16.2 1.0
CE1 A:HIS377 4.7 14.1 1.0
OXT A:29D818 4.8 17.3 1.0
O A:HOH1334 4.8 37.1 1.0
NE1 A:TRP381 4.8 17.1 1.0
OD2 A:ASP453 4.9 20.3 1.0
CD1 A:TYR552 5.0 17.5 1.0

Zinc binding site 2 out of 2 in 4mcr

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

b:18.9
occ:1.00
 O A:HOH1339 2.0 17.6 1.0
OD1 A:ASP387 2.0 17.5 1.0
OD2 A:ASP453 2.0 20.3 1.0
NE2 A:HIS377 2.0 14.2 1.0
CG A:ASP453 2.7 18.7 1.0
OD1 A:ASP453 2.8 22.1 1.0
CG A:ASP387 2.9 17.0 1.0
CE1 A:HIS377 3.0 14.1 1.0
CD2 A:HIS377 3.0 14.2 1.0
OD2 A:ASP387 3.2 18.5 1.0
ZN A:ZN801 3.3 17.1 1.0
OE2 A:GLU425 3.6 16.5 1.0
ND1 A:HIS377 4.1 14.9 1.0
CG A:HIS377 4.2 14.5 1.0
CB A:ASP453 4.2 17.8 1.0
CB A:ASP387 4.2 16.0 1.0
CD A:GLU425 4.3 14.2 1.0
OAG A:29D818 4.3 19.1 1.0
CB A:PRO388 4.3 14.9 1.0
CBS A:29D818 4.3 16.9 1.0
CAW A:29D818 4.3 20.2 1.0
ND2 A:ASN519 4.4 17.8 1.0
OE1 A:GLU425 4.4 17.1 1.0
O A:HOH1334 4.5 37.1 1.0
CA A:PRO388 4.6 16.0 1.0
CA A:ASP387 4.6 16.0 1.0
C A:ASP387 4.7 16.9 1.0
N A:PRO388 4.7 16.2 1.0
OG A:SER454 4.8 12.7 0.7
N A:29D818 4.9 16.9 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: Sun Oct 27 02:20:27 2024

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