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

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

All present enzymatic activity of A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with Folyldi-Gamma-L-Glutamic Acid (Pteroyltri- 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 Folyldi-Gamma-L-Glutamic Acid (Pteroyltri- Gamma-L-Glutamic Acid), PDB code: 4mcq was solved by M.Navratil, C.Barinka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.96 / 2.00
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.646, 130.140, 159.867, 90.00, 90.00, 90.00
R / Rfree (%) 13.7 / 17.2

Other elements in 4mcq:

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

Zinc binding site 1 out of 2 in 4mcq

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

b:18.7
occ:1.00
 O A:HOH1309 2.0 17.8 1.0
OD2 A:ASP387 2.0 19.5 1.0
OE2 A:GLU425 2.1 17.4 1.0
NE2 A:HIS553 2.1 17.4 1.0
OAF A:29C818 2.2 21.6 1.0
OE1 A:GLU425 2.2 19.1 1.0
CD A:GLU425 2.5 16.0 1.0
CE1 A:HIS553 3.0 16.4 1.0
CG A:ASP387 3.0 19.6 1.0
CBL A:29C818 3.1 20.2 1.0
CD2 A:HIS553 3.1 16.3 1.0
ZN A:ZN802 3.3 21.3 1.0
OD1 A:ASP387 3.3 18.5 1.0
N A:29C818 3.8 19.6 1.0
CA A:29C818 4.0 19.1 1.0
CE1 A:TYR552 4.0 17.3 1.0
CAT A:29C818 4.1 20.8 1.0
CG A:GLU425 4.1 16.9 1.0
ND1 A:HIS553 4.1 16.4 1.0
O A:HOH916 4.1 16.1 1.0
CG A:HIS553 4.2 16.1 1.0
CB A:ASP387 4.3 17.2 1.0
OH A:TYR552 4.4 18.4 1.0
NE2 A:HIS377 4.5 15.6 1.0
C A:29C818 4.5 18.9 1.0
CZ A:TYR552 4.6 18.0 1.0
CD1 A:TRP381 4.7 19.1 1.0
CE1 A:HIS377 4.7 16.4 1.0
OXT A:29C818 4.8 19.1 1.0
O A:HOH1304 4.8 36.2 1.0
NE1 A:TRP381 4.9 20.0 1.0
OD2 A:ASP453 4.9 20.7 1.0
CD1 A:TYR552 5.0 19.1 1.0

Zinc binding site 2 out of 2 in 4mcq

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

b:21.3
occ:1.00
 O A:HOH1309 2.0 17.8 1.0
OD1 A:ASP387 2.0 18.5 1.0
OD2 A:ASP453 2.0 20.7 1.0
NE2 A:HIS377 2.0 15.6 1.0
CG A:ASP453 2.7 20.7 1.0
OD1 A:ASP453 2.8 22.6 1.0
CG A:ASP387 2.9 19.6 1.0
CE1 A:HIS377 3.0 16.4 1.0
CD2 A:HIS377 3.0 15.8 1.0
OD2 A:ASP387 3.2 19.5 1.0
ZN A:ZN801 3.3 18.7 1.0
OE2 A:GLU425 3.6 17.4 1.0
ND1 A:HIS377 4.1 17.1 1.0
CG A:HIS377 4.2 16.2 1.0
CB A:ASP453 4.2 19.1 1.0
CB A:ASP387 4.2 17.2 1.0
CD A:GLU425 4.3 16.0 1.0
CB A:PRO388 4.3 15.9 1.0
OAF A:29C818 4.3 21.6 1.0
OE1 A:GLU425 4.4 19.1 1.0
CBL A:29C818 4.4 20.2 1.0
ND2 A:ASN519 4.4 18.6 1.0
CAT A:29C818 4.4 20.8 1.0
O A:HOH1304 4.5 36.2 1.0
CA A:PRO388 4.6 16.6 1.0
CA A:ASP387 4.6 17.4 1.0
N A:PRO388 4.6 16.1 1.0
C A:ASP387 4.6 16.6 1.0
OG A:SER454 4.7 13.1 0.7
N A:29C818 4.9 19.6 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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