Atomistry » Zinc » PDB 3f7k-3fkg » 3fed
Atomistry »
  Zinc »
    PDB 3f7k-3fkg »
      3fed »

Zinc in PDB 3fed: The High Resolution Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II) in Complex with A Transition State Analog of Glu-Glu

Enzymatic activity of The High Resolution Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II) in Complex with A Transition State Analog of Glu-Glu

All present enzymatic activity of The High Resolution Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II) in Complex with A Transition State Analog of Glu-Glu:
3.4.17.21;

Protein crystallography data

The structure of The High Resolution Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II) in Complex with A Transition State Analog of Glu-Glu, PDB code: 3fed was solved by J.Lubkowski, C.Barinka, K.Hlouchova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.29
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 122.731, 104.086, 77.634, 90.00, 108.19, 90.00
R / Rfree (%) 13.1 / 14.7

Other elements in 3fed:

The structure of The High Resolution Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II) in Complex with A Transition State Analog of Glu-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 The High Resolution Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II) in Complex with A Transition State Analog of Glu-Glu (pdb code 3fed). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The High Resolution Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II) in Complex with A Transition State Analog of Glu-Glu, PDB code: 3fed:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3fed

Go back to Zinc Binding Sites List in 3fed
Zinc binding site 1 out of 2 in the The High Resolution Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II) in Complex with A Transition State Analog of Glu-Glu


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The High Resolution Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II) in Complex with A Transition State Analog of Glu-Glu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1751

b:10.5
occ:0.90
 O61 A:BIX1 1.9 9.9 0.8
OD2 A:ASP377 2.0 11.3 1.0
OE2 A:GLU415 2.0 12.2 1.0
NE2 A:HIS543 2.0 10.9 1.0
OE1 A:GLU415 2.5 11.3 1.0
CD A:GLU415 2.6 10.1 1.0
CG A:ASP377 3.0 11.8 1.0
CE1 A:HIS543 3.0 11.4 1.0
P6 A:BIX1 3.0 10.7 0.8
CD2 A:HIS543 3.1 12.0 1.0
O6 A:BIX1 3.1 12.9 0.8
OD1 A:ASP377 3.4 11.9 1.0
O A:HOH955 3.8 13.0 1.0
OH A:TYR542 3.9 13.5 1.0
CE1 A:TYR542 3.9 12.7 1.0
ZN A:ZN1752 3.9 10.6 0.8
CA A:BIX1 4.0 12.0 0.8
CG A:GLU415 4.1 11.3 1.0
ND1 A:HIS543 4.1 11.2 1.0
C1 A:BIX1 4.1 11.7 0.8
CG A:HIS543 4.2 10.7 1.0
CB A:ASP377 4.2 12.5 1.0
CZ A:TYR542 4.3 11.6 1.0
C A:BIX1 4.3 12.9 0.8
C5 A:BIX1 4.4 13.9 0.8
OC A:BIX1 4.5 12.4 0.8
OE1 A:GLU414 4.5 13.1 1.0
O A:HOH1262 4.5 12.7 0.5
CD1 A:TRP371 4.5 10.5 1.0
NE1 A:TRP371 4.7 11.1 1.0
CE1 A:HIS367 4.7 10.4 1.0
NE2 A:HIS367 4.8 11.0 1.0
CD1 A:TYR542 4.9 13.0 1.0
O A:BIX1 4.9 12.9 0.8

Zinc binding site 2 out of 2 in 3fed

Go back to Zinc Binding Sites List in 3fed
Zinc binding site 2 out of 2 in the The High Resolution Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II) in Complex with A Transition State Analog of Glu-Glu


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The High Resolution Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II) in Complex with A Transition State Analog of Glu-Glu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1752

b:10.6
occ:0.80
 OD1 A:ASP377 2.0 11.9 1.0
O6 A:BIX1 2.1 12.9 0.8
NE2 A:HIS367 2.1 11.0 1.0
O A:HOH1262 2.2 12.7 0.5
OD2 A:ASP443 2.3 14.2 1.0
OD1 A:ASP443 2.3 15.6 1.0
CG A:ASP443 2.6 14.9 1.0
CG A:ASP377 3.1 11.8 1.0
CE1 A:HIS367 3.1 10.4 1.0
CD2 A:HIS367 3.1 10.8 1.0
P6 A:BIX1 3.4 10.7 0.8
OD2 A:ASP377 3.6 11.3 1.0
OE2 A:GLU414 3.6 14.7 1.0
ZN A:ZN1751 3.9 10.5 0.9
OE1 A:GLU414 4.0 13.1 1.0
C5 A:BIX1 4.0 13.9 0.8
O61 A:BIX1 4.0 9.9 0.8
CD A:GLU414 4.1 13.2 1.0
OE2 A:GLU415 4.1 12.2 1.0
CB A:ASP443 4.2 13.2 1.0
ND1 A:HIS367 4.2 10.5 1.0
OG A:SER444 4.3 18.1 1.0
CB A:ASP377 4.3 12.5 1.0
CG A:HIS367 4.3 10.0 1.0
O A:HOH1319 4.3 36.0 1.0
CB A:PRO378 4.4 12.0 1.0
CA A:PRO378 4.5 11.1 1.0
CA A:ASP377 4.6 12.2 1.0
C1 A:BIX1 4.7 11.7 0.8
N A:PRO378 4.7 10.8 1.0
C A:ASP377 4.8 11.3 1.0
N A:SER444 4.9 12.2 1.0
OG A:SER509 4.9 14.8 1.0
CD A:GLU415 4.9 10.1 1.0
O A:HOH980 4.9 35.6 1.0

Reference:

K.Hlouchova, C.Barinka, J.Konvalinka, J.Lubkowski. Structural Insight Into the Evolutionary and Pharmacologic Homology of Glutamate Carboxypeptidases II and III Febs J. V. 276 4448 2009.
ISSN: ISSN 1742-464X
PubMed: 19678840
DOI: 10.1111/J.1742-4658.2009.07152.X
Page generated: Thu Oct 24 13:08:59 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy