Atomistry » Zinc » PDB 6fdw-6fjk » 6fe5
Atomistry »
  Zinc »
    PDB 6fdw-6fjk »
      6fe5 »

Zinc in PDB 6fe5: X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) - the E424M Inactive Mutant, in Complex with A Inhibitor Jhu 2249

Enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) - the E424M Inactive Mutant, in Complex with A Inhibitor Jhu 2249

All present enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) - the E424M Inactive Mutant, in Complex with A Inhibitor Jhu 2249:
3.4.17.21;

Protein crystallography data

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) - the E424M Inactive Mutant, in Complex with A Inhibitor Jhu 2249, PDB code: 6fe5 was solved by C.Barinka, Z.Novakova, L.Motlova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.52
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.702, 130.687, 159.829, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 17.9

Other elements in 6fe5:

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) - the E424M Inactive Mutant, in Complex with A Inhibitor Jhu 2249 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) - the E424M Inactive Mutant, in Complex with A Inhibitor Jhu 2249 (pdb code 6fe5). 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) - the E424M Inactive Mutant, in Complex with A Inhibitor Jhu 2249, PDB code: 6fe5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6fe5

Go back to Zinc Binding Sites List in 6fe5
Zinc binding site 1 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) - the E424M Inactive Mutant, in Complex with A Inhibitor Jhu 2249


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) - the E424M Inactive Mutant, in Complex with A Inhibitor Jhu 2249 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn816

b:23.0
occ:1.00
O A:HOH1305 2.0 21.1 1.0
NE2 A:HIS553 2.0 20.2 1.0
OD2 A:ASP387 2.0 26.2 1.0
OE2 A:GLU425 2.1 21.7 1.0
OE1 A:GLU425 2.4 21.9 1.0
CD A:GLU425 2.6 22.2 1.0
OAF A:D6E821 2.9 23.5 1.0
CG A:ASP387 2.9 23.9 1.0
CE1 A:HIS553 3.0 21.0 1.0
CD2 A:HIS553 3.1 23.2 1.0
ZN A:ZN817 3.3 22.1 1.0
OD1 A:ASP387 3.3 20.9 1.0
CAR A:D6E821 3.7 24.5 1.0
CE1 A:TYR552 4.0 23.1 1.0
CA A:D6E821 4.1 23.6 1.0
ND1 A:HIS553 4.1 21.8 1.0
O A:HOH980 4.1 22.6 1.0
N A:D6E821 4.1 22.4 1.0
CG A:GLU425 4.1 21.4 1.0
CG A:HIS553 4.2 21.8 1.0
CB A:ASP387 4.3 23.1 1.0
OH A:TYR552 4.5 23.5 1.0
NE2 A:HIS377 4.5 21.1 1.0
NAN A:D6E821 4.5 23.6 1.0
CD1 A:TRP381 4.6 22.1 1.0
CZ A:TYR552 4.6 23.9 1.0
CE1 A:HIS377 4.7 20.6 1.0
C A:D6E821 4.7 25.1 1.0
NE1 A:TRP381 4.8 22.6 1.0
SD A:MET424 4.8 22.5 1.0
OXT A:D6E821 4.9 23.5 1.0
O A:HOH1171 4.9 32.2 1.0
CAU A:D6E821 4.9 25.0 1.0
CD1 A:TYR552 4.9 23.9 1.0
OD2 A:ASP453 5.0 21.5 1.0

Zinc binding site 2 out of 2 in 6fe5

Go back to Zinc Binding Sites List in 6fe5
Zinc binding site 2 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) - the E424M Inactive Mutant, in Complex with A Inhibitor Jhu 2249


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) - the E424M Inactive Mutant, in Complex with A Inhibitor Jhu 2249 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn817

b:22.1
occ:1.00
O A:HOH1305 1.8 21.1 1.0
OD2 A:ASP453 2.0 21.5 1.0
NE2 A:HIS377 2.0 21.1 1.0
OD1 A:ASP387 2.1 20.9 1.0
CG A:ASP453 2.7 23.1 1.0
OD1 A:ASP453 2.8 23.3 1.0
CG A:ASP387 3.0 23.9 1.0
CE1 A:HIS377 3.0 20.6 1.0
CD2 A:HIS377 3.1 20.7 1.0
ZN A:ZN816 3.3 23.0 1.0
OD2 A:ASP387 3.3 26.2 1.0
CE A:MET424 3.7 21.1 1.0
OE2 A:GLU425 3.7 21.7 1.0
SD A:MET424 4.0 22.5 1.0
ND1 A:HIS377 4.1 21.3 1.0
CB A:ASP453 4.1 21.3 1.0
CG A:HIS377 4.2 20.0 1.0
CB A:ASP387 4.2 23.1 1.0
CB A:PRO388 4.4 21.5 1.0
CD A:GLU425 4.4 22.2 1.0
O A:HOH1171 4.4 32.2 1.0
ND2 A:ASN519 4.4 20.1 1.0
CA A:ASP387 4.6 23.7 1.0
CA A:PRO388 4.6 21.5 1.0
OE1 A:GLU425 4.6 21.9 1.0
C A:ASP387 4.7 23.4 1.0
OAF A:D6E821 4.7 23.5 1.0
CAR A:D6E821 4.7 24.5 1.0
OG A:SER454 4.7 23.8 1.0
N A:PRO388 4.7 22.5 1.0
NAN A:D6E821 4.8 23.6 1.0
OAE A:D6E821 5.0 26.7 1.0

Reference:

C.Barinka, Z.Novakova, N.Hin, D.Bim, D.V.Ferraris, B.Duvall, G.Kabarriti, R.Tsukamoto, M.Budesinsky, L.Motlova, C.Rojas, B.S.Slusher, T.A.Rokob, L.Rulisek, T.Tsukamoto. Structural and Computational Basis For Potent Inhibition of Glutamate Carboxypeptidase II By Carbamate-Based Inhibitors. Bioorg.Med.Chem. V. 27 255 2019.
ISSN: ESSN 1464-3391
PubMed: 30552009
DOI: 10.1016/J.BMC.2018.11.022
Page generated: Wed Dec 16 11:47:27 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy