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Zinc in PDB 3rbu: N-Terminally Avitev-Tagged Human Glutamate Carboxypeptidase II in Complex with 2-Pmpa

Enzymatic activity of N-Terminally Avitev-Tagged Human Glutamate Carboxypeptidase II in Complex with 2-Pmpa

All present enzymatic activity of N-Terminally Avitev-Tagged Human Glutamate Carboxypeptidase II in Complex with 2-Pmpa:
3.4.17.21;

Protein crystallography data

The structure of N-Terminally Avitev-Tagged Human Glutamate Carboxypeptidase II in Complex with 2-Pmpa, PDB code: 3rbu was solved by J.Tykvart, P.Sacha, C.Barinka, J.Starkova, T.Knedlik, J.Lubkowski, J.Konvalinka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.46 / 1.60
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.247, 130.559, 158.897, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 18.2

Other elements in 3rbu:

The structure of N-Terminally Avitev-Tagged Human Glutamate Carboxypeptidase II in Complex with 2-Pmpa also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the N-Terminally Avitev-Tagged Human Glutamate Carboxypeptidase II in Complex with 2-Pmpa (pdb code 3rbu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the N-Terminally Avitev-Tagged Human Glutamate Carboxypeptidase II in Complex with 2-Pmpa, PDB code: 3rbu:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3rbu

Go back to Zinc Binding Sites List in 3rbu
Zinc binding site 1 out of 2 in the N-Terminally Avitev-Tagged Human Glutamate Carboxypeptidase II in Complex with 2-Pmpa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of N-Terminally Avitev-Tagged Human Glutamate Carboxypeptidase II in Complex with 2-Pmpa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1751

b:19.7
occ:1.00
NE2 A:HIS553 2.0 17.6 1.0
OE2 A:GLU425 2.0 19.2 1.0
OD2 A:ASP387 2.0 19.9 1.0
O1 A:G881800 2.1 20.9 1.0
O2 A:G881800 2.1 42.3 1.0
OE1 A:GLU425 2.4 17.0 1.0
CD A:GLU425 2.5 17.6 1.0
P1 A:G881800 2.7 48.2 1.0
CE1 A:HIS553 3.0 19.1 1.0
CG A:ASP387 3.0 18.4 1.0
CD2 A:HIS553 3.0 19.6 1.0
ZN A:ZN1752 3.3 18.4 1.0
OD1 A:ASP387 3.3 18.1 1.0
O3 A:G881800 3.6 33.1 1.0
O A:HOH2015 3.9 19.2 1.0
CE1 A:TYR552 4.1 23.0 1.0
ND1 A:HIS553 4.1 18.4 1.0
CG A:GLU425 4.1 18.4 1.0
OE1 A:GLU424 4.1 17.6 1.0
CG A:HIS553 4.1 18.8 1.0
C1 A:G881800 4.2 20.9 1.0
OH A:TYR552 4.2 23.8 1.0
C2 A:G881800 4.3 24.2 1.0
CB A:ASP387 4.3 18.8 1.0
NE2 A:HIS377 4.5 17.9 1.0
CD1 A:TRP381 4.5 19.5 1.0
CZ A:TYR552 4.5 21.7 1.0
CE1 A:HIS377 4.6 16.8 1.0
NE1 A:TRP381 4.6 20.1 1.0
C3 A:G881800 4.6 23.9 1.0
O5 A:G881800 4.8 20.9 1.0
OD2 A:ASP453 5.0 18.4 1.0

Zinc binding site 2 out of 2 in 3rbu

Go back to Zinc Binding Sites List in 3rbu
Zinc binding site 2 out of 2 in the N-Terminally Avitev-Tagged Human Glutamate Carboxypeptidase II in Complex with 2-Pmpa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of N-Terminally Avitev-Tagged Human Glutamate Carboxypeptidase II in Complex with 2-Pmpa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1752

b:18.4
occ:1.00
OD2 A:ASP453 1.9 18.4 1.0
O1 A:G881800 2.0 20.9 1.0
OD1 A:ASP387 2.0 18.1 1.0
NE2 A:HIS377 2.1 17.9 1.0
CG A:ASP453 2.6 20.6 1.0
OD1 A:ASP453 2.7 23.0 1.0
CG A:ASP387 2.9 18.4 1.0
CE1 A:HIS377 3.0 16.8 1.0
CD2 A:HIS377 3.1 15.9 1.0
P1 A:G881800 3.2 48.2 1.0
ZN A:ZN1751 3.3 19.7 1.0
OD2 A:ASP387 3.3 19.9 1.0
OE1 A:GLU424 3.6 17.6 1.0
O3 A:G881800 3.7 33.1 1.0
OE2 A:GLU425 3.7 19.2 1.0
O A:HOH2787 4.0 38.6 1.0
CD A:GLU424 4.1 18.8 1.0
CB A:ASP453 4.1 18.2 1.0
ND1 A:HIS377 4.2 17.0 1.0
O2 A:G881800 4.2 42.3 1.0
CG A:HIS377 4.2 15.2 1.0
ND2 A:ASN519 4.2 20.7 1.0
CB A:ASP387 4.2 18.8 1.0
OE2 A:GLU424 4.3 19.9 1.0
CB A:PRO388 4.4 17.6 1.0
CD A:GLU425 4.4 17.6 1.0
C1 A:G881800 4.5 20.9 1.0
CA A:ASP387 4.6 18.7 1.0
CA A:PRO388 4.6 17.5 1.0
C A:ASP387 4.7 19.5 1.0
OG A:SER454 4.7 22.7 1.0
OE1 A:GLU425 4.7 17.0 1.0
N A:PRO388 4.7 18.6 1.0

Reference:

J.Tykvart, P.Sacha, C.Barinka, T.Knedlik, J.Starkova, J.Lubkowski, J.Konvalinka. Efficient and Versatile One-Step Affinity Purification of in Vivo Biotinylated Proteins: Expression, Characterization and Structure Analysis of Recombinant Human Glutamate Carboxypeptidase II. Protein Expr.Purif. V. 82 106 2012.
ISSN: ISSN 1046-5928
PubMed: 22178733
DOI: 10.1016/J.PEP.2011.11.016
Page generated: Wed Dec 16 04:47:04 2020

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