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Calcium 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
Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total only one binding site of Calcium was determined in the Structure of Peptidyl-Alpha-Hydroxyglycine Alpha-Amidating Lyase (Pal), PDB code: 3fvz:

Calcium binding site 1 out of 1 in 3fvz

Go back to Calcium Binding Sites List in 3fvz
Calcium 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 Calcium with other atoms in the Ca 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:Ca823

b:50.7
occ:1.00
 O A:LEU587 2.3 53.2 1.0
OD1 A:ASP787 2.4 54.1 1.0
O A:HOH25 2.5 44.6 1.0
O A:VAL520 2.5 52.0 1.0
O A:HOH54 2.6 47.4 1.0
O A:HOH56 2.7 45.6 1.0
O1 A:GOL824 2.8 51.0 1.0
CG A:ASP787 3.4 54.4 1.0
C A:LEU587 3.5 52.6 1.0
C1 A:GOL824 3.5 53.2 1.0
OD2 A:ASP787 3.6 55.3 1.0
C A:VAL520 3.7 52.3 1.0
N A:VAL520 4.0 52.5 1.0
N A:LEU587 4.3 52.4 1.0
N A:SER588 4.4 52.7 1.0
CA A:LEU587 4.5 52.4 1.0
CA A:VAL520 4.5 52.2 1.0
OD1 A:ASP638 4.5 56.5 1.0
CA A:SER588 4.5 52.7 1.0
N A:ALA521 4.7 52.4 1.0
CB A:ALA521 4.7 52.8 1.0
CB A:SER588 4.7 52.6 1.0
OD2 A:ASP638 4.8 54.3 1.0
O A:HOH24 4.8 44.4 1.0
CB A:ASP787 4.8 54.1 1.0
CA A:ALA521 4.8 52.9 1.0
C2 A:GOL824 4.9 53.2 1.0
CA A:GLY519 4.9 52.6 1.0
CB A:LEU587 4.9 52.3 1.0
C A:GLY519 4.9 52.7 1.0
O A:ILE788 4.9 54.2 1.0
CG2 A:VAL520 4.9 51.1 1.0
O2 A:GOL824 5.0 50.7 1.0
O A:HOH48 5.0 52.3 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: Sat Jul 13 10:19:35 2024

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