Atomistry » Zinc » PDB 3d7h-3dgd » 3d7h
Atomistry »
  Zinc »
    PDB 3d7h-3dgd »
      3d7h »

Zinc in PDB 3d7h: A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcibzl, A Urea-Based Inhibitor

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

All present enzymatic activity of A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcibzl, 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 Dcibzl, A Urea-Based Inhibitor, PDB code: 3d7h 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 / 1.55
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.274, 130.511, 158.732, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 20.9

Other elements in 3d7h:

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

Iodine (I) 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 Dcibzl, A Urea-Based Inhibitor (pdb code 3d7h). 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 Dcibzl, A Urea-Based Inhibitor, PDB code: 3d7h:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3d7h

Go back to Zinc Binding Sites List in 3d7h
Zinc binding site 1 out of 2 in the A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcibzl, 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 Dcibzl, A Urea-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1751

b:21.0
occ:1.00
 O A:HOH2257 2.0 18.2 1.0
OD2 A:ASP387 2.0 22.6 1.0
NE2 A:HIS553 2.1 18.2 1.0
OE2 A:GLU425 2.2 18.3 1.0
OE1 A:GLU425 2.4 18.8 1.0
O31 A:YC21 2.6 18.6 1.0
CD A:GLU425 2.6 16.7 1.0
CE1 A:HIS553 3.0 19.0 1.0
CG A:ASP387 3.0 20.3 1.0
CD2 A:HIS553 3.1 18.5 1.0
ZN A:ZN1752 3.3 21.0 1.0
OD1 A:ASP387 3.3 20.6 1.0
C11 A:YC21 3.4 20.0 1.0
C6 A:YC21 4.0 20.8 1.0
N10 A:YC21 4.0 19.7 1.0
CE1 A:TYR552 4.1 20.6 1.0
OE1 A:GLU424 4.1 19.0 1.0
ND1 A:HIS553 4.1 18.2 1.0
CG A:GLU425 4.2 17.1 1.0
O A:HOH1783 4.2 20.5 1.0
CG A:HIS553 4.2 18.2 1.0
N12 A:YC21 4.2 20.1 1.0
CB A:ASP387 4.3 19.5 1.0
OH A:TYR552 4.4 20.2 1.0
C13 A:YC21 4.5 22.1 1.0
NE2 A:HIS377 4.5 16.5 1.0
C7 A:YC21 4.6 22.5 1.0
CZ A:TYR552 4.6 20.6 1.0
CD1 A:TRP381 4.7 19.3 1.0
CE1 A:HIS377 4.7 17.5 1.0
NE1 A:TRP381 4.8 20.3 1.0
O8 A:YC21 4.8 23.0 1.0
OD2 A:ASP453 4.8 21.1 1.0
CD A:GLU424 5.0 18.8 1.0

Zinc binding site 2 out of 2 in 3d7h

Go back to Zinc Binding Sites List in 3d7h
Zinc binding site 2 out of 2 in the A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcibzl, 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 Dcibzl, A Urea-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1752

b:21.0
occ:1.00
 OD2 A:ASP453 1.9 21.1 1.0
O A:HOH2257 2.0 18.2 1.0
NE2 A:HIS377 2.0 16.5 1.0
OD1 A:ASP387 2.0 20.6 1.0
CG A:ASP453 2.7 19.1 1.0
OD1 A:ASP453 2.8 23.5 1.0
CG A:ASP387 2.9 20.3 1.0
CE1 A:HIS377 3.0 17.5 1.0
CD2 A:HIS377 3.0 18.2 1.0
OD2 A:ASP387 3.3 22.6 1.0
ZN A:ZN1751 3.3 21.0 1.0
OE1 A:GLU424 3.6 19.0 1.0
OE2 A:GLU425 3.7 18.3 1.0
CD A:GLU424 4.0 18.8 1.0
ND1 A:HIS377 4.1 19.8 1.0
CB A:ASP453 4.1 20.2 1.0
CG A:HIS377 4.2 16.7 1.0
CB A:ASP387 4.2 19.5 1.0
OE2 A:GLU424 4.2 19.7 1.0
ND2 A:ASN519 4.3 19.7 1.0
CB A:PRO388 4.3 18.4 1.0
CD A:GLU425 4.3 16.7 1.0
CA A:ASP387 4.5 17.8 1.0
CA A:PRO388 4.5 17.9 1.0
C11 A:YC21 4.6 20.0 1.0
O31 A:YC21 4.6 18.6 1.0
N A:PRO388 4.6 19.0 1.0
C A:ASP387 4.6 19.1 1.0
N12 A:YC21 4.7 20.1 1.0
OE1 A:GLU425 4.7 18.8 1.0
O A:HOH2258 4.7 30.4 1.0
OG A:SER454 4.8 18.6 0.7
C13 A:YC21 4.8 22.1 1.0
O30 A:YC21 4.9 25.3 1.0
C28 A:YC21 5.0 23.3 1.0
CG A:GLU424 5.0 16.9 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 12:05:41 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy