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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

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