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Zinc in PDB 2pvw: A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with 2-(Phosphonomethyl)Pentanedioic Acid (2-Pmpa)

Enzymatic activity of A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with 2-(Phosphonomethyl)Pentanedioic Acid (2-Pmpa)

All present enzymatic activity of A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with 2-(Phosphonomethyl)Pentanedioic Acid (2-Pmpa):
3.4.17.21;

Protein crystallography data

The structure of A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with 2-(Phosphonomethyl)Pentanedioic Acid (2-Pmpa), PDB code: 2pvw 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 / 1.71
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.849, 130.822, 159.452, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 20.7

Other elements in 2pvw:

The structure of A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with 2-(Phosphonomethyl)Pentanedioic Acid (2-Pmpa) 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 A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with 2-(Phosphonomethyl)Pentanedioic Acid (2-Pmpa) (pdb code 2pvw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with 2-(Phosphonomethyl)Pentanedioic Acid (2-Pmpa), PDB code: 2pvw:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2pvw

Go back to Zinc Binding Sites List in 2pvw
Zinc binding site 1 out of 2 in the A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with 2-(Phosphonomethyl)Pentanedioic Acid (2-Pmpa)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with 2-(Phosphonomethyl)Pentanedioic Acid (2-Pmpa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1751

b:25.9
occ:1.00
NE2 A:HIS553 2.0 23.4 1.0
OD2 A:ASP387 2.0 26.7 1.0
OE2 A:GLU425 2.1 22.1 1.0
O2 A:G881768 2.1 29.3 1.0
OE1 A:GLU425 2.5 24.3 1.0
CD A:GLU425 2.6 22.1 1.0
O1 A:G881768 2.7 27.3 1.0
P1 A:G881768 2.9 25.8 1.0
CE1 A:HIS553 2.9 22.1 1.0
CG A:ASP387 3.0 25.7 1.0
CD2 A:HIS553 3.1 24.9 1.0
OD1 A:ASP387 3.5 24.9 1.0
ZN A:ZN1752 3.6 26.1 1.0
CE1 A:TYR552 3.9 25.8 1.0
OH A:TYR552 3.9 26.2 1.0
O3 A:G881768 4.0 25.4 1.0
O A:HOH1783 4.0 26.7 1.0
ND1 A:HIS553 4.1 24.2 1.0
C2 A:G881768 4.1 27.5 1.0
CG A:GLU425 4.1 22.6 1.0
C1 A:G881768 4.2 27.1 1.0
CG A:HIS553 4.2 23.2 1.0
CZ A:TYR552 4.3 25.8 1.0
CB A:ASP387 4.3 23.0 1.0
C3 A:G881768 4.4 31.6 1.0
O5 A:G881768 4.5 28.2 1.0
OE1 A:GLU424 4.5 25.8 1.0
CD1 A:TRP381 4.6 25.3 1.0
NE1 A:TRP381 4.7 23.6 1.0
NE2 A:HIS377 4.8 23.4 1.0
CE1 A:HIS377 4.8 22.2 1.0
CD1 A:TYR552 4.9 25.1 1.0

Zinc binding site 2 out of 2 in 2pvw

Go back to Zinc Binding Sites List in 2pvw
Zinc binding site 2 out of 2 in the A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with 2-(Phosphonomethyl)Pentanedioic Acid (2-Pmpa)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of A High Resolution Structure of Human Glutamate Carboxypeptidase II (Gcpii) in Complex with 2-(Phosphonomethyl)Pentanedioic Acid (2-Pmpa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1752

b:26.1
occ:1.00
OD2 A:ASP453 1.9 27.5 1.0
OD1 A:ASP387 2.0 24.9 1.0
O1 A:G881768 2.0 27.3 1.0
NE2 A:HIS377 2.1 23.4 1.0
CG A:ASP453 2.7 30.4 1.0
OD1 A:ASP453 2.8 31.9 1.0
CG A:ASP387 3.0 25.7 1.0
CD2 A:HIS377 3.1 23.0 1.0
CE1 A:HIS377 3.1 22.2 1.0
P1 A:G881768 3.2 25.8 1.0
OD2 A:ASP387 3.4 26.7 1.0
O3 A:G881768 3.5 25.4 1.0
OE1 A:GLU424 3.6 25.8 1.0
ZN A:ZN1751 3.6 25.9 1.0
OE2 A:GLU425 3.7 22.1 1.0
O2 A:G881768 4.1 29.3 1.0
OE2 A:GLU424 4.1 29.9 1.0
CD A:GLU424 4.1 29.7 1.0
CB A:ASP453 4.1 25.2 1.0
ND1 A:HIS377 4.2 22.3 1.0
CG A:HIS377 4.2 19.6 1.0
ND2 A:ASN519 4.2 25.8 1.0
CB A:ASP387 4.3 23.0 1.0
CB A:PRO388 4.3 23.0 1.0
CD A:GLU425 4.5 22.1 1.0
CA A:PRO388 4.6 22.9 1.0
C1 A:G881768 4.6 27.1 1.0
CA A:ASP387 4.6 23.9 1.0
C A:ASP387 4.7 23.2 1.0
N A:PRO388 4.7 23.6 1.0
OG A:SER454 4.7 31.9 1.0
OE1 A:GLU425 4.9 24.3 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 03:49:16 2020

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