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Zinc in PDB 3fvz: Structure of Peptidyl-Alpha-Hydroxyglycine Alpha-Amidating Lyase (Pal)

Enzymatic activity of Structure of Peptidyl-Alpha-Hydroxyglycine Alpha-Amidating Lyase (Pal)

All present enzymatic activity of Structure of Peptidyl-Alpha-Hydroxyglycine Alpha-Amidating Lyase (Pal):
4.3.2.5;

Protein crystallography data

The structure of Structure of Peptidyl-Alpha-Hydroxyglycine Alpha-Amidating Lyase (Pal), PDB code: 3fvz was solved by E.E.Chufan, M.De, B.A.Eipper, R.E.Mains, L.M.Amzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.22 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.176, 75.056, 97.474, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 26.3

Other elements in 3fvz:

The structure of Structure of Peptidyl-Alpha-Hydroxyglycine Alpha-Amidating Lyase (Pal) also contains other interesting chemical elements:

Iron (Fe) 1 atom
Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Peptidyl-Alpha-Hydroxyglycine Alpha-Amidating Lyase (Pal) (pdb code 3fvz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Structure of Peptidyl-Alpha-Hydroxyglycine Alpha-Amidating Lyase (Pal), PDB code: 3fvz:

Zinc binding site 1 out of 1 in 3fvz

Go back to Zinc Binding Sites List in 3fvz
Zinc binding site 1 out of 1 in the Structure of Peptidyl-Alpha-Hydroxyglycine Alpha-Amidating Lyase (Pal)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Peptidyl-Alpha-Hydroxyglycine Alpha-Amidating Lyase (Pal) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn821

b:61.6
occ:1.00
 OXT A:ACT1 2.0 59.9 1.0
NE2 A:HIS585 2.1 47.9 1.0
NE2 A:HIS786 2.1 50.5 1.0
NE2 A:HIS690 2.1 53.4 1.0
CE1 A:HIS585 3.0 48.8 1.0
CD2 A:HIS786 3.0 50.8 1.0
CE1 A:HIS690 3.0 52.4 1.0
C A:ACT1 3.1 59.9 1.0
CD2 A:HIS585 3.1 48.6 1.0
CE1 A:HIS786 3.1 50.8 1.0
CD2 A:HIS690 3.2 53.7 1.0
OH A:TYR654 3.2 53.4 1.0
O A:ACT1 3.3 59.7 1.0
CE1 A:TYR654 3.5 52.3 1.0
CZ A:TYR654 3.8 52.7 1.0
ND1 A:HIS585 4.1 50.1 1.0
CG A:HIS585 4.2 50.6 1.0
ND1 A:HIS690 4.2 52.8 1.0
ND1 A:HIS786 4.2 51.2 1.0
CG A:HIS786 4.2 52.3 1.0
CG A:HIS690 4.3 53.3 1.0
CH3 A:ACT1 4.4 59.9 1.0
O3 A:GOL824 4.7 55.0 1.0
CD1 A:TYR654 4.8 51.8 1.0
CZ3 A:TRP538 4.8 54.2 1.0
NH2 A:ARG533 4.9 54.2 1.0
CE A:MET784 5.0 57.0 1.0

Reference:

E.E.Chufan, M.De, B.A.Eipper, R.E.Mains, L.M.Amzel. Amidation of Bioactive Peptides: the Structure of the Lyase Domain of the Amidating Enzyme. Structure V. 17 965 2009.
ISSN: ISSN 0969-2126
PubMed: 19604476
DOI: 10.1016/J.STR.2009.05.008
Page generated: Wed Dec 16 04:19:33 2020

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