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Zinc in PDB 2pvv: Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with L-Serine-O-Sulfate

Enzymatic activity of Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with L-Serine-O-Sulfate

All present enzymatic activity of Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with L-Serine-O-Sulfate:
3.4.17.21;

Protein crystallography data

The structure of Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with L-Serine-O-Sulfate, PDB code: 2pvv 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) 30.00 / 2.11
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.617, 130.220, 158.975, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 21.2

Other elements in 2pvv:

The structure of Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with L-Serine-O-Sulfate 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 Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with L-Serine-O-Sulfate (pdb code 2pvv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with L-Serine-O-Sulfate, PDB code: 2pvv:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2pvv

Go back to Zinc Binding Sites List in 2pvv
Zinc binding site 1 out of 2 in the Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with L-Serine-O-Sulfate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with L-Serine-O-Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1751

b:24.1
occ:1.00
OE2 A:GLU425 2.0 14.4 1.0
OD2 A:ASP387 2.0 21.9 1.0
NE2 A:HIS553 2.1 19.4 1.0
O A:HOH2263 2.2 17.3 1.0
OE1 A:GLU425 2.4 19.2 1.0
CD A:GLU425 2.5 15.0 1.0
CG A:ASP387 2.9 21.2 1.0
CD2 A:HIS553 3.1 17.4 1.0
CE1 A:HIS553 3.1 19.4 1.0
OD1 A:ASP387 3.2 22.9 1.0
ZN A:ZN1752 3.2 21.3 1.0
O A:HOH2264 3.5 27.5 1.0
O A:HOH1784 4.0 16.4 1.0
CG A:GLU425 4.0 14.1 1.0
CE1 A:TYR552 4.1 20.1 1.0
OE1 A:GLU424 4.1 15.8 1.0
OH A:TYR552 4.2 24.8 1.0
ND1 A:HIS553 4.2 18.8 1.0
N A:OSE1768 4.2 23.9 1.0
CG A:HIS553 4.2 20.5 1.0
CB A:ASP387 4.3 19.6 1.0
NE2 A:HIS377 4.4 14.4 1.0
CA A:OSE1768 4.4 22.8 1.0
CE1 A:HIS377 4.5 17.2 1.0
CZ A:TYR552 4.5 20.2 1.0
CD1 A:TRP381 4.6 18.6 1.0
C A:OSE1768 4.6 22.6 1.0
NE1 A:TRP381 4.7 22.3 1.0
OXT A:OSE1768 4.7 22.4 1.0
OD2 A:ASP453 4.9 17.0 1.0

Zinc binding site 2 out of 2 in 2pvv

Go back to Zinc Binding Sites List in 2pvv
Zinc binding site 2 out of 2 in the Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with L-Serine-O-Sulfate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with L-Serine-O-Sulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1752

b:21.3
occ:1.00
O A:HOH2263 1.8 17.3 1.0
NE2 A:HIS377 2.0 14.4 1.0
OD2 A:ASP453 2.0 17.0 1.0
OD1 A:ASP387 2.1 22.9 1.0
OD1 A:ASP453 2.7 21.1 1.0
CG A:ASP453 2.7 20.2 1.0
CE1 A:HIS377 2.9 17.2 1.0
CD2 A:HIS377 3.0 13.9 1.0
CG A:ASP387 3.0 21.2 1.0
ZN A:ZN1751 3.2 24.1 1.0
OD2 A:ASP387 3.3 21.9 1.0
OE2 A:GLU425 3.6 14.4 1.0
OE1 A:GLU424 3.7 15.8 1.0
O A:HOH2272 3.9 35.6 1.0
O A:HOH2264 4.0 27.5 1.0
ND1 A:HIS377 4.0 16.7 1.0
CD A:GLU424 4.1 19.8 1.0
CG A:HIS377 4.1 14.7 1.0
CB A:ASP453 4.2 18.6 1.0
ND2 A:ASN519 4.3 17.7 1.0
CB A:PRO388 4.3 20.7 1.0
CB A:ASP387 4.3 19.6 1.0
CD A:GLU425 4.4 15.0 1.0
OE2 A:GLU424 4.4 16.6 1.0
CA A:PRO388 4.6 19.8 1.0
CA A:ASP387 4.6 19.8 1.0
N A:PRO388 4.6 19.8 1.0
N A:OSE1768 4.6 23.9 1.0
OG A:SER454 4.6 19.7 1.0
C A:ASP387 4.6 18.7 1.0
OE1 A:GLU425 4.7 19.2 1.0

Reference:

C.Barinka, M.Rovenska, P.Mlcochova, K.Hlouchova, A.Plechanovova, P.Majer, T.Tsukamoto, B.S.Slusher, J.Konvalinka, J.Lubkowski. Structural Insight Into the Pharmacophore Pocket of Human Glutamate Carboxypeptidase II. J.Med.Chem. V. 50 3267 2007.
ISSN: ISSN 0022-2623
PubMed: 17567119
DOI: 10.1021/JM070133W
Page generated: Wed Dec 16 03:49:17 2020

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