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Zinc in PDB 2jbk: Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with Quisqualic Acid (Quisqualate, Alpha-Amino-3,5-Dioxo-1,2,4- Oxadiazolidine-2-Propanoic Acid)

Enzymatic activity of Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with Quisqualic Acid (Quisqualate, Alpha-Amino-3,5-Dioxo-1,2,4- Oxadiazolidine-2-Propanoic Acid)

All present enzymatic activity of Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with Quisqualic Acid (Quisqualate, Alpha-Amino-3,5-Dioxo-1,2,4- Oxadiazolidine-2-Propanoic Acid):
3.4.17.21;

Protein crystallography data

The structure of Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with Quisqualic Acid (Quisqualate, Alpha-Amino-3,5-Dioxo-1,2,4- Oxadiazolidine-2-Propanoic Acid), PDB code: 2jbk was solved by J.R.Mesters, K.Henning, R.Hilgenfeld, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.00 / 2.99
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 103.144, 130.758, 159.992, 90.00, 90.00, 90.00
R / Rfree (%) 21 / n/a

Other elements in 2jbk:

The structure of Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with Quisqualic Acid (Quisqualate, Alpha-Amino-3,5-Dioxo-1,2,4- Oxadiazolidine-2-Propanoic 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 Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with Quisqualic Acid (Quisqualate, Alpha-Amino-3,5-Dioxo-1,2,4- Oxadiazolidine-2-Propanoic Acid) (pdb code 2jbk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with Quisqualic Acid (Quisqualate, Alpha-Amino-3,5-Dioxo-1,2,4- Oxadiazolidine-2-Propanoic Acid), PDB code: 2jbk:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2jbk

Go back to Zinc Binding Sites List in 2jbk
Zinc binding site 1 out of 2 in the Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with Quisqualic Acid (Quisqualate, Alpha-Amino-3,5-Dioxo-1,2,4- Oxadiazolidine-2-Propanoic Acid)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with Quisqualic Acid (Quisqualate, Alpha-Amino-3,5-Dioxo-1,2,4- Oxadiazolidine-2-Propanoic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:35.0
occ:1.00
 OE2 A:GLU425 1.9 35.0 1.0
OD2 A:ASP387 1.9 35.0 1.0
O A:HOH2018 2.0 35.0 1.0
NE2 A:HIS553 2.1 35.0 1.0
CD A:GLU425 2.5 35.0 1.0
OE1 A:GLU425 2.6 35.0 1.0
CG A:ASP387 2.9 35.0 1.0
O A:HOH2020 2.9 35.0 1.0
CE1 A:HIS553 3.0 35.0 1.0
ZN A:ZN802 3.1 35.0 1.0
OD1 A:ASP387 3.1 35.0 1.0
CD2 A:HIS553 3.2 35.0 1.0
OE1 A:GLU424 3.7 35.0 1.0
CG A:GLU425 4.0 35.0 1.0
ND1 A:HIS553 4.2 35.0 1.0
C02 A:QUS1764 4.2 35.0 1.0
CB A:ASP387 4.2 35.0 1.0
CE1 A:TYR552 4.2 35.0 1.0
CG A:HIS553 4.3 35.0 1.0
CE1 A:HIS377 4.4 35.0 1.0
NP3 A:QUS1764 4.4 35.0 1.0
NE2 A:HIS377 4.4 35.0 1.0
OH A:TYR552 4.5 35.0 1.0
C01 A:QUS1764 4.6 35.0 1.0
CD1 A:TRP381 4.6 35.0 1.0
O16 A:QUS1764 4.7 35.0 1.0
OD2 A:ASP453 4.7 35.0 1.0
NE1 A:TRP381 4.7 35.0 1.0
CZ A:TYR552 4.8 35.0 1.0
CD A:GLU424 4.8 35.0 1.0
CB A:GLU425 4.9 35.0 1.0

Zinc binding site 2 out of 2 in 2jbk

Go back to Zinc Binding Sites List in 2jbk
Zinc binding site 2 out of 2 in the Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with Quisqualic Acid (Quisqualate, Alpha-Amino-3,5-Dioxo-1,2,4- Oxadiazolidine-2-Propanoic Acid)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with Quisqualic Acid (Quisqualate, Alpha-Amino-3,5-Dioxo-1,2,4- Oxadiazolidine-2-Propanoic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:35.0
occ:1.00
 O A:HOH2018 1.5 35.0 1.0
NE2 A:HIS377 1.8 35.0 1.0
OD2 A:ASP453 1.9 35.0 1.0
OD1 A:ASP387 2.0 35.0 1.0
CE1 A:HIS377 2.6 35.0 1.0
CG A:ASP453 2.8 35.0 1.0
CD2 A:HIS377 3.0 35.0 1.0
OE1 A:GLU424 3.0 35.0 1.0
CG A:ASP387 3.0 35.0 1.0
OD1 A:ASP453 3.0 35.0 1.0
ZN A:ZN801 3.1 35.0 1.0
OD2 A:ASP387 3.3 35.0 1.0
OE2 A:GLU425 3.6 35.0 1.0
ND1 A:HIS377 3.7 35.0 1.0
CD A:GLU424 3.8 35.0 1.0
CG A:HIS377 4.0 35.0 1.0
O A:HOH2020 4.0 35.0 1.0
ND2 A:ASN519 4.2 35.0 1.0
CB A:ASP453 4.2 35.0 1.0
OE2 A:GLU424 4.2 35.0 1.0
CD A:GLU425 4.3 35.0 1.0
CB A:ASP387 4.3 35.0 1.0
CB A:PRO388 4.4 35.0 1.0
CA A:PRO388 4.6 35.0 1.0
N A:PRO388 4.6 35.0 1.0
C A:ASP387 4.7 35.0 1.0
CG A:GLU424 4.7 35.0 1.0
CA A:ASP387 4.7 35.0 1.0
OE1 A:GLU425 4.7 35.0 1.0
NP3 A:QUS1764 4.8 35.0 1.0

Reference:

J.R.Mesters, K.Henning, R.Hilgenfeld. Human Glutamate Carboxypeptidase II Inhibition: Structures of Gcpii in Complex with Two Potent Inhibitors, Quisqualate and 2-Pmpa. Acta Crystallogr.,Sect.D V. 63 508 2007.
ISSN: ISSN 0907-4449
PubMed: 17372356
DOI: 10.1107/S090744490700902X
Page generated: Thu Oct 17 01:12:12 2024

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