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Calcium in PDB 5d29: X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Hydroxamate Inhibitor JHU241

Enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Hydroxamate Inhibitor JHU241

All present enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Hydroxamate Inhibitor JHU241:
3.4.17.21;

Protein crystallography data

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Hydroxamate Inhibitor JHU241, PDB code: 5d29 was solved by C.Barinka, Z.Novakova, J.Pavlicek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.82 / 1.80
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 100.191, 130.459, 157.196, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 20.5

Other elements in 5d29:

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Hydroxamate Inhibitor JHU241 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 X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Hydroxamate Inhibitor JHU241 (pdb code 5d29). 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 X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Hydroxamate Inhibitor JHU241, PDB code: 5d29:

Calcium binding site 1 out of 1 in 5d29

Go back to Calcium Binding Sites List in 5d29
Calcium binding site 1 out of 1 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Hydroxamate Inhibitor JHU241


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Hydroxamate Inhibitor JHU241 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca815

b:17.4
occ:1.00
 OE2 A:GLU436 2.3 18.4 1.0
O A:TYR272 2.3 17.4 1.0
O A:THR269 2.4 19.8 1.0
O A:HOH962 2.4 18.3 1.0
OE2 A:GLU433 2.4 18.3 1.0
OG1 A:THR269 2.4 17.4 1.0
OE1 A:GLU433 2.4 19.6 1.0
CD A:GLU433 2.8 18.7 1.0
C A:THR269 3.3 19.5 1.0
CB A:THR269 3.3 20.2 1.0
CD A:GLU436 3.4 20.0 1.0
C A:TYR272 3.4 18.6 1.0
OE1 A:GLU436 3.8 18.2 1.0
CA A:THR269 3.9 19.3 1.0
N A:TYR272 4.0 18.6 1.0
CA A:PRO273 4.2 19.6 1.0
N A:PRO270 4.2 18.8 0.5
N A:ALA274 4.3 17.2 1.0
CB A:ASP266 4.3 18.4 1.0
N A:PRO270 4.3 18.8 0.5
N A:PRO273 4.3 19.0 1.0
CG A:GLU433 4.3 18.0 1.0
CA A:TYR272 4.4 19.3 1.0
CA A:PRO270 4.4 18.3 0.5
C A:PRO273 4.4 19.6 1.0
O A:ASP266 4.5 18.8 1.0
N A:GLY271 4.5 18.3 1.0
N A:ASP266 4.5 17.3 1.0
CA A:PRO270 4.5 18.2 0.5
N A:THR269 4.6 19.9 1.0
O A:ALA264 4.6 18.1 1.0
CG2 A:THR269 4.7 19.6 1.0
CG A:GLU436 4.7 17.6 1.0
C A:PRO270 4.7 17.9 0.5
C A:PRO270 4.7 17.9 0.5
OD2 A:ASP266 4.8 22.6 1.0
CA A:ASP266 4.9 19.0 1.0
CB A:GLU436 4.9 17.1 1.0
C A:GLY271 5.0 19.2 1.0
CB A:ALA274 5.0 19.0 1.0

Reference:

Z.Novakova, K.Wozniak, A.Jancarik, R.Rais, Y.Wu, J.Pavlicek, D.Ferraris, B.Havlinova, J.Ptacek, J.Vavra, N.Hin, C.Rojas, P.Majer, B.S.Slusher, T.Tsukamoto, C.Barinka. Unprecedented Binding Mode of Hydroxamate-Based Inhibitors of Glutamate Carboxypeptidase II: Structural Characterization and Biological Activity. J.Med.Chem. V. 59 4539 2016.
ISSN: ISSN 0022-2623
PubMed: 27074627
DOI: 10.1021/ACS.JMEDCHEM.5B01806
Page generated: Wed Jul 9 04:58:56 2025

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