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Zinc in PDB 5of0: X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii), the E424M Inactive Mutant, in Complex with A Inhibitor Cfbzog

Enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii), the E424M Inactive Mutant, in Complex with A Inhibitor Cfbzog

All present enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii), the E424M Inactive Mutant, in Complex with A Inhibitor Cfbzog:
3.4.17.21;

Protein crystallography data

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii), the E424M Inactive Mutant, in Complex with A Inhibitor Cfbzog, PDB code: 5of0 was solved by Z.Novakova, L.Motlova, C.Barinka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.25 / 1.48
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.467, 130.461, 159.574, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 17.2

Other elements in 5of0:

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii), the E424M Inactive Mutant, in Complex with A Inhibitor Cfbzog also contains other interesting chemical elements:

Fluorine (F) 1 atom
Calcium (Ca) 1 atom
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii), the E424M Inactive Mutant, in Complex with A Inhibitor Cfbzog (pdb code 5of0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii), the E424M Inactive Mutant, in Complex with A Inhibitor Cfbzog, PDB code: 5of0:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5of0

Go back to Zinc Binding Sites List in 5of0
Zinc binding site 1 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii), the E424M Inactive Mutant, in Complex with A Inhibitor Cfbzog


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii), the E424M Inactive Mutant, in Complex with A Inhibitor Cfbzog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn818

b:29.9
occ:1.00
O A:HOH1282 1.9 29.3 1.0
NE2 A:HIS553 2.0 27.9 1.0
OE2 A:GLU425 2.0 29.1 1.0
OD2 A:ASP387 2.0 31.9 1.0
OE1 A:GLU425 2.5 29.1 1.0
CD A:GLU425 2.6 30.5 1.0
OAE A:9TB822 2.9 33.0 1.0
CG A:ASP387 2.9 30.3 1.0
CE1 A:HIS553 3.0 27.7 1.0
CD2 A:HIS553 3.1 29.1 1.0
ZN A:ZN819 3.3 28.6 1.0
OD1 A:ASP387 3.3 27.6 1.0
CBA A:9TB822 3.8 33.6 1.0
O A:HOH1039 4.0 30.0 1.0
CE1 A:TYR552 4.1 30.5 1.0
ND1 A:HIS553 4.1 29.1 1.0
CG A:GLU425 4.1 28.9 1.0
CG A:HIS553 4.2 28.6 1.0
CBE A:9TB822 4.2 30.8 1.0
CB A:ASP387 4.3 30.6 1.0
NAV A:9TB822 4.3 30.7 1.0
OH A:TYR552 4.5 31.0 1.0
NE2 A:HIS377 4.5 27.8 1.0
CD1 A:TRP381 4.6 29.4 1.0
CE1 A:HIS377 4.6 27.9 1.0
N A:9TB822 4.7 33.6 1.0
CZ A:TYR552 4.7 31.2 1.0
CAY A:9TB822 4.7 30.7 1.0
NE1 A:TRP381 4.8 29.9 1.0
SD A:MET424 4.8 30.1 1.0
CA A:9TB822 4.9 38.3 1.0
OAC A:9TB822 4.9 30.0 1.0
CD1 A:TYR552 5.0 32.6 1.0

Zinc binding site 2 out of 2 in 5of0

Go back to Zinc Binding Sites List in 5of0
Zinc binding site 2 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii), the E424M Inactive Mutant, in Complex with A Inhibitor Cfbzog


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii), the E424M Inactive Mutant, in Complex with A Inhibitor Cfbzog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn819

b:28.6
occ:1.00
O A:HOH1282 1.9 29.3 1.0
OD1 A:ASP387 2.0 27.6 1.0
OD2 A:ASP453 2.0 29.5 1.0
NE2 A:HIS377 2.0 27.8 1.0
CG A:ASP453 2.7 32.5 1.0
OD1 A:ASP453 2.8 32.7 1.0
CG A:ASP387 2.9 30.3 1.0
CE1 A:HIS377 3.0 27.9 1.0
CD2 A:HIS377 3.1 27.3 1.0
ZN A:ZN818 3.3 29.9 1.0
OD2 A:ASP387 3.3 31.9 1.0
OE2 A:GLU425 3.7 29.1 1.0
CE A:MET424 3.7 29.3 1.0
SD A:MET424 4.0 30.1 1.0
ND1 A:HIS377 4.1 27.9 1.0
CB A:ASP453 4.1 30.6 1.0
CG A:HIS377 4.2 27.1 1.0
CB A:ASP387 4.2 30.6 1.0
CB A:PRO388 4.4 28.4 1.0
ND2 A:ASN519 4.4 27.8 1.0
CD A:GLU425 4.4 30.5 1.0
CA A:ASP387 4.6 29.4 1.0
CA A:PRO388 4.6 28.9 1.0
OAE A:9TB822 4.6 33.0 1.0
C A:ASP387 4.7 29.5 1.0
OE1 A:GLU425 4.7 29.1 1.0
CBA A:9TB822 4.7 33.6 1.0
N A:PRO388 4.7 29.0 1.0
OG A:SER454 4.7 28.3 0.8
O A:HOH920 4.8 38.2 0.6
N A:9TB822 4.9 33.6 1.0
OXT A:9TB822 4.9 38.1 1.0
CA A:9TB822 4.9 38.3 1.0

Reference:

R.Nakajima, Z.Novakova, W.Tueckmantel, L.Motlova, C.Barinka, A.P.Kozikowski. 2-Aminoadipic Acid-C(O)-Glutamate Based Prostate-Specific Membrane Antigen Ligands For Potential Use As Theranostics. Acs Med Chem Lett V. 9 1099 2018.
ISSN: ISSN 1948-5875
PubMed: 30429952
DOI: 10.1021/ACSMEDCHEMLETT.8B00318
Page generated: Wed Dec 16 06:38:00 2020

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