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Zinc in PDB 5ely: X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Hydroxamate Inhibitor JHU242

Enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Hydroxamate Inhibitor JHU242

All present enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Hydroxamate Inhibitor JHU242:
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 JHU242, PDB code: 5ely 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) 40.00 / 1.81
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.060, 130.827, 158.386, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 19.9

Other elements in 5ely:

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Hydroxamate Inhibitor JHU242 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 (Gcpii) in Complex with A Hydroxamate Inhibitor JHU242 (pdb code 5ely). 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 (Gcpii) in Complex with A Hydroxamate Inhibitor JHU242, PDB code: 5ely:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5ely

Go back to Zinc Binding Sites List in 5ely
Zinc binding site 1 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Hydroxamate Inhibitor JHU242


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 (Gcpii) in Complex with A Hydroxamate Inhibitor JHU242 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:21.2
occ:1.00
 OE2 A:GLU425 2.0 19.6 1.0
OD2 A:ASP387 2.0 22.2 1.0
OAC A:5PU817 2.1 24.9 1.0
NE2 A:HIS553 2.1 20.8 1.0
OAD A:5PU817 2.3 19.8 1.0
OE1 A:GLU425 2.5 20.1 1.0
CD A:GLU425 2.6 17.1 1.0
CAQ A:5PU817 2.9 22.0 1.0
NAN A:5PU817 3.0 22.4 1.0
CG A:ASP387 3.0 22.5 1.0
CE1 A:HIS553 3.0 19.3 1.0
CD2 A:HIS553 3.1 22.9 1.0
OD1 A:ASP387 3.3 20.9 1.0
ZN A:ZN802 3.4 20.4 1.0
O A:HOH1126 3.6 21.2 1.0
CE1 A:TYR552 4.0 21.2 1.0
OXT A:ACT818 4.1 39.2 1.0
O A:HOH950 4.1 21.8 1.0
CG A:GLU425 4.1 17.0 1.0
ND1 A:HIS553 4.2 21.1 1.0
OH A:TYR552 4.2 21.5 1.0
OE1 A:GLU424 4.2 19.5 1.0
CG A:HIS553 4.2 21.6 1.0
CB A:ASP387 4.3 22.4 1.0
CAK A:5PU817 4.4 20.3 1.0
NE2 A:HIS377 4.5 18.2 1.0
CZ A:TYR552 4.5 21.9 1.0
C A:ACT818 4.6 36.0 1.0
CE1 A:HIS377 4.7 18.1 1.0
CD1 A:TRP381 4.7 21.6 1.0
NE1 A:TRP381 4.8 23.3 1.0
CAL A:5PU817 4.9 22.2 1.0
O A:ACT818 5.0 37.6 1.0

Zinc binding site 2 out of 2 in 5ely

Go back to Zinc Binding Sites List in 5ely
Zinc binding site 2 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Hydroxamate Inhibitor JHU242


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 (Gcpii) in Complex with A Hydroxamate Inhibitor JHU242 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:20.4
occ:1.00
 OAD A:5PU817 2.0 19.8 1.0
NE2 A:HIS377 2.0 18.2 1.0
OD1 A:ASP387 2.1 20.9 1.0
OD2 A:ASP453 2.1 18.9 1.0
O A:HOH1126 2.2 21.2 1.0
OD1 A:ASP453 2.5 22.6 1.0
CG A:ASP453 2.6 21.1 1.0
CG A:ASP387 2.9 22.5 1.0
NAN A:5PU817 3.0 22.4 1.0
CE1 A:HIS377 3.0 18.1 1.0
CD2 A:HIS377 3.0 16.0 1.0
OD2 A:ASP387 3.2 22.2 1.0
ZN A:ZN801 3.4 21.2 1.0
OE2 A:GLU425 3.7 19.6 1.0
OE1 A:GLU424 3.8 19.5 1.0
CAQ A:5PU817 3.8 22.0 1.0
OAC A:5PU817 4.1 24.9 1.0
ND1 A:HIS377 4.1 17.3 1.0
CB A:ASP453 4.1 18.8 1.0
OE2 A:GLU424 4.2 21.2 1.0
CD A:GLU424 4.2 21.9 1.0
CG A:HIS377 4.2 14.5 1.0
CB A:ASP387 4.2 22.4 1.0
CB A:PRO388 4.3 19.5 1.0
ND2 A:ASN519 4.4 18.3 1.0
CD A:GLU425 4.5 17.1 1.0
CA A:ASP387 4.5 21.2 1.0
O A:HOH1159 4.5 26.6 1.0
OG A:SER454 4.5 21.8 1.0
CA A:PRO388 4.5 19.2 1.0
N A:PRO388 4.7 19.9 1.0
C A:ASP387 4.7 20.2 1.0
O A:HOH1113 4.7 24.2 1.0
OE1 A:GLU425 4.9 20.1 1.0
N A:SER454 5.0 21.4 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: Sun Oct 27 15:23:20 2024

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