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Zinc in PDB 3d7g: A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcmc, A Urea-Based Inhibitor

Enzymatic activity of A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcmc, A Urea-Based Inhibitor

All present enzymatic activity of A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcmc, A Urea-Based Inhibitor:
3.4.17.21;

Protein crystallography data

The structure of A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcmc, A Urea-Based Inhibitor, PDB code: 3d7g 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 / 1.75
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.790, 129.694, 159.299, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20.4

Other elements in 3d7g:

The structure of A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcmc, A Urea-Based Inhibitor 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 Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcmc, A Urea-Based Inhibitor (pdb code 3d7g). 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 Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcmc, A Urea-Based Inhibitor, PDB code: 3d7g:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3d7g

Go back to Zinc Binding Sites List in 3d7g
Zinc binding site 1 out of 2 in the A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcmc, A Urea-Based Inhibitor


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 Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcmc, A Urea-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1751

b:20.4
occ:1.00
O A:HOH1769 1.9 18.9 1.0
NE2 A:HIS553 2.0 17.2 1.0
OD2 A:ASP387 2.1 21.4 1.0
OE2 A:GLU425 2.2 16.0 1.0
OE1 A:GLU425 2.4 16.0 1.0
CD A:GLU425 2.6 15.3 1.0
O20 A:MUD1 2.7 17.3 1.0
CE1 A:HIS553 3.0 18.0 1.0
CG A:ASP387 3.0 19.2 1.0
CD2 A:HIS553 3.1 18.7 1.0
ZN A:ZN1752 3.3 20.3 1.0
OD1 A:ASP387 3.3 18.3 1.0
C11 A:MUD1 3.5 21.3 1.0
C6 A:MUD1 3.9 19.7 1.0
N10 A:MUD1 4.0 20.2 1.0
CE1 A:TYR552 4.1 18.5 1.0
O A:HOH1784 4.1 19.4 1.0
OE1 A:GLU424 4.1 19.7 1.0
ND1 A:HIS553 4.1 15.6 1.0
CG A:GLU425 4.2 16.3 1.0
CG A:HIS553 4.2 17.2 1.0
CB A:ASP387 4.4 19.7 1.0
OH A:TYR552 4.4 19.8 1.0
N12 A:MUD1 4.4 18.9 1.0
C7 A:MUD1 4.5 22.5 1.0
NE2 A:HIS377 4.6 16.8 1.0
CD1 A:TRP381 4.6 18.1 1.0
CZ A:TYR552 4.6 17.7 1.0
C13 A:MUD1 4.7 22.9 1.0
CE1 A:HIS377 4.7 16.7 1.0
NE1 A:TRP381 4.8 18.2 1.0
O8 A:MUD1 4.9 22.2 1.0
OD2 A:ASP453 4.9 20.5 1.0
CD A:GLU424 5.0 19.8 1.0

Zinc binding site 2 out of 2 in 3d7g

Go back to Zinc Binding Sites List in 3d7g
Zinc binding site 2 out of 2 in the A High Resolution Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcmc, A Urea-Based Inhibitor


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 Crystal Structure of Human Glutamate Carboxypeptidase II (Gcpii) in A Complex with Dcmc, A Urea-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1752

b:20.3
occ:1.00
OD1 A:ASP387 1.9 18.3 1.0
OD2 A:ASP453 2.0 20.5 1.0
O A:HOH1769 2.0 18.9 1.0
NE2 A:HIS377 2.0 16.8 1.0
CG A:ASP453 2.7 21.1 1.0
OD1 A:ASP453 2.8 23.3 1.0
CG A:ASP387 2.9 19.2 1.0
CE1 A:HIS377 3.0 16.7 1.0
CD2 A:HIS377 3.1 17.8 1.0
OD2 A:ASP387 3.2 21.4 1.0
ZN A:ZN1751 3.3 20.4 1.0
OE1 A:GLU424 3.6 19.7 1.0
OE2 A:GLU425 3.6 16.0 1.0
CD A:GLU424 4.0 19.8 1.0
ND1 A:HIS377 4.1 17.4 1.0
OE2 A:GLU424 4.1 19.1 1.0
CG A:HIS377 4.2 17.0 1.0
CB A:ASP453 4.2 18.7 1.0
CB A:ASP387 4.2 19.7 1.0
ND2 A:ASN519 4.2 17.9 1.0
CB A:PRO388 4.3 16.2 1.0
CD A:GLU425 4.3 15.3 1.0
C A:ASP387 4.5 19.7 1.0
CA A:PRO388 4.5 17.8 1.0
C11 A:MUD1 4.6 21.3 1.0
CA A:ASP387 4.6 18.7 1.0
O20 A:MUD1 4.6 17.3 1.0
O A:HOH2363 4.7 29.9 1.0
OE1 A:GLU425 4.7 16.0 1.0
N A:PRO388 4.7 18.2 1.0
OG A:SER454 4.7 19.8 1.0
N12 A:MUD1 4.8 18.9 1.0
O18 A:MUD1 4.9 28.3 1.0
N10 A:MUD1 4.9 20.2 1.0
C13 A:MUD1 5.0 22.9 1.0
CG A:GLU424 5.0 15.4 1.0

Reference:

C.Barinka, Y.Byun, C.L.Dusich, S.R.Banerjee, Y.Chen, M.Castanares, A.P.Kozikowski, R.C.Mease, M.G.Pomper, J.Lubkowski. Interactions Between Human Glutamate Carboxypeptidase II and Urea-Based Inhibitors: Structural Characterization J.Med.Chem. V. 51 7737 2008.
ISSN: ISSN 0022-2623
PubMed: 19053759
DOI: 10.1021/JM800765E
Page generated: Wed Dec 16 04:12:17 2020

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