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Zinc in PDB 4ome: X-Ray Structure of Human Glutamate Carboxypeptidase II in Complex with Dccbl, A Urea Based Inhibitor with Distal Carborane Moiety

Enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II in Complex with Dccbl, A Urea Based Inhibitor with Distal Carborane Moiety

All present enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II in Complex with Dccbl, A Urea Based Inhibitor with Distal Carborane Moiety:
3.4.17.21;

Protein crystallography data

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II in Complex with Dccbl, A Urea Based Inhibitor with Distal Carborane Moiety, PDB code: 4ome was solved by C.Barinka, J.Ptacek, Z.Novakova, Y.Byun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.43 / 1.79
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.316, 130.564, 158.073, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 18.4

Other elements in 4ome:

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II in Complex with Dccbl, A Urea Based Inhibitor with Distal Carborane Moiety 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 in Complex with Dccbl, A Urea Based Inhibitor with Distal Carborane Moiety (pdb code 4ome). 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 in Complex with Dccbl, A Urea Based Inhibitor with Distal Carborane Moiety, PDB code: 4ome:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4ome

Go back to Zinc Binding Sites List in 4ome
Zinc binding site 1 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II in Complex with Dccbl, A Urea Based Inhibitor with Distal Carborane Moiety


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 in Complex with Dccbl, A Urea Based Inhibitor with Distal Carborane Moiety within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn815

b:10.8
occ:1.00
O A:HOH1454 2.0 10.1 1.0
NE2 A:HIS553 2.0 16.6 1.0
OD2 A:ASP387 2.1 16.9 1.0
OE2 A:GLU425 2.2 14.9 1.0
OE1 A:GLU425 2.4 14.4 1.0
OD A:DGQ819 2.5 17.5 1.0
CD A:GLU425 2.6 14.7 1.0
CE1 A:HIS553 2.9 16.1 1.0
CG A:ASP387 3.0 16.8 1.0
CD2 A:HIS553 3.1 16.2 1.0
ZN A:ZN816 3.3 10.9 1.0
CJ A:DGQ819 3.4 18.6 1.0
OD1 A:ASP387 3.4 15.7 1.0
NC A:DGQ819 3.9 15.9 1.0
CE1 A:TYR552 4.1 16.4 1.0
ND1 A:HIS553 4.1 16.1 1.0
CK A:DGQ819 4.1 15.7 1.0
CG A:GLU425 4.1 14.3 1.0
OE1 A:GLU424 4.1 14.2 1.0
O A:HOH915 4.1 10.8 1.0
CG A:HIS553 4.2 16.2 1.0
CB A:ASP387 4.3 16.5 1.0
NB A:DGQ819 4.3 16.2 1.0
OH A:TYR552 4.3 16.2 1.0
CH A:DGQ819 4.5 21.0 1.0
CM A:DGQ819 4.6 16.5 1.0
NE2 A:HIS377 4.6 13.6 1.0
CZ A:TYR552 4.6 16.6 1.0
CD1 A:TRP381 4.7 16.1 1.0
CE1 A:HIS377 4.8 13.4 1.0
NE1 A:TRP381 4.8 16.4 1.0
OG A:DGQ819 4.8 17.2 1.0
OD2 A:ASP453 4.8 17.9 1.0

Zinc binding site 2 out of 2 in 4ome

Go back to Zinc Binding Sites List in 4ome
Zinc binding site 2 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II in Complex with Dccbl, A Urea Based Inhibitor with Distal Carborane Moiety


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 in Complex with Dccbl, A Urea Based Inhibitor with Distal Carborane Moiety within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn816

b:10.9
occ:1.00
O A:HOH1454 1.9 10.1 1.0
OD2 A:ASP453 2.0 17.9 1.0
OD1 A:ASP387 2.0 15.7 1.0
NE2 A:HIS377 2.0 13.6 1.0
CG A:ASP453 2.7 17.8 1.0
OD1 A:ASP453 2.8 18.5 1.0
CG A:ASP387 2.9 16.8 1.0
CE1 A:HIS377 3.0 13.4 1.0
CD2 A:HIS377 3.1 13.6 1.0
OD2 A:ASP387 3.3 16.9 1.0
ZN A:ZN815 3.3 10.8 1.0
OE2 A:GLU425 3.6 14.9 1.0
OE1 A:GLU424 3.7 14.2 1.0
CD A:GLU424 4.1 14.1 1.0
ND1 A:HIS377 4.1 14.1 1.0
CB A:ASP453 4.2 16.3 1.0
CG A:HIS377 4.2 13.9 1.0
OE2 A:GLU424 4.2 13.5 1.0
ND2 A:ASN519 4.3 15.1 1.0
CB A:ASP387 4.3 16.5 1.0
CD A:GLU425 4.3 14.7 1.0
CB A:PRO388 4.3 15.2 1.0
CJ A:DGQ819 4.5 18.6 1.0
OD A:DGQ819 4.5 17.5 1.0
CA A:PRO388 4.6 15.3 1.0
CA A:ASP387 4.6 16.3 1.0
OE1 A:GLU425 4.6 14.4 1.0
N A:PRO388 4.7 15.7 1.0
C A:ASP387 4.7 15.9 1.0
O A:HOH1455 4.7 15.9 1.0
NB A:DGQ819 4.7 16.2 1.0
CH A:DGQ819 4.8 21.0 1.0
OG A:SER454 4.8 16.3 0.8
NC A:DGQ819 4.8 15.9 1.0
CG A:GLU424 5.0 13.7 1.0

Reference:

C.Barinka, J.Ptacek, Z.Novakova, Y.Byun. X-Ray Structure of Human Glutamate Carboxypeptidase II in Complex with Dccbl, A Urea Based Inhibitor with Distal Carborane Moiety To Be Published.
Page generated: Wed Dec 16 05:39:16 2020

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