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Zinc in PDB 3sjg: Human Glutamate Carboxypeptidase II (E424A Inactive Mutant ) in Complex with N-Acetyl-Aspartyl-Aminooctanoic Acid

Enzymatic activity of Human Glutamate Carboxypeptidase II (E424A Inactive Mutant ) in Complex with N-Acetyl-Aspartyl-Aminooctanoic Acid

All present enzymatic activity of Human Glutamate Carboxypeptidase II (E424A Inactive Mutant ) in Complex with N-Acetyl-Aspartyl-Aminooctanoic Acid:
3.4.17.21;

Protein crystallography data

The structure of Human Glutamate Carboxypeptidase II (E424A Inactive Mutant ) in Complex with N-Acetyl-Aspartyl-Aminooctanoic Acid, PDB code: 3sjg was solved by A.Plechanovova, Y.Byun, G.Alquicer, L.Skultetyova, P.Mlcochova, A.Nemcova, H.Kim, M.Navratil, R.Mease, J.Lubkowski, M.Pomper, J.Konvalinka, L.Rulisek, C.Barinka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.05 / 1.65
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.266, 129.993, 159.121, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 18.3

Other elements in 3sjg:

The structure of Human Glutamate Carboxypeptidase II (E424A Inactive Mutant ) in Complex with N-Acetyl-Aspartyl-Aminooctanoic 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 Human Glutamate Carboxypeptidase II (E424A Inactive Mutant ) in Complex with N-Acetyl-Aspartyl-Aminooctanoic Acid (pdb code 3sjg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Glutamate Carboxypeptidase II (E424A Inactive Mutant ) in Complex with N-Acetyl-Aspartyl-Aminooctanoic Acid, PDB code: 3sjg:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3sjg

Go back to Zinc Binding Sites List in 3sjg
Zinc binding site 1 out of 2 in the Human Glutamate Carboxypeptidase II (E424A Inactive Mutant ) in Complex with N-Acetyl-Aspartyl-Aminooctanoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Glutamate Carboxypeptidase II (E424A Inactive Mutant ) in Complex with N-Acetyl-Aspartyl-Aminooctanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1751

b:16.6
occ:1.00
 O A:HOH2271 2.0 17.1 1.0
NE2 A:HIS553 2.0 20.2 1.0
OD2 A:ASP387 2.1 20.9 1.0
OE2 A:GLU425 2.1 20.4 1.0
OE1 A:GLU425 2.4 22.4 1.0
OAF A:SDR1 2.5 28.8 1.0
CD A:GLU425 2.6 20.0 1.0
CE1 A:HIS553 3.0 21.6 1.0
CG A:ASP387 3.0 22.5 1.0
CD2 A:HIS553 3.1 21.8 1.0
CAU A:SDR1 3.2 29.4 1.0
OD1 A:ASP387 3.3 20.4 1.0
ZN A:ZN1752 3.3 16.0 1.0
NAP A:SDR1 3.8 28.9 1.0
N A:SDR1 3.9 28.5 1.0
CA A:SDR1 4.0 29.2 1.0
CAW A:SDR1 4.1 29.1 1.0
ND1 A:HIS553 4.1 21.2 1.0
CG A:GLU425 4.1 20.0 1.0
CE1 A:TYR552 4.1 23.2 1.0
O A:HOH1815 4.1 16.8 1.0
CG A:HIS553 4.2 21.8 1.0
O A:HOH2272 4.2 33.0 1.0
CB A:ASP387 4.3 22.1 1.0
OH A:TYR552 4.4 25.2 1.0
NE2 A:HIS377 4.5 20.1 1.0
C A:SDR1 4.6 29.6 1.0
CAR A:SDR1 4.6 31.5 1.0
CD1 A:TRP381 4.6 23.0 1.0
CE1 A:HIS377 4.6 21.3 1.0
O A:SDR1 4.7 27.7 1.0
NE1 A:TRP381 4.7 23.7 1.0
CZ A:TYR552 4.7 23.4 1.0
OD2 A:ASP453 5.0 21.2 1.0
O A:HOH1808 5.0 17.5 1.0

Zinc binding site 2 out of 2 in 3sjg

Go back to Zinc Binding Sites List in 3sjg
Zinc binding site 2 out of 2 in the Human Glutamate Carboxypeptidase II (E424A Inactive Mutant ) in Complex with N-Acetyl-Aspartyl-Aminooctanoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Glutamate Carboxypeptidase II (E424A Inactive Mutant ) in Complex with N-Acetyl-Aspartyl-Aminooctanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1752

b:16.0
occ:1.00
 O A:HOH2271 2.0 17.1 1.0
OD2 A:ASP453 2.0 21.2 1.0
OD1 A:ASP387 2.0 20.4 1.0
NE2 A:HIS377 2.0 20.1 1.0
CG A:ASP453 2.7 23.8 1.0
OD1 A:ASP453 2.7 23.9 1.0
CG A:ASP387 2.9 22.5 1.0
CE1 A:HIS377 3.0 21.3 1.0
CD2 A:HIS377 3.0 17.5 1.0
OD2 A:ASP387 3.3 20.9 1.0
ZN A:ZN1751 3.3 16.6 1.0
CAR A:SDR1 3.6 31.5 1.0
OE2 A:GLU425 3.7 20.4 1.0
NAP A:SDR1 3.8 28.9 1.0
O A:HOH2272 3.9 33.0 1.0
OAC A:SDR1 4.0 33.2 1.0
CAW A:SDR1 4.1 29.1 1.0
ND1 A:HIS377 4.1 19.5 1.0
CB A:ASP453 4.1 20.1 1.0
CG A:HIS377 4.2 19.1 1.0
CAU A:SDR1 4.2 29.4 1.0
CB A:ASP387 4.2 22.1 1.0
O A:HOH2273 4.3 29.3 1.0
CB A:PRO388 4.3 19.3 1.0
CD A:GLU425 4.4 20.0 1.0
ND2 A:ASN519 4.4 21.1 1.0
OAF A:SDR1 4.5 28.8 1.0
CAB A:SDR1 4.5 32.3 1.0
CA A:ASP387 4.6 20.9 1.0
CA A:PRO388 4.6 19.6 1.0
C A:ASP387 4.7 20.9 1.0
OE1 A:GLU425 4.7 22.4 1.0
N A:PRO388 4.7 20.2 1.0
N A:SDR1 4.7 28.5 1.0
OG A:SER454 4.9 20.8 0.7

Reference:

A.Plechanovova, Y.Byun, G.Alquicer, L.Skultetyova, P.Mlcochova, A.Nemcova, H.J.Kim, M.Navratil, R.Mease, J.Lubkowski, M.Pomper, J.Konvalinka, L.Rulisek, C.Barinka. Novel Substrate-Based Inhibitors of Human Glutamate Carboxypeptidase II with Enhanced Lipophilicity. J.Med.Chem. V. 54 7535 2011.
ISSN: ISSN 0022-2623
PubMed: 21923190
DOI: 10.1021/JM200807M
Page generated: Sat Oct 26 15:51:41 2024

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