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Zinc in PDB 3d7d: A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A Urea-Based Inhibitor

Enzymatic activity of A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A Urea-Based Inhibitor

All present enzymatic activity of A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A Urea-Based Inhibitor:
3.4.17.21;

Protein crystallography data

The structure of A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A Urea-Based Inhibitor, PDB code: 3d7d was solved by J.Lubkowski, C.Barinka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.69
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.930, 130.497, 159.187, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 19.9

Other elements in 3d7d:

The structure of A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A Urea-Based Inhibitor also contains other interesting chemical elements:

Fluorine (F) 1 atom
Chlorine (Cl) 1 atom
Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A Urea-Based Inhibitor (pdb code 3d7d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A Urea-Based Inhibitor, PDB code: 3d7d:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3d7d

Go back to Zinc Binding Sites List in 3d7d
Zinc binding site 1 out of 2 in the A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A Urea-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A Urea-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1751

b:20.2
occ:1.00
 O A:HOH2378 2.0 18.1 1.0
OD2 A:ASP387 2.0 20.4 1.0
NE2 A:HIS553 2.1 17.6 1.0
OE2 A:GLU425 2.2 17.6 1.0
OE1 A:GLU425 2.5 16.9 1.0
CD A:GLU425 2.6 15.4 1.0
O27 A:FBD1 2.7 18.5 1.0
CE1 A:HIS553 3.0 18.0 1.0
CG A:ASP387 3.0 20.7 1.0
CD2 A:HIS553 3.1 18.4 1.0
ZN A:ZN1752 3.3 19.9 1.0
OD1 A:ASP387 3.3 20.2 1.0
C11 A:FBD1 3.5 19.9 1.0
C6 A:FBD1 4.0 20.0 1.0
CE1 A:TYR552 4.0 17.6 1.0
N10 A:FBD1 4.0 19.6 1.0
OE1 A:GLU424 4.1 19.3 1.0
ND1 A:HIS553 4.1 15.6 1.0
O A:HOH1784 4.1 19.2 1.0
CG A:GLU425 4.2 16.3 1.0
CG A:HIS553 4.2 17.4 1.0
CB A:ASP387 4.3 19.6 1.0
OH A:TYR552 4.4 19.3 1.0
N12 A:FBD1 4.4 18.2 1.0
C7 A:FBD1 4.5 21.8 1.0
NE2 A:HIS377 4.6 15.1 1.0
CZ A:TYR552 4.6 16.8 1.0
C13 A:FBD1 4.6 22.6 1.0
CD1 A:TRP381 4.6 18.7 1.0
CE1 A:HIS377 4.7 14.1 1.0
NE1 A:TRP381 4.8 19.4 1.0
O9 A:FBD1 4.8 21.5 1.0
OD2 A:ASP453 4.9 20.8 1.0
O A:HOH2379 4.9 33.4 1.0

Zinc binding site 2 out of 2 in 3d7d

Go back to Zinc Binding Sites List in 3d7d
Zinc binding site 2 out of 2 in the A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A Urea-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcfbd, A Urea-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1752

b:19.9
occ:1.00
 O A:HOH2378 1.9 18.1 1.0
OD1 A:ASP387 1.9 20.2 1.0
OD2 A:ASP453 2.0 20.8 1.0
NE2 A:HIS377 2.0 15.1 1.0
CG A:ASP453 2.7 20.4 1.0
OD1 A:ASP453 2.8 22.6 1.0
CG A:ASP387 2.9 20.7 1.0
CE1 A:HIS377 3.0 14.1 1.0
CD2 A:HIS377 3.1 17.4 1.0
OD2 A:ASP387 3.2 20.4 1.0
ZN A:ZN1751 3.3 20.2 1.0
OE1 A:GLU424 3.6 19.3 1.0
OE2 A:GLU425 3.7 17.6 1.0
CD A:GLU424 4.1 18.3 1.0
ND1 A:HIS377 4.1 17.5 1.0
CG A:HIS377 4.2 16.8 1.0
CB A:ASP453 4.2 18.6 1.0
OE2 A:GLU424 4.2 19.3 1.0
CB A:ASP387 4.2 19.6 1.0
ND2 A:ASN519 4.3 17.4 1.0
CB A:PRO388 4.3 16.1 1.0
CD A:GLU425 4.4 15.4 1.0
C A:ASP387 4.5 19.1 1.0
O A:HOH2379 4.5 33.4 1.0
CA A:PRO388 4.5 17.1 1.0
C11 A:FBD1 4.6 19.9 1.0
O27 A:FBD1 4.6 18.5 1.0
CA A:ASP387 4.6 18.7 1.0
OE1 A:GLU425 4.7 16.9 1.0
N A:PRO388 4.7 18.4 1.0
N12 A:FBD1 4.7 18.2 1.0
OG A:SER454 4.8 14.4 0.7
O25 A:FBD1 4.9 26.2 1.0
C13 A:FBD1 4.9 22.6 1.0
N10 A:FBD1 5.0 19.6 1.0

Reference:

C.Barinka, Y.Byun, C.L.Dusich, S.R.Banerjee, Y.Chen, M.Castanares, A.P.Kozikowski, R.C.Mease, M.G.Pomper, J.Lubkowski. Interactions Between Human Glutamate Carboxypeptidase II and Urea-Based Inhibitors: Structural Characterization J.Med.Chem. V. 51 7737 2008.
ISSN: ISSN 0022-2623
PubMed: 19053759
DOI: 10.1021/JM800765E
Page generated: Thu Oct 24 12:05:01 2024

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