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

Zinc in PDB 3fec: Crystal Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II), Pseudo-Unliganded

Enzymatic activity of Crystal Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II), Pseudo-Unliganded

All present enzymatic activity of Crystal Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II), Pseudo-Unliganded:
3.4.17.21;

Protein crystallography data

The structure of Crystal Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II), Pseudo-Unliganded, PDB code: 3fec was solved by C.Barinka, J.Lubkowski, K.Hlouchova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.49
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 122.767, 104.322, 78.008, 90.00, 107.69, 90.00
R / Rfree (%) 15.9 / 18.3

Other elements in 3fec:

The structure of Crystal Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II), Pseudo-Unliganded 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 Crystal Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II), Pseudo-Unliganded (pdb code 3fec). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II), Pseudo-Unliganded, PDB code: 3fec:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3fec

Go back to Zinc Binding Sites List in 3fec
Zinc binding site 1 out of 4 in the Crystal Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II), Pseudo-Unliganded


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II), Pseudo-Unliganded within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1751

b:21.5
occ:0.50
 ZN A:ZN1751 0.0 21.5 0.5
ZN A:ZN1751 0.5 16.3 0.5
O A:HOH802 1.8 17.2 0.4
O1 A:MPO741 1.8 26.2 0.4
OD2 A:ASP377 2.1 20.0 1.0
NE2 A:HIS543 2.1 18.8 1.0
O A:HOH801 2.1 13.9 0.4
OE2 A:GLU415 2.3 19.6 1.0
OE1 A:GLU415 2.5 19.9 1.0
O2 A:MPO741 2.6 29.2 0.4
S1 A:MPO741 2.7 30.1 0.4
CD A:GLU415 2.7 18.3 1.0
CE1 A:HIS543 2.9 19.0 1.0
O A:HOH806 3.0 12.7 0.4
CG A:ASP377 3.1 19.8 1.0
CD2 A:HIS543 3.2 20.0 1.0
OD1 A:ASP377 3.4 19.9 1.0
C3 A:MPO741 3.4 27.6 0.4
O3 A:MPO741 3.5 30.6 0.4
O A:HOH805 3.5 15.6 0.4
ZN A:ZN1752 3.7 18.5 0.4
N A:GLU742 3.8 22.7 0.4
CA A:GLU742 3.8 22.4 0.4
ZN A:ZN1752 3.9 20.2 0.4
OH A:TYR542 4.0 25.2 1.0
C1 A:MPO741 4.0 22.6 0.4
C A:GLU742 4.0 22.7 0.4
CE1 A:TYR542 4.1 24.8 1.0
OE1 A:GLU414 4.1 20.1 1.0
ND1 A:HIS543 4.2 18.2 1.0
C2 A:MPO741 4.2 28.4 0.4
O A:HOH833 4.2 18.5 1.0
CG A:GLU415 4.3 16.8 1.0
CG A:HIS543 4.3 18.3 1.0
CB A:ASP377 4.4 18.0 1.0
CZ A:TYR542 4.4 23.9 1.0
O A:GLU742 4.4 21.1 0.4
OXT A:GLU742 4.5 23.4 0.4
CE1 A:HIS367 4.7 16.2 1.0
CD1 A:TRP371 4.7 18.2 1.0
N1 A:MPO741 4.7 30.3 0.4
NE2 A:HIS367 4.7 16.6 1.0
NE1 A:TRP371 4.8 18.8 1.0

Zinc binding site 2 out of 4 in 3fec

Go back to Zinc Binding Sites List in 3fec
Zinc binding site 2 out of 4 in the Crystal Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II), Pseudo-Unliganded


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II), Pseudo-Unliganded within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1751

b:16.3
occ:0.45
 ZN A:ZN1751 0.0 16.3 0.5
ZN A:ZN1751 0.5 21.5 0.5
OE2 A:GLU415 1.9 19.6 1.0
OD2 A:ASP377 2.0 20.0 1.0
NE2 A:HIS543 2.0 18.8 1.0
O1 A:MPO741 2.1 26.2 0.4
O A:HOH802 2.3 17.2 0.4
O A:HOH801 2.3 13.9 0.4
OE1 A:GLU415 2.4 19.9 1.0
CD A:GLU415 2.5 18.3 1.0
CG A:ASP377 2.9 19.8 1.0
CE1 A:HIS543 3.0 19.0 1.0
CD2 A:HIS543 3.0 20.0 1.0
O2 A:MPO741 3.1 29.2 0.4
S1 A:MPO741 3.1 30.1 0.4
OD1 A:ASP377 3.3 19.9 1.0
O A:HOH806 3.4 12.7 0.4
ZN A:ZN1752 3.7 18.5 0.4
O A:HOH805 3.8 15.6 0.4
O A:HOH833 3.8 18.5 1.0
O3 A:MPO741 3.8 30.6 0.4
C3 A:MPO741 3.8 27.6 0.4
ZN A:ZN1752 4.0 20.2 0.4
CG A:GLU415 4.0 16.8 1.0
ND1 A:HIS543 4.1 18.2 1.0
CA A:GLU742 4.1 22.4 0.4
N A:GLU742 4.1 22.7 0.4
CG A:HIS543 4.2 18.3 1.0
OE1 A:GLU414 4.2 20.1 1.0
CB A:ASP377 4.2 18.0 1.0
CE1 A:TYR542 4.2 24.8 1.0
OH A:TYR542 4.3 25.2 1.0
C A:GLU742 4.4 22.7 0.4
CD1 A:TRP371 4.4 18.2 1.0
C1 A:MPO741 4.4 22.6 0.4
CE1 A:HIS367 4.5 16.2 1.0
NE1 A:TRP371 4.6 18.8 1.0
C2 A:MPO741 4.6 28.4 0.4
CZ A:TYR542 4.6 23.9 1.0
NE2 A:HIS367 4.7 16.6 1.0
O A:GLU742 4.7 21.1 0.4
OXT A:GLU742 4.9 23.4 0.4
O A:ASP377 5.0 18.6 1.0

Zinc binding site 3 out of 4 in 3fec

Go back to Zinc Binding Sites List in 3fec
Zinc binding site 3 out of 4 in the Crystal Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II), Pseudo-Unliganded


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II), Pseudo-Unliganded within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1752

b:20.2
occ:0.40
 ZN A:ZN1752 0.0 20.2 0.4
ZN A:ZN1752 0.3 18.5 0.4
O A:HOH805 1.9 15.6 0.4
OD1 A:ASP443 2.0 20.8 1.0
O3 A:MPO741 2.1 30.6 0.4
OD1 A:ASP377 2.1 19.9 1.0
NE2 A:HIS367 2.2 16.6 1.0
O A:HOH801 2.3 13.9 0.4
OD2 A:ASP443 2.4 22.1 1.0
CG A:ASP443 2.5 21.6 1.0
O1 A:MPO741 3.1 26.2 0.4
CG A:ASP377 3.1 19.8 1.0
CE1 A:HIS367 3.1 16.2 1.0
S1 A:MPO741 3.1 30.1 0.4
CD2 A:HIS367 3.1 18.3 1.0
O A:HOH806 3.2 12.7 0.4
OD2 A:ASP377 3.6 20.0 1.0
O A:HOH804 3.8 21.6 0.4
ZN A:ZN1751 3.9 21.5 0.5
ZN A:ZN1751 4.0 16.3 0.5
OE1 A:GLU414 4.0 20.1 1.0
CB A:ASP443 4.1 19.6 1.0
O2 A:MPO741 4.1 29.2 0.4
OE2 A:GLU414 4.2 22.8 1.0
C1 A:MPO741 4.2 22.6 0.4
CB A:PRO378 4.2 18.5 1.0
OG A:SER444 4.2 16.5 0.5
CD A:GLU414 4.2 23.9 1.0
ND1 A:HIS367 4.2 15.8 1.0
CB A:ASP377 4.3 18.0 1.0
CG A:HIS367 4.3 16.9 1.0
OE2 A:GLU415 4.3 19.6 1.0
CA A:PRO378 4.4 17.5 1.0
O A:HOH802 4.5 17.2 0.4
CA A:ASP377 4.5 18.2 1.0
N A:PRO378 4.6 17.2 1.0
N A:SER444 4.7 18.0 1.0
C A:ASP377 4.7 17.8 1.0
N A:GLU742 4.8 22.7 0.4
OG A:SER509 4.9 19.6 1.0
CA A:ASP443 4.9 17.6 1.0

Zinc binding site 4 out of 4 in 3fec

Go back to Zinc Binding Sites List in 3fec
Zinc binding site 4 out of 4 in the Crystal Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II), Pseudo-Unliganded


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II), Pseudo-Unliganded within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1752

b:18.5
occ:0.40
 ZN A:ZN1752 0.0 18.5 0.4
ZN A:ZN1752 0.3 20.2 0.4
OD1 A:ASP377 2.0 19.9 1.0
O A:HOH805 2.0 15.6 0.4
NE2 A:HIS367 2.0 16.6 1.0
O A:HOH801 2.1 13.9 0.4
O3 A:MPO741 2.1 30.6 0.4
OD1 A:ASP443 2.3 20.8 1.0
OD2 A:ASP443 2.6 22.1 1.0
CG A:ASP443 2.8 21.6 1.0
O1 A:MPO741 2.8 26.2 0.4
CE1 A:HIS367 2.9 16.2 1.0
CG A:ASP377 3.0 19.8 1.0
S1 A:MPO741 3.0 30.1 0.4
CD2 A:HIS367 3.1 18.3 1.0
O A:HOH806 3.2 12.7 0.4
OD2 A:ASP377 3.4 20.0 1.0
ZN A:ZN1751 3.7 21.5 0.5
ZN A:ZN1751 3.7 16.3 0.5
OE1 A:GLU414 3.8 20.1 1.0
O A:HOH804 4.0 21.6 0.4
OE2 A:GLU415 4.1 19.6 1.0
ND1 A:HIS367 4.1 15.8 1.0
O2 A:MPO741 4.1 29.2 0.4
CD A:GLU414 4.1 23.9 1.0
OE2 A:GLU414 4.1 22.8 1.0
C1 A:MPO741 4.1 22.6 0.4
CG A:HIS367 4.2 16.9 1.0
CB A:PRO378 4.2 18.5 1.0
CB A:ASP377 4.3 18.0 1.0
O A:HOH802 4.3 17.2 0.4
CB A:ASP443 4.4 19.6 1.0
OG A:SER444 4.4 16.5 0.5
CA A:PRO378 4.4 17.5 1.0
CA A:ASP377 4.5 18.2 1.0
N A:PRO378 4.6 17.2 1.0
N A:GLU742 4.6 22.7 0.4
C A:ASP377 4.6 17.8 1.0
CD A:GLU415 4.8 18.3 1.0
N A:SER444 4.9 18.0 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 13:08:29 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