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Zinc in PDB 3iww: Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dbibzl, A Urea-Based Inhibitor

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

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

Protein crystallography data

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

Resolution Low / High (Å) 20.00 / 2.30
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.068, 130.035, 157.951, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 20.6

Other elements in 3iww:

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

Zinc binding site 1 out of 2 in 3iww

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

b:28.7
occ:1.00
OE2 A:GLU425 2.0 23.1 1.0
OD2 A:ASP387 2.1 20.4 1.0
NE2 A:HIS553 2.2 14.8 1.0
O A:HOH36 2.3 20.5 1.0
OE1 A:GLU425 2.5 23.6 1.0
CD A:GLU425 2.6 22.8 1.0
O31 A:YZE1 2.7 29.4 0.8
CG A:ASP387 3.1 18.8 1.0
CE1 A:HIS553 3.1 17.8 1.0
ZN A:ZN1752 3.3 27.7 1.0
CD2 A:HIS553 3.3 16.4 1.0
OD1 A:ASP387 3.4 27.0 1.0
C11 A:YZE1 3.5 30.8 0.8
OE1 A:GLU424 4.0 22.5 1.0
C6 A:YZE1 4.0 31.0 0.8
N10 A:YZE1 4.1 30.2 0.8
CG A:GLU425 4.1 18.4 1.0
CE1 A:TYR552 4.1 19.7 1.0
O A:HOH1783 4.2 21.9 1.0
ND1 A:HIS553 4.2 18.8 1.0
N12 A:YZE1 4.3 29.5 0.8
CB A:ASP387 4.3 20.0 1.0
OH A:TYR552 4.3 26.7 1.0
CG A:HIS553 4.4 17.3 1.0
NE2 A:HIS377 4.5 18.6 1.0
C13 A:YZE1 4.6 31.9 0.8
CE1 A:HIS377 4.6 17.8 1.0
C7 A:YZE1 4.6 32.5 0.8
CZ A:TYR552 4.7 21.4 1.0
OD2 A:ASP453 4.8 28.4 1.0
CD1 A:TRP381 4.8 16.3 1.0
NE1 A:TRP381 4.8 17.6 1.0
O8 A:YZE1 4.9 34.1 0.8
CD A:GLU424 4.9 23.6 1.0

Zinc binding site 2 out of 2 in 3iww

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

b:27.7
occ:1.00
OD2 A:ASP453 1.9 28.4 1.0
O A:HOH36 1.9 20.5 1.0
NE2 A:HIS377 1.9 18.6 1.0
OD1 A:ASP387 2.0 27.0 1.0
CG A:ASP453 2.6 28.2 1.0
OD1 A:ASP453 2.8 28.6 1.0
CG A:ASP387 2.8 18.8 1.0
CE1 A:HIS377 2.9 17.8 1.0
CD2 A:HIS377 2.9 13.1 1.0
OD2 A:ASP387 3.0 20.4 1.0
ZN A:ZN1751 3.3 28.7 1.0
OE2 A:GLU425 3.5 23.1 1.0
OE1 A:GLU424 3.6 22.5 1.0
CD A:GLU424 4.0 23.6 1.0
ND1 A:HIS377 4.0 15.2 1.0
CG A:HIS377 4.1 15.4 1.0
CB A:ASP453 4.1 26.4 1.0
CB A:ASP387 4.2 20.0 1.0
OE2 A:GLU424 4.2 24.7 1.0
CB A:PRO388 4.3 17.4 1.0
ND2 A:ASN519 4.3 22.4 1.0
CD A:GLU425 4.4 22.8 1.0
CA A:PRO388 4.5 16.4 1.0
N A:PRO388 4.6 16.8 1.0
CA A:ASP387 4.6 18.7 1.0
O30 A:YZE1 4.6 35.3 0.8
C A:ASP387 4.7 17.5 1.0
O31 A:YZE1 4.7 29.4 0.8
C11 A:YZE1 4.7 30.8 0.8
N12 A:YZE1 4.7 29.5 0.8
OG A:SER454 4.7 32.1 1.0
OE1 A:GLU425 4.8 23.6 1.0
C13 A:YZE1 4.9 31.9 0.8
C28 A:YZE1 4.9 34.7 0.8

Reference:

H.Wang, Y.Byun, C.Barinka, M.Pullambhatla, H.E.Bhang, J.J.Fox, J.Lubkowski, R.C.Mease, M.G.Pomper. Bioisosterism of Urea-Based Gcpii Inhibitors: Synthesis and Structure-Activity Relationship Studies. Bioorg.Med.Chem.Lett. V. 20 392 2010.
ISSN: ISSN 0960-894X
PubMed: 19897367
DOI: 10.1016/J.BMCL.2009.10.061
Page generated: Wed Dec 16 04:27:14 2020

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