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Zinc in PDB 3bi0: X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Transition State Analog of Glu-Glu

Enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Transition State Analog of Glu-Glu

All present enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Transition State Analog of Glu-Glu:
3.4.17.21;

Protein crystallography data

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Transition State Analog of Glu-Glu, PDB code: 3bi0 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 / 1.67
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.405, 130.797, 159.140, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 21.1

Other elements in 3bi0:

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Transition State Analog of Glu-Glu 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) in Complex with A Transition State Analog of Glu-Glu (pdb code 3bi0). 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) in Complex with A Transition State Analog of Glu-Glu, PDB code: 3bi0:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3bi0

Go back to Zinc Binding Sites List in 3bi0
Zinc binding site 1 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Transition State Analog of Glu-Glu


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) in Complex with A Transition State Analog of Glu-Glu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1751

b:20.4
occ:1.00
NE2 A:HIS553 2.0 19.2 1.0
OD2 A:ASP387 2.0 21.8 1.0
OE2 A:GLU425 2.1 18.3 1.0
O61 A:BIX1 2.1 20.9 1.0
OE1 A:GLU425 2.5 17.0 1.0
CD A:GLU425 2.6 16.6 1.0
O6 A:BIX1 2.8 17.9 1.0
P6 A:BIX1 2.9 20.1 1.0
CE1 A:HIS553 2.9 17.2 1.0
CG A:ASP387 3.0 18.6 1.0
CD2 A:HIS553 3.1 19.2 1.0
OD1 A:ASP387 3.4 20.0 1.0
ZN A:ZN1752 3.7 20.6 1.0
CE1 A:TYR552 3.8 19.9 1.0
O A:HOH1783 3.9 22.1 1.0
OH A:TYR552 4.0 20.2 1.0
ND1 A:HIS553 4.1 18.5 1.0
CG A:GLU425 4.1 17.7 1.0
CA A:BIX1 4.2 19.4 1.0
C1 A:BIX1 4.2 18.1 1.0
CG A:HIS553 4.2 18.6 1.0
C5 A:BIX1 4.3 23.3 1.0
CZ A:TYR552 4.3 18.9 1.0
CB A:ASP387 4.3 18.0 1.0
C A:BIX1 4.4 20.2 1.0
CD1 A:TRP381 4.4 21.2 1.0
OC A:BIX1 4.6 20.7 1.0
OE1 A:GLU424 4.6 19.1 1.0
NE1 A:TRP381 4.6 18.9 1.0
NE2 A:HIS377 4.8 16.8 1.0
CE1 A:HIS377 4.8 14.4 1.0
CD1 A:TYR552 4.9 19.3 1.0
O A:BIX1 5.0 18.8 1.0

Zinc binding site 2 out of 2 in 3bi0

Go back to Zinc Binding Sites List in 3bi0
Zinc binding site 2 out of 2 in the X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Transition State Analog of Glu-Glu


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) in Complex with A Transition State Analog of Glu-Glu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1752

b:20.6
occ:1.00
OD2 A:ASP453 2.0 21.8 1.0
O6 A:BIX1 2.0 17.9 1.0
OD1 A:ASP387 2.0 20.0 1.0
NE2 A:HIS377 2.1 16.8 1.0
CG A:ASP453 2.7 19.4 1.0
OD1 A:ASP453 2.7 20.1 1.0
CG A:ASP387 3.0 18.6 1.0
CE1 A:HIS377 3.0 14.4 1.0
CD2 A:HIS377 3.1 16.9 1.0
P6 A:BIX1 3.3 20.1 1.0
OD2 A:ASP387 3.4 21.8 1.0
OE1 A:GLU424 3.6 19.1 1.0
ZN A:ZN1751 3.7 20.4 1.0
OE2 A:GLU425 3.7 18.3 1.0
C5 A:BIX1 3.7 23.3 1.0
CD A:GLU424 4.1 22.8 1.0
OE2 A:GLU424 4.1 23.7 1.0
CB A:ASP453 4.1 19.8 1.0
O61 A:BIX1 4.1 20.9 1.0
ND1 A:HIS377 4.2 16.1 1.0
CG A:HIS377 4.2 15.8 1.0
CB A:ASP387 4.3 18.0 1.0
ND2 A:ASN519 4.4 19.9 1.0
CB A:PRO388 4.4 16.3 1.0
O A:HOH2397 4.5 43.5 1.0
CD A:GLU425 4.5 16.6 1.0
CA A:ASP387 4.6 17.4 1.0
C1 A:BIX1 4.6 18.1 1.0
O A:HOH2358 4.6 41.4 1.0
CA A:PRO388 4.6 17.8 1.0
C A:ASP387 4.7 17.5 1.0
OG A:SER454 4.7 21.2 1.0
N A:PRO388 4.7 17.1 1.0
OE1 A:GLU425 5.0 17.0 1.0

Reference:

C.Barinka, K.Hlouchova, M.Rovenska, P.Majer, M.Dauter, N.Hin, Y.S.Ko, T.Tsukamoto, B.S.Slusher, J.Konvalinka, J.Lubkowski. Structural Basis of Interactions Between Human Glutamate Carboxypeptidase II and Its Substrate Analogs J.Mol.Biol. V. 376 1438 2008.
ISSN: ISSN 0022-2836
PubMed: 18234225
DOI: 10.1016/J.JMB.2007.12.066
Page generated: Thu Oct 24 11:30:09 2024

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