Atomistry » Zinc » PDB 2ja8-2jt6 » 2jbj
Atomistry »
  Zinc »
    PDB 2ja8-2jt6 »
      2jbj »

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: Thu Oct 17 01:11:58 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy