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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: Wed Dec 16 04:18:15 2020

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