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Calcium 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
Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total only one binding site of Calcium was 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:

Calcium binding site 1 out of 1 in 3bxm

Go back to Calcium Binding Sites List in 3bxm
Calcium binding site 1 out of 1 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 Calcium with other atoms in the Ca 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:Ca1753

b:18.6
occ:1.00
 O A:TYR272 2.3 19.4 1.0
OE2 A:GLU436 2.3 19.9 1.0
O A:HOH1772 2.4 20.2 1.0
O A:THR269 2.4 19.4 1.0
OE2 A:GLU433 2.5 18.7 1.0
OE1 A:GLU433 2.5 18.4 1.0
OG1 A:THR269 2.5 18.4 1.0
CD A:GLU433 2.9 18.5 1.0
C A:THR269 3.3 18.2 1.0
CB A:THR269 3.3 19.6 1.0
C A:TYR272 3.4 19.3 1.0
CD A:GLU436 3.4 18.2 1.0
OE1 A:GLU436 3.9 19.0 1.0
CA A:THR269 4.0 19.0 1.0
N A:TYR272 4.0 19.7 1.0
CA A:PRO273 4.2 20.4 1.0
CB A:ASP266 4.2 20.4 1.0
N A:PRO270 4.3 19.3 1.0
N A:ALA274 4.3 19.5 1.0
N A:PRO273 4.3 20.2 1.0
CA A:TYR272 4.3 20.3 1.0
CG A:GLU433 4.4 17.1 1.0
C A:PRO273 4.4 21.3 1.0
N A:ASP266 4.5 17.7 1.0
CA A:PRO270 4.5 18.8 1.0
N A:GLY271 4.5 19.9 1.0
O A:ALA264 4.6 21.7 1.0
O A:ASP266 4.6 20.0 1.0
N A:THR269 4.7 19.4 1.0
CG A:GLU436 4.7 15.9 1.0
CG2 A:THR269 4.7 20.5 1.0
C A:PRO270 4.8 20.0 1.0
OD2 A:ASP266 4.8 21.4 1.0
CB A:GLU436 4.9 18.7 1.0
CA A:ASP266 4.9 19.0 1.0
CB A:ALA274 4.9 20.7 1.0
C A:GLY271 5.0 21.0 1.0
CA A:GLU433 5.0 17.1 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: Tue Jul 8 11:15:40 2025

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