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Zinc in PDB 5f09: Structure of Inactive Gcpii Mutant in Complex with Beta-Citryl Glutamate

Enzymatic activity of Structure of Inactive Gcpii Mutant in Complex with Beta-Citryl Glutamate

All present enzymatic activity of Structure of Inactive Gcpii Mutant in Complex with Beta-Citryl Glutamate:
3.4.17.21;

Protein crystallography data

The structure of Structure of Inactive Gcpii Mutant in Complex with Beta-Citryl Glutamate, PDB code: 5f09 was solved by J.Tykvart, M.Navratil, P.Pachl, J.Konvalinka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.85
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 100.901, 130.923, 159.136, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 18.1

Other elements in 5f09:

The structure of Structure of Inactive Gcpii Mutant in Complex with Beta-Citryl 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 Structure of Inactive Gcpii Mutant in Complex with Beta-Citryl Glutamate (pdb code 5f09). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Inactive Gcpii Mutant in Complex with Beta-Citryl Glutamate, PDB code: 5f09:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5f09

Go back to Zinc Binding Sites List in 5f09
Zinc binding site 1 out of 2 in the Structure of Inactive Gcpii Mutant in Complex with Beta-Citryl Glutamate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Inactive Gcpii Mutant in Complex with Beta-Citryl Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn815

b:28.0
occ:1.00
OD2 A:ASP387 2.0 28.7 1.0
OE2 A:GLU425 2.1 25.6 1.0
NE2 A:HIS553 2.1 26.9 1.0
O A:HOH933 2.2 24.4 0.3
O A:HOH902 2.2 28.4 1.0
OE1 A:GLU425 2.5 28.1 1.0
CD A:GLU425 2.6 25.9 1.0
OAK A:BC8819 2.6 37.6 0.7
CG A:ASP387 3.0 26.2 1.0
CE1 A:HIS553 3.0 26.5 1.0
CD2 A:HIS553 3.1 27.3 1.0
OD1 A:ASP387 3.2 25.6 1.0
ZN A:ZN816 3.4 26.7 1.0
O A:HOH1197 3.7 17.6 0.3
CAJ A:BC8819 3.7 38.1 0.7
CE1 A:TYR552 4.0 29.4 1.0
O A:HOH967 4.1 21.9 1.0
CG A:GLU425 4.1 24.6 1.0
ND1 A:HIS553 4.2 27.7 1.0
CA A:BC8819 4.2 32.2 0.7
CG A:HIS553 4.2 27.6 1.0
OH A:TYR552 4.2 31.4 1.0
O A:HOH1335 4.2 27.0 0.3
CB A:ASP387 4.3 26.9 1.0
N A:BC8819 4.4 37.4 0.7
CZ A:TYR552 4.5 30.0 1.0
NE2 A:HIS377 4.5 23.1 1.0
C A:BC8819 4.6 29.7 0.7
CD1 A:TRP381 4.6 28.7 1.0
OAI A:BC8819 4.6 37.2 0.7
CE1 A:HIS377 4.6 23.3 1.0
NE1 A:TRP381 4.7 29.2 1.0
OXT A:BC8819 4.7 25.8 0.7
CAD A:BC8819 4.8 37.0 0.7

Zinc binding site 2 out of 2 in 5f09

Go back to Zinc Binding Sites List in 5f09
Zinc binding site 2 out of 2 in the Structure of Inactive Gcpii Mutant in Complex with Beta-Citryl Glutamate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Inactive Gcpii Mutant in Complex with Beta-Citryl Glutamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn816

b:26.7
occ:1.00
OD1 A:ASP387 1.9 25.6 1.0
OD2 A:ASP453 2.0 24.3 1.0
NE2 A:HIS377 2.1 23.1 1.0
O A:HOH902 2.2 28.4 1.0
O A:HOH1197 2.5 17.6 0.3
CG A:ASP453 2.7 24.7 1.0
OD1 A:ASP453 2.7 25.6 1.0
CG A:ASP387 2.9 26.2 1.0
CE1 A:HIS377 3.0 23.3 1.0
CD2 A:HIS377 3.1 22.2 1.0
OD2 A:ASP387 3.3 28.7 1.0
ZN A:ZN815 3.4 28.0 1.0
OE2 A:GLU425 3.8 25.6 1.0
OAI A:BC8819 4.1 37.2 0.7
OAK A:BC8819 4.1 37.6 0.7
ND1 A:HIS377 4.2 22.9 1.0
CB A:ASP453 4.2 24.3 1.0
CG A:HIS377 4.2 21.5 1.0
CB A:ASP387 4.2 26.9 1.0
O A:HOH933 4.3 24.4 0.3
ND2 A:ASN519 4.3 25.7 1.0
CB A:PRO388 4.4 23.6 1.0
O A:HOH1335 4.4 27.0 0.3
CAJ A:BC8819 4.5 38.1 0.7
CD A:GLU425 4.5 25.9 1.0
CA A:ASP387 4.6 26.6 1.0
CA A:PRO388 4.6 24.1 1.0
OG A:SER454 4.7 28.5 1.0
C A:ASP387 4.7 25.7 1.0
N A:PRO388 4.7 24.2 1.0
O A:HOH1090 4.8 45.6 1.0
OE1 A:GLU425 4.8 28.1 1.0
CAD A:BC8819 4.9 37.0 0.7
O A:HOH983 4.9 21.1 0.3

Reference:

M.Navratil, J.Tykvart, J.Schimer, P.Pachl, V.Navratil, T.A.Rokob, K.Hlouchova, L.Rulisek, J.Konvalinka. Comparison of Human Glutamate Carboxypeptidases II and III Reveals Their Divergent Substrate Specificities. Febs J. V. 283 2528 2016.
ISSN: ISSN 1742-464X
PubMed: 27208881
DOI: 10.1111/FEBS.13761
Page generated: Wed Dec 16 06:11:07 2020

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