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

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

All present enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (the E424A Inactive Mutant) in Complex with N-Acetyl-Aspartyl-Methionine:
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-Methionine, PDB code: 3sjx 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) 28.21 / 1.66
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.539, 129.937, 159.194, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 20.4

Other elements in 3sjx:

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

Zinc binding site 1 out of 2 in 3sjx

Go back to Zinc Binding Sites List in 3sjx
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-Methionine


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-Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1751

b:14.7
occ:1.00
 O A:HOH2214 2.0 13.5 1.0
OD2 A:ASP387 2.0 19.6 1.0
NE2 A:HIS553 2.1 21.0 1.0
OE2 A:GLU425 2.1 18.9 1.0
OE1 A:GLU425 2.4 20.0 1.0
CD A:GLU425 2.6 19.2 1.0
OAF A:QRG1 2.7 24.4 1.0
CG A:ASP387 3.0 20.2 1.0
CE1 A:HIS553 3.0 20.6 1.0
CD2 A:HIS553 3.1 21.5 1.0
ZN A:ZN1752 3.3 14.1 1.0
OD1 A:ASP387 3.3 19.3 1.0
CAR A:QRG1 3.4 26.2 1.0
NAL A:QRG1 3.9 23.0 1.0
N A:QRG1 4.1 24.2 1.0
CA A:QRG1 4.1 25.4 1.0
CG A:GLU425 4.1 18.4 1.0
ND1 A:HIS553 4.1 19.4 1.0
O A:HOH1814 4.2 13.4 1.0
CAT A:QRG1 4.2 23.7 1.0
CG A:HIS553 4.2 21.5 1.0
O A:HOH2191 4.2 18.5 1.0
CE1 A:TYR552 4.3 22.9 1.0
CB A:ASP387 4.3 20.1 1.0
NE2 A:HIS377 4.5 17.6 1.0
CD1 A:TRP381 4.6 21.0 1.0
OH A:TYR552 4.6 22.7 1.0
NE1 A:TRP381 4.6 23.7 1.0
CAO A:QRG1 4.7 29.1 1.0
CE1 A:HIS377 4.7 18.3 1.0
C A:QRG1 4.7 25.3 1.0
OXT A:QRG1 4.7 25.2 1.0
CZ A:TYR552 4.9 20.9 1.0
OD2 A:ASP453 5.0 18.9 1.0

Zinc binding site 2 out of 2 in 3sjx

Go back to Zinc Binding Sites List in 3sjx
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-Methionine


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-Methionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1752

b:14.1
occ:1.00
 O A:HOH2214 1.9 13.5 1.0
OD1 A:ASP387 2.0 19.3 1.0
OD2 A:ASP453 2.0 18.9 1.0
NE2 A:HIS377 2.0 17.6 1.0
CG A:ASP453 2.7 19.5 1.0
OD1 A:ASP453 2.8 21.7 1.0
CG A:ASP387 2.9 20.2 1.0
CE1 A:HIS377 3.0 18.3 1.0
CD2 A:HIS377 3.0 16.4 1.0
ZN A:ZN1751 3.3 14.7 1.0
OD2 A:ASP387 3.3 19.6 1.0
OE2 A:GLU425 3.7 18.9 1.0
CAO A:QRG1 3.8 29.1 1.0
NAL A:QRG1 3.9 23.0 1.0
O A:HOH2191 3.9 18.5 1.0
OAC A:QRG1 4.1 29.8 1.0
ND1 A:HIS377 4.1 17.7 1.0
CAT A:QRG1 4.2 23.7 1.0
CB A:ASP453 4.2 18.3 1.0
CG A:HIS377 4.2 17.1 1.0
O A:HOH2219 4.2 25.4 1.0
CB A:ASP387 4.2 20.1 1.0
CB A:PRO388 4.3 17.7 1.0
CD A:GLU425 4.3 19.2 1.0
CAB A:QRG1 4.4 26.8 1.0
CAR A:QRG1 4.4 26.2 1.0
ND2 A:ASN519 4.4 19.4 1.0
OAF A:QRG1 4.6 24.4 1.0
CA A:ASP387 4.6 19.1 1.0
OE1 A:GLU425 4.6 20.0 1.0
CA A:PRO388 4.6 17.6 1.0
C A:ASP387 4.7 19.4 1.0
N A:PRO388 4.7 18.3 1.0
N A:QRG1 4.8 24.2 1.0
OG A:SER454 5.0 18.5 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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