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Zinc 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
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 JHU241 (pdb code 5d29). 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 JHU241, PDB code: 5d29:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5d29

Go back to Zinc Binding Sites List in 5d29
Zinc binding site 1 out of 2 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 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 JHU241 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn813

b:21.0
occ:1.00
 OD2 A:ASP387 2.0 22.3 1.0
OE2 A:GLU425 2.0 19.8 1.0
OAC A:5Q1818 2.1 23.4 1.0
NE2 A:HIS553 2.1 19.4 1.0
OAD A:5Q1818 2.2 20.3 1.0
OE1 A:GLU425 2.5 20.0 1.0
CD A:GLU425 2.6 20.2 1.0
CAQ A:5Q1818 2.9 22.8 1.0
NAN A:5Q1818 2.9 19.9 1.0
CG A:ASP387 3.0 21.6 1.0
CE1 A:HIS553 3.1 19.9 1.0
CD2 A:HIS553 3.1 19.8 1.0
OD1 A:ASP387 3.4 23.2 1.0
ZN A:ZN814 3.4 21.3 1.0
O A:HOH974 3.6 25.9 1.0
CE1 A:TYR552 4.0 22.1 1.0
O A:HOH955 4.0 22.4 1.0
CG A:GLU425 4.1 16.5 1.0
OH A:TYR552 4.1 21.2 1.0
OE1 A:GLU424 4.2 21.2 1.0
ND1 A:HIS553 4.2 21.0 1.0
CG A:HIS553 4.2 21.2 1.0
CB A:ASP387 4.3 23.0 1.0
CH3 A:ACT817 4.4 29.2 1.0
CAK A:5Q1818 4.4 22.9 1.0
NE2 A:HIS377 4.4 16.3 1.0
CZ A:TYR552 4.5 23.4 1.0
CE1 A:HIS377 4.6 19.1 1.0
O A:ACT817 4.6 31.4 1.0
CD1 A:TRP381 4.7 20.5 1.0
C A:ACT817 4.7 31.0 1.0
NE1 A:TRP381 4.8 22.4 1.0
CD1 A:TYR552 5.0 21.1 1.0

Zinc binding site 2 out of 2 in 5d29

Go back to Zinc Binding Sites List in 5d29
Zinc binding site 2 out of 2 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 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 JHU241 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn814

b:21.3
occ:1.00
 OAD A:5Q1818 1.9 20.3 1.0
NE2 A:HIS377 2.0 16.3 1.0
OD1 A:ASP387 2.1 23.2 1.0
O A:HOH974 2.1 25.9 1.0
OD2 A:ASP453 2.1 20.3 1.0
OD1 A:ASP453 2.5 21.6 1.0
CG A:ASP453 2.6 20.3 1.0
NAN A:5Q1818 2.9 19.9 1.0
CG A:ASP387 2.9 21.6 1.0
CD2 A:HIS377 3.0 17.2 1.0
CE1 A:HIS377 3.0 19.1 1.0
OD2 A:ASP387 3.2 22.3 1.0
ZN A:ZN813 3.4 21.0 1.0
OE2 A:GLU425 3.7 19.8 1.0
OE1 A:GLU424 3.8 21.2 1.0
CAQ A:5Q1818 3.8 22.8 1.0
OE2 A:GLU424 4.0 20.5 1.0
CD A:GLU424 4.1 22.6 1.0
ND1 A:HIS377 4.1 17.1 1.0
OAC A:5Q1818 4.1 23.4 1.0
CB A:ASP453 4.1 19.7 1.0
CG A:HIS377 4.1 16.8 1.0
CB A:ASP387 4.2 23.0 1.0
CB A:PRO388 4.3 19.6 1.0
OAF A:5Q1818 4.4 27.0 1.0
ND2 A:ASN519 4.4 18.0 1.0
CD A:GLU425 4.5 20.2 1.0
CA A:ASP387 4.5 21.1 1.0
OG A:SER454 4.6 24.2 1.0
CA A:PRO388 4.6 19.4 1.0
O A:HOH1002 4.6 29.6 1.0
N A:PRO388 4.7 20.5 1.0
C A:ASP387 4.7 21.7 1.0
OE1 A:GLU425 4.8 20.0 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 Dec 16 06:07:47 2020

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