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Zinc in PDB 3sje: X-Ray Structure of Human Glutamate Carboxypeptidase II (the E424A Inactive Mutant) in Complex with N-Acetyl-Aspartyl-Aminononanoic Acid

Enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (the E424A Inactive Mutant) in Complex with N-Acetyl-Aspartyl-Aminononanoic Acid

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

Protein crystallography data

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (the E424A Inactive Mutant) in Complex with N-Acetyl-Aspartyl-Aminononanoic Acid, PDB code: 3sje 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) 29.57 / 1.70
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.824, 130.231, 159.171, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 18.8

Other elements in 3sje:

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (the E424A Inactive Mutant) in Complex with N-Acetyl-Aspartyl-Aminononanoic 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 X-Ray Structure of Human Glutamate Carboxypeptidase II (the E424A Inactive Mutant) in Complex with N-Acetyl-Aspartyl-Aminononanoic Acid (pdb code 3sje). 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 (the E424A Inactive Mutant) in Complex with N-Acetyl-Aspartyl-Aminononanoic Acid, PDB code: 3sje:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3sje

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


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 (the E424A Inactive Mutant) in Complex with N-Acetyl-Aspartyl-Aminononanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1751

b:17.0
occ:1.00
 O A:HOH2157 2.0 20.1 1.0
NE2 A:HIS553 2.0 19.5 1.0
OD1 A:ASP387 2.1 24.4 1.0
OE2 A:GLU425 2.1 21.2 1.0
OAF A:SDR1 2.4 31.5 0.8
OE1 A:GLU425 2.5 25.8 1.0
CD A:GLU425 2.6 22.3 1.0
CE1 A:HIS553 3.0 22.4 1.0
CG A:ASP387 3.0 23.7 1.0
CD2 A:HIS553 3.1 21.4 1.0
CAU A:SDR1 3.1 35.1 0.8
ZN A:ZN1752 3.4 15.8 1.0
OD2 A:ASP387 3.4 20.0 1.0
NAP A:SDR1 3.8 31.8 0.8
N A:SDR1 3.8 33.9 0.8
CA A:SDR1 3.9 35.5 0.8
CAW A:SDR1 4.0 33.5 0.8
ND1 A:HIS553 4.1 20.2 1.0
O A:HOH2165 4.1 47.6 1.0
CE1 A:TYR552 4.1 27.8 1.0
CG A:GLU425 4.1 21.4 1.0
O A:HOH1815 4.2 16.0 1.0
CG A:HIS553 4.2 21.7 1.0
CB A:ASP387 4.3 22.4 1.0
OH A:TYR552 4.3 30.4 1.0
NE2 A:HIS377 4.5 20.1 1.0
C A:SDR1 4.5 34.5 0.8
CZ A:TYR552 4.7 26.6 1.0
CD1 A:TRP381 4.7 23.0 1.0
CE1 A:HIS377 4.7 19.6 1.0
CAR A:SDR1 4.7 39.5 0.8
NE1 A:TRP381 4.7 24.4 1.0
O A:SDR1 4.8 33.2 0.8

Zinc binding site 2 out of 2 in 3sje

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


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 (the E424A Inactive Mutant) in Complex with N-Acetyl-Aspartyl-Aminononanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1752

b:15.8
occ:1.00
 O A:HOH2157 1.9 20.1 1.0
OD2 A:ASP387 1.9 20.0 1.0
OD2 A:ASP453 2.0 24.0 1.0
NE2 A:HIS377 2.0 20.1 1.0
CG A:ASP453 2.7 25.3 1.0
OD1 A:ASP453 2.7 27.0 1.0
CG A:ASP387 2.9 23.7 1.0
CE1 A:HIS377 3.0 19.6 1.0
CD2 A:HIS377 3.0 18.3 1.0
OD1 A:ASP387 3.3 24.4 1.0
ZN A:ZN1751 3.4 17.0 1.0
OE2 A:GLU425 3.7 21.2 1.0
CAR A:SDR1 3.8 39.5 0.8
NAP A:SDR1 3.8 31.8 0.8
O A:HOH2165 3.8 47.6 1.0
OAC A:SDR1 4.1 41.6 0.8
CAW A:SDR1 4.1 33.5 0.8
ND1 A:HIS377 4.1 19.8 1.0
CG A:HIS377 4.1 18.7 1.0
CB A:ASP453 4.1 20.5 1.0
CB A:ASP387 4.2 22.4 1.0
CB A:PRO388 4.2 18.9 1.0
CAU A:SDR1 4.2 35.1 0.8
ND2 A:ASN519 4.4 24.7 1.0
CAB A:SDR1 4.4 40.6 0.8
CD A:GLU425 4.4 22.3 1.0
OAF A:SDR1 4.5 31.5 0.8
CA A:PRO388 4.5 20.2 1.0
CA A:ASP387 4.5 21.6 1.0
N A:PRO388 4.7 20.4 1.0
C A:ASP387 4.7 21.3 1.0
N A:SDR1 4.7 33.9 0.8
OE1 A:GLU425 4.8 25.8 1.0
OG A:SER454 4.8 27.0 1.0

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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