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Zinc in PDB 3ff3: The High Resolution Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II) in Complex with L-Glutamate

Enzymatic activity of The High Resolution Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II) in Complex with L-Glutamate

All present enzymatic activity of The High Resolution Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II) in Complex with L-Glutamate:
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 L-Glutamate, PDB code: 3ff3 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) 19.96 / 1.37
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 122.535, 104.128, 77.584, 90.00, 107.98, 90.00
R / Rfree (%) 13.2 / 15.5

Other elements in 3ff3:

The structure of The High Resolution Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II) in Complex with L-Glutamate 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 L-Glutamate (pdb code 3ff3). 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 L-Glutamate, PDB code: 3ff3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3ff3

Go back to Zinc Binding Sites List in 3ff3
Zinc binding site 1 out of 2 in the The High Resolution Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II) in Complex with L-Glutamate


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 L-Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1751

b:8.1
occ:0.80
 OD2 A:ASP377 2.0 10.3 1.0
NE2 A:HIS543 2.1 7.7 1.0
O A:HOH1603 2.1 13.1 1.0
OE2 A:GLU415 2.2 10.8 1.0
O A:HOH1610 2.4 21.6 1.0
OE1 A:GLU415 2.4 9.1 1.0
CD A:GLU415 2.6 8.8 1.0
CG A:ASP377 3.0 10.3 1.0
CE1 A:HIS543 3.0 8.3 1.0
CD2 A:HIS543 3.1 8.6 1.0
O A:HOH971 3.3 17.4 0.8
OD1 A:ASP377 3.4 9.7 1.0
ZN A:ZN1752 3.7 10.6 0.7
O A:HOH875 3.7 18.2 0.6
N A:GLU1 3.9 8.2 0.8
CA A:GLU1 4.0 6.8 0.8
O A:HOH1084 4.0 8.5 1.0
CG A:GLU415 4.1 7.8 1.0
OH A:TYR542 4.2 11.1 1.0
ND1 A:HIS543 4.2 8.3 1.0
OE1 A:GLU414 4.2 9.7 1.0
CE1 A:TYR542 4.2 8.9 1.0
CG A:HIS543 4.2 8.2 1.0
C A:GLU1 4.3 7.6 0.8
CB A:ASP377 4.3 9.4 1.0
CD1 A:TRP371 4.5 7.3 1.0
O A:GLU1 4.6 7.7 0.8
CZ A:TYR542 4.6 10.0 1.0
CE1 A:HIS367 4.6 8.3 1.0
NE1 A:TRP371 4.7 7.9 1.0
NE2 A:HIS367 4.7 8.2 1.0
OXT A:GLU1 4.8 8.2 0.8

Zinc binding site 2 out of 2 in 3ff3

Go back to Zinc Binding Sites List in 3ff3
Zinc binding site 2 out of 2 in the The High Resolution Structure of Human Glutamate Carboxypeptidase III (Gcpiii/Naaladase II) in Complex with L-Glutamate


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 L-Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1752

b:10.6
occ:0.70
 O A:HOH875 2.0 18.2 0.6
OD1 A:ASP377 2.1 9.7 1.0
NE2 A:HIS367 2.1 8.2 1.0
O A:HOH1603 2.3 13.1 1.0
OD1 A:ASP443 2.3 10.3 0.7
OD2 A:ASP443 2.6 12.9 0.7
CG A:ASP443 2.8 11.2 0.7
CE1 A:HIS367 3.0 8.3 1.0
CG A:ASP377 3.0 10.3 1.0
CD2 A:HIS367 3.2 8.2 1.0
O A:HOH971 3.2 17.4 0.8
OD2 A:ASP377 3.5 10.3 1.0
ZN A:ZN1751 3.7 8.1 0.8
O A:HOH780 3.8 34.6 1.0
OE1 A:GLU414 3.9 9.7 1.0
OE2 A:GLU414 4.1 11.2 1.0
O A:HOH789 4.1 28.3 1.0
CD A:GLU414 4.1 8.8 1.0
O A:HOH1610 4.2 21.6 1.0
ND1 A:HIS367 4.2 7.3 1.0
OE2 A:GLU415 4.2 10.8 1.0
CB A:PRO378 4.2 8.2 1.0
CB A:ASP377 4.3 9.4 1.0
CB A:ASP443 4.3 10.6 0.3
CG A:HIS367 4.3 7.1 1.0
OG A:SER444 4.3 6.9 0.5
CB A:ASP443 4.4 9.9 0.7
CA A:PRO378 4.5 7.2 1.0
N A:GLU1 4.5 8.2 0.8
CA A:ASP377 4.6 8.0 1.0
N A:PRO378 4.6 7.3 1.0
C A:ASP377 4.7 8.2 1.0
CD A:GLU415 4.9 8.8 1.0
OD2 A:ASP443 4.9 17.1 0.3
N A:SER444 4.9 8.3 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 04:18:22 2020

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