Atomistry » Zinc » PDB 2bn7-2c6n » 2c6c
Atomistry »
  Zinc »
    PDB 2bn7-2c6n »
      2c6c »

Zinc in PDB 2c6c: Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with Gpi-18431 (S)-2-(4-Iodobenzylphosphonomethyl)-Pentanedioic Acid

Enzymatic activity of Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with Gpi-18431 (S)-2-(4-Iodobenzylphosphonomethyl)-Pentanedioic Acid

All present enzymatic activity of Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with Gpi-18431 (S)-2-(4-Iodobenzylphosphonomethyl)-Pentanedioic Acid:
3.4.17.21;

Protein crystallography data

The structure of Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with Gpi-18431 (S)-2-(4-Iodobenzylphosphonomethyl)-Pentanedioic Acid, PDB code: 2c6c was solved by J.R.Mesters, C.Barinka, W.Li, T.Tsukamoto, P.Majer, B.S.Slusher, J.Konvalinka, R.Hilgenfeld, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.00
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 103.127, 131.189, 161.225, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 22.5

Other elements in 2c6c:

The structure of Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with Gpi-18431 (S)-2-(4-Iodobenzylphosphonomethyl)-Pentanedioic Acid also contains other interesting chemical elements:

Iodine (I) 1 atom
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 Gpi-18431 (S)-2-(4-Iodobenzylphosphonomethyl)-Pentanedioic Acid (pdb code 2c6c). 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 Gpi-18431 (S)-2-(4-Iodobenzylphosphonomethyl)-Pentanedioic Acid, PDB code: 2c6c:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2c6c

Go back to Zinc Binding Sites List in 2c6c
Zinc binding site 1 out of 2 in the Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with Gpi-18431 (S)-2-(4-Iodobenzylphosphonomethyl)-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 Gpi-18431 (S)-2-(4-Iodobenzylphosphonomethyl)-Pentanedioic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1751

b:23.2
occ:1.00
 OD2 A:ASP387 1.9 23.6 1.0
O2 A:24I1767 1.9 23.7 1.0
OE2 A:GLU425 2.0 19.1 1.0
NE2 A:HIS553 2.1 21.0 1.0
OE1 A:GLU425 2.4 21.4 1.0
CD A:GLU425 2.5 20.7 1.0
CE1 A:HIS553 3.0 20.8 1.0
CG A:ASP387 3.0 26.5 1.0
P1 A:24I1767 3.0 22.0 1.0
CD2 A:HIS553 3.1 19.6 1.0
O1 A:24I1767 3.2 21.0 1.0
OD1 A:ASP387 3.5 25.9 1.0
ZN A:ZN1752 3.8 23.4 1.0
CE1 A:TYR552 3.9 25.5 1.0
O A:HOH2069 3.9 22.3 1.0
OH A:TYR552 4.0 24.9 1.0
CG A:GLU425 4.0 20.6 1.0
C10 A:24I1767 4.1 21.5 1.0
ND1 A:HIS553 4.1 21.7 1.0
C7 A:24I1767 4.2 21.2 1.0
CG A:HIS553 4.2 21.4 1.0
CZ A:TYR552 4.3 25.3 1.0
CB A:ASP387 4.3 26.1 1.0
C9 A:24I1767 4.4 21.9 1.0
C6 A:24I1767 4.5 25.2 1.0
CD1 A:TRP381 4.5 22.2 1.0
O4 A:24I1767 4.6 22.9 1.0
OE1 A:GLU424 4.6 19.2 1.0
NE1 A:TRP381 4.7 24.3 1.0
CE1 A:HIS377 4.7 22.1 1.0
C8 A:24I1767 4.7 28.4 1.0
NE2 A:HIS377 4.8 20.8 1.0
CD1 A:TYR552 4.9 27.1 1.0

Zinc binding site 2 out of 2 in 2c6c

Go back to Zinc Binding Sites List in 2c6c
Zinc binding site 2 out of 2 in the Membrane-Bound Glutamate Carboxypeptidase II (Gcpii) in Complex with Gpi-18431 (S)-2-(4-Iodobenzylphosphonomethyl)-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 Gpi-18431 (S)-2-(4-Iodobenzylphosphonomethyl)-Pentanedioic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1752

b:23.4
occ:1.00
 O1 A:24I1767 1.9 21.0 1.0
OD2 A:ASP453 2.0 22.1 1.0
OD1 A:ASP387 2.0 25.9 1.0
NE2 A:HIS377 2.1 20.8 1.0
CG A:ASP453 2.7 22.6 1.0
OD1 A:ASP453 2.8 24.8 1.0
CG A:ASP387 3.0 26.5 1.0
CE1 A:HIS377 3.0 22.1 1.0
CD2 A:HIS377 3.0 22.8 1.0
OD2 A:ASP387 3.3 23.6 1.0
P1 A:24I1767 3.4 22.0 1.0
OE2 A:GLU424 3.5 23.3 1.0
OE2 A:GLU425 3.7 19.1 1.0
OE1 A:GLU424 3.7 19.2 1.0
ZN A:ZN1751 3.8 23.2 1.0
C4 A:24I1767 3.8 33.7 1.0
CD A:GLU424 3.9 21.5 1.0
O2 A:24I1767 4.0 23.7 1.0
ND1 A:HIS377 4.1 22.3 1.0
CG A:HIS377 4.2 21.7 1.0
CB A:ASP453 4.2 22.4 1.0
C6 A:24I1767 4.3 25.2 1.0
C8 A:24I1767 4.3 28.4 1.0
CB A:PRO388 4.3 24.1 1.0
ND2 A:ASN519 4.3 23.8 1.0
CB A:ASP387 4.4 26.1 1.0
CD A:GLU425 4.5 20.7 1.0
C2 A:24I1767 4.5 34.8 1.0
C7 A:24I1767 4.6 21.2 1.0
CA A:PRO388 4.6 23.7 1.0
CA A:ASP387 4.7 23.6 1.0
N A:PRO388 4.7 23.7 1.0
C A:ASP387 4.7 23.1 1.0
OG A:SER454 4.9 31.6 1.0
OE1 A:GLU425 5.0 21.4 1.0

Reference:

J.R.Mesters, C.Barinka, W.Li, T.Tsukamoto, P.Majer, B.S.Slusher, J.Konvalinka, R.Hilgenfeld. Structure of Glutamate Carboxypeptidase II, A Drug Target in Neuronal Damage and Prostate Cancer. Embo J. V. 25 1375 2006.
ISSN: ISSN 0261-4189
PubMed: 16467855
DOI: 10.1038/SJ.EMBOJ.7600969
Page generated: Wed Oct 16 22:12:43 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy