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Zinc in PDB 3bi1: X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Transition State Analog of Methotrexate-Glu

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

All present enzymatic activity of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Transition State Analog of Methotrexate-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 Methotrexate-Glu, PDB code: 3bi1 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) 15.00 / 1.50
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.116, 130.462, 159.456, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 16.9

Other elements in 3bi1:

The structure of X-Ray Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with A Transition State Analog of Methotrexate-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 Methotrexate-Glu (pdb code 3bi1). 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 Methotrexate-Glu, PDB code: 3bi1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3bi1

Go back to Zinc Binding Sites List in 3bi1
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 Methotrexate-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 Methotrexate-Glu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1751

b:17.3
occ:1.00
OD2 A:ASP387 2.0 18.6 1.0
OE2 A:GLU425 2.0 16.9 1.0
O8 A:3BI1 2.0 16.9 1.0
NE2 A:HIS553 2.1 14.9 1.0
OE1 A:GLU425 2.5 16.4 1.0
CD A:GLU425 2.6 15.5 1.0
O7 A:3BI1 2.7 19.2 1.0
P A:3BI1 2.9 17.1 1.0
CE1 A:HIS553 3.0 16.2 1.0
CG A:ASP387 3.0 15.7 1.0
CD2 A:HIS553 3.1 15.1 1.0
OD1 A:ASP387 3.4 18.7 1.0
ZN A:ZN1752 3.7 18.9 1.0
CE1 A:TYR552 3.8 15.4 1.0
O A:HOH1782 3.9 18.5 1.0
OH A:TYR552 4.0 17.9 1.0
CG A:GLU425 4.1 15.1 1.0
C19 A:3BI1 4.1 16.4 1.0
ND1 A:HIS553 4.1 16.7 1.0
C18 A:3BI1 4.2 19.3 1.0
C20 A:3BI1 4.2 17.1 1.0
CG A:HIS553 4.2 16.5 1.0
CZ A:TYR552 4.3 16.0 1.0
CB A:ASP387 4.3 16.6 1.0
C24 A:3BI1 4.4 20.6 1.0
CD1 A:TRP381 4.5 16.0 1.0
O A:HOH2214 4.5 34.8 0.4
O5 A:3BI1 4.5 20.1 1.0
OE1 A:GLU424 4.6 17.1 1.0
NE1 A:TRP381 4.6 16.7 1.0
NE2 A:HIS377 4.8 14.5 1.0
CD1 A:TYR552 4.8 16.2 1.0
CE1 A:HIS377 4.8 14.1 1.0

Zinc binding site 2 out of 2 in 3bi1

Go back to Zinc Binding Sites List in 3bi1
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 Methotrexate-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 Methotrexate-Glu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1752

b:18.9
occ:1.00
O7 A:3BI1 1.9 19.2 1.0
OD2 A:ASP453 1.9 19.6 1.0
OD1 A:ASP387 1.9 18.7 1.0
NE2 A:HIS377 2.0 14.5 1.0
CG A:ASP453 2.6 18.8 1.0
OD1 A:ASP453 2.7 21.5 1.0
O A:HOH2214 2.7 34.8 0.4
CG A:ASP387 3.0 15.7 1.0
CD2 A:HIS377 3.0 15.4 1.0
CE1 A:HIS377 3.0 14.1 1.0
P A:3BI1 3.3 17.1 1.0
OD2 A:ASP387 3.4 18.6 1.0
OE1 A:GLU424 3.7 17.1 1.0
ZN A:ZN1751 3.7 17.3 1.0
C18 A:3BI1 3.7 19.3 1.0
OE2 A:GLU425 3.8 16.9 1.0
OE2 A:GLU424 4.0 20.6 1.0
CD A:GLU424 4.1 16.6 1.0
O8 A:3BI1 4.1 16.9 1.0
ND1 A:HIS377 4.1 14.8 1.0
CB A:ASP453 4.1 17.9 1.0
CG A:HIS377 4.2 13.8 1.0
CB A:ASP387 4.3 16.6 1.0
ND2 A:ASN519 4.3 18.3 1.0
CB A:PRO388 4.4 16.0 1.0
CD A:GLU425 4.5 15.5 1.0
C19 A:3BI1 4.6 16.4 1.0
CA A:ASP387 4.6 16.0 1.0
CA A:PRO388 4.6 15.2 1.0
C A:ASP387 4.7 17.0 1.0
N A:PRO388 4.7 16.9 1.0
O A:HOH2214 4.7 27.6 0.6
OG A:SER454 4.8 20.5 1.0
OE1 A:GLU425 5.0 16.4 1.0
O1 A:3BI1 5.0 31.1 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 11:30:31 2024

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