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Zinc in PDB 2jbj: Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with 2-Pmpa (2-Phosphonomethyl-Pentanedioic Acid)

Enzymatic activity of Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with 2-Pmpa (2-Phosphonomethyl-Pentanedioic Acid)

All present enzymatic activity of Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with 2-Pmpa (2-Phosphonomethyl-Pentanedioic Acid):
3.4.17.21;

Protein crystallography data

The structure of Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with 2-Pmpa (2-Phosphonomethyl-Pentanedioic Acid), PDB code: 2jbj 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) 101.02 / 2.19
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 100.755, 130.982, 159.611, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 23.8

Other elements in 2jbj:

The structure of Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with 2-Pmpa (2-Phosphonomethyl-Pentanedioic 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 2-Pmpa (2-Phosphonomethyl-Pentanedioic Acid) (pdb code 2jbj). 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 2-Pmpa (2-Phosphonomethyl-Pentanedioic Acid), PDB code: 2jbj:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2jbj

Go back to Zinc Binding Sites List in 2jbj
Zinc binding site 1 out of 2 in the Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with 2-Pmpa (2-Phosphonomethyl-Pentanedioic 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 2-Pmpa (2-Phosphonomethyl-Pentanedioic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1751

b:51.2
occ:1.00
OD2 A:ASP387 1.9 31.1 1.0
OE2 A:GLU425 2.0 27.6 1.0
O2 A:G881768 2.1 39.6 1.0
NE2 A:HIS553 2.2 34.0 1.0
OE1 A:GLU425 2.6 30.2 1.0
O1 A:G881768 2.6 31.7 1.0
CD A:GLU425 2.6 31.0 1.0
P1 A:G881768 2.9 29.8 1.0
CG A:ASP387 2.9 33.5 1.0
CD2 A:HIS553 3.1 29.0 1.0
CE1 A:HIS553 3.2 33.6 1.0
OD1 A:ASP387 3.3 36.2 1.0
ZN A:ZN1752 3.6 49.6 1.0
CE1 A:TYR552 3.9 29.7 1.0
C2 A:G881768 3.9 33.3 1.0
O A:HOH2175 4.0 33.0 1.0
O3 A:G881768 4.0 32.5 1.0
C1 A:G881768 4.1 33.1 1.0
CG A:GLU425 4.1 29.5 1.0
OH A:TYR552 4.1 35.0 1.0
CB A:ASP387 4.2 32.1 1.0
ND1 A:HIS553 4.3 34.8 1.0
CG A:HIS553 4.3 37.4 1.0
CZ A:TYR552 4.3 34.4 1.0
C3 A:G881768 4.4 35.0 1.0
CD1 A:TRP381 4.5 33.1 1.0
OE1 A:GLU424 4.5 36.6 1.0
NE1 A:TRP381 4.7 34.1 1.0
O4 A:G881768 4.7 35.9 1.0
O A:HOH2400 4.8 27.8 1.0
NE2 A:HIS377 4.8 31.0 1.0
CE1 A:HIS377 4.8 28.0 1.0
CD1 A:TYR552 4.9 32.1 1.0

Zinc binding site 2 out of 2 in 2jbj

Go back to Zinc Binding Sites List in 2jbj
Zinc binding site 2 out of 2 in the Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with 2-Pmpa (2-Phosphonomethyl-Pentanedioic 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 2-Pmpa (2-Phosphonomethyl-Pentanedioic Acid) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1752

b:49.6
occ:1.00
O1 A:G881768 2.0 31.7 1.0
NE2 A:HIS377 2.1 31.0 1.0
OD1 A:ASP387 2.2 36.2 1.0
OD2 A:ASP453 2.2 40.5 1.0
OD1 A:ASP453 2.5 33.2 1.0
CG A:ASP453 2.7 33.6 1.0
CD2 A:HIS377 3.1 29.5 1.0
CE1 A:HIS377 3.1 28.0 1.0
CG A:ASP387 3.1 33.5 1.0
P1 A:G881768 3.3 29.8 1.0
OD2 A:ASP387 3.4 31.1 1.0
OE1 A:GLU424 3.5 36.6 1.0
O3 A:G881768 3.5 32.5 1.0
ZN A:ZN1751 3.6 51.2 1.0
OE2 A:GLU425 3.7 27.6 1.0
OE2 A:GLU424 4.0 33.4 1.0
CD A:GLU424 4.0 33.1 1.0
O A:HOH2402 4.0 57.3 1.0
ND2 A:ASN519 4.1 31.4 1.0
ND1 A:HIS377 4.2 30.1 1.0
CG A:HIS377 4.2 31.7 1.0
CB A:ASP453 4.3 32.1 1.0
O2 A:G881768 4.3 39.6 1.0
CB A:PRO388 4.4 31.9 1.0
CB A:ASP387 4.4 32.1 1.0
CD A:GLU425 4.6 31.0 1.0
C1 A:G881768 4.6 33.1 1.0
CA A:PRO388 4.6 31.5 1.0
CA A:ASP387 4.6 32.5 1.0
C A:ASP387 4.7 31.9 1.0
OG A:SER454 4.7 35.7 1.0
N A:PRO388 4.7 31.4 1.0
OE1 A:GLU425 5.0 30.2 1.0
OD1 A:ASN519 5.0 33.8 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: Wed Dec 16 03:31:58 2020

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