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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

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