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Zinc in PDB 3bxm: Structure of An Inactive Mutant of Human Glutamate Carboxypeptidase II [Gcpii(E424A)] in Complex with N-Acetyl-Asp-Glu (Naag)

Enzymatic activity of Structure of An Inactive Mutant of Human Glutamate Carboxypeptidase II [Gcpii(E424A)] in Complex with N-Acetyl-Asp-Glu (Naag)

All present enzymatic activity of Structure of An Inactive Mutant of Human Glutamate Carboxypeptidase II [Gcpii(E424A)] in Complex with N-Acetyl-Asp-Glu (Naag):
3.4.17.21;

Protein crystallography data

The structure of Structure of An Inactive Mutant of Human Glutamate Carboxypeptidase II [Gcpii(E424A)] in Complex with N-Acetyl-Asp-Glu (Naag), PDB code: 3bxm was solved by J.Lubkowski, C.Barinka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.71
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.063, 129.801, 159.589, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 21.3

Other elements in 3bxm:

The structure of Structure of An Inactive Mutant of Human Glutamate Carboxypeptidase II [Gcpii(E424A)] in Complex with N-Acetyl-Asp-Glu (Naag) 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 Structure of An Inactive Mutant of Human Glutamate Carboxypeptidase II [Gcpii(E424A)] in Complex with N-Acetyl-Asp-Glu (Naag) (pdb code 3bxm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of An Inactive Mutant of Human Glutamate Carboxypeptidase II [Gcpii(E424A)] in Complex with N-Acetyl-Asp-Glu (Naag), PDB code: 3bxm:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3bxm

Go back to Zinc Binding Sites List in 3bxm
Zinc binding site 1 out of 2 in the Structure of An Inactive Mutant of Human Glutamate Carboxypeptidase II [Gcpii(E424A)] in Complex with N-Acetyl-Asp-Glu (Naag)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of An Inactive Mutant of Human Glutamate Carboxypeptidase II [Gcpii(E424A)] in Complex with N-Acetyl-Asp-Glu (Naag) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1751

b:21.7
occ:1.00
 O I:HOH2187 2.0 19.5 1.0
OD2 A:ASP387 2.0 20.9 1.0
NE2 A:HIS553 2.1 19.7 1.0
OE2 A:GLU425 2.1 18.7 1.0
OE1 A:GLU425 2.4 19.2 1.0
CD A:GLU425 2.6 17.7 1.0
O I:ASP2 2.6 22.5 1.0
CG A:ASP387 2.9 21.2 1.0
CE1 A:HIS553 3.0 20.6 1.0
CD2 A:HIS553 3.1 21.0 1.0
C I:ASP2 3.3 24.0 1.0
ZN A:ZN1752 3.3 21.6 1.0
OD1 A:ASP387 3.3 21.8 1.0
N I:GLU3 3.9 23.5 1.0
N I:ASP2 3.9 25.3 1.0
CA I:GLU3 4.0 24.8 1.0
CG A:GLU425 4.1 17.8 1.0
CA I:ASP2 4.1 22.5 1.0
ND1 A:HIS553 4.1 19.2 1.0
O A:HOH1782 4.2 23.6 1.0
CE1 A:TYR552 4.2 20.9 1.0
CG A:HIS553 4.2 19.4 1.0
CB A:ASP387 4.3 20.9 1.0
O A:HOH2210 4.3 33.7 1.0
OH A:TYR552 4.5 22.7 1.0
C I:GLU3 4.5 25.5 1.0
NE2 A:HIS377 4.5 19.4 1.0
CD1 A:TRP381 4.6 20.0 1.0
C I:ACE1 4.7 27.1 1.0
CE1 A:HIS377 4.7 19.5 1.0
CZ A:TYR552 4.7 21.5 1.0
O I:GLU3 4.8 25.2 1.0
NE1 A:TRP381 4.8 20.4 1.0
OD2 A:ASP453 5.0 23.5 1.0
CH3 I:ACE1 5.0 26.8 1.0

Zinc binding site 2 out of 2 in 3bxm

Go back to Zinc Binding Sites List in 3bxm
Zinc binding site 2 out of 2 in the Structure of An Inactive Mutant of Human Glutamate Carboxypeptidase II [Gcpii(E424A)] in Complex with N-Acetyl-Asp-Glu (Naag)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of An Inactive Mutant of Human Glutamate Carboxypeptidase II [Gcpii(E424A)] in Complex with N-Acetyl-Asp-Glu (Naag) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1752

b:21.6
occ:1.00
 OD1 A:ASP387 2.0 21.8 1.0
O I:HOH2187 2.0 19.5 1.0
OD2 A:ASP453 2.0 23.5 1.0
NE2 A:HIS377 2.0 19.4 1.0
CG A:ASP453 2.7 23.0 1.0
OD1 A:ASP453 2.8 24.7 1.0
CG A:ASP387 2.9 21.2 1.0
CE1 A:HIS377 3.0 19.5 1.0
CD2 A:HIS377 3.1 19.7 1.0
OD2 A:ASP387 3.2 20.9 1.0
ZN A:ZN1751 3.3 21.7 1.0
OE2 A:GLU425 3.7 18.7 1.0
C I:ACE1 3.9 27.1 1.0
O A:HOH2210 3.9 33.7 1.0
N I:ASP2 4.0 25.3 1.0
O I:ACE1 4.1 28.2 1.0
ND1 A:HIS377 4.1 20.8 1.0
CA I:ASP2 4.2 22.5 1.0
CG A:HIS377 4.2 19.9 1.0
CB A:ASP453 4.2 21.3 1.0
CB A:ASP387 4.3 20.9 1.0
O A:HOH2211 4.3 26.2 1.0
C I:ASP2 4.3 24.0 1.0
CB A:PRO388 4.3 19.3 1.0
CD A:GLU425 4.4 17.7 1.0
CH3 I:ACE1 4.4 26.8 1.0
ND2 A:ASN519 4.5 21.4 1.0
O I:ASP2 4.6 22.5 1.0
OE1 A:GLU425 4.6 19.2 1.0
CA A:PRO388 4.6 19.8 1.0
CA A:ASP387 4.6 19.7 1.0
N A:PRO388 4.7 20.0 1.0
C A:ASP387 4.7 19.9 1.0
N I:GLU3 4.7 23.5 1.0
OG A:SER454 5.0 22.7 1.0

Reference:

V.Klusak, C.Barinka, A.Plechanovova, P.Mlcochova, J.Konvalinka, L.Rulisek, J.Lubkowski. Reaction Mechanism of Glutamate Carboxypeptidase II Revealed By Mutagenesis, X-Ray Crystallography, and Computational Methods. Biochemistry V. 48 4126 2009.
ISSN: ISSN 0006-2960
PubMed: 19301871
DOI: 10.1021/BI900220S
Page generated: Wed Dec 16 04:09:51 2020

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