Atomistry » Zinc » PDB 5ehf-5evd » 5ely
Atomistry »
  Zinc »
    PDB 5ehf-5evd »
      5ely »

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: Wed Dec 16 06:10:09 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy