Calcium in PDB 8yk5: Structure of Glycerophosphoethanolamine Ethanolaminephosphodiesterase From Streptomyces Sanglieri

All present enzymatic activity of Structure of Glycerophosphoethanolamine Ethanolaminephosphodiesterase From Streptomyces Sanglieri:
3.1.4.3;

The structure of Structure of Glycerophosphoethanolamine Ethanolaminephosphodiesterase From Streptomyces Sanglieri, PDB code: 8yk5 was solved by K.Murayama, D.Sugimori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.25 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	143.742, 179.184, 88.45, 90, 120.44, 90
R / Rfree (%)	18.3 / 21

The binding sites of Calcium atom in the Structure of Glycerophosphoethanolamine Ethanolaminephosphodiesterase From Streptomyces Sanglieri (pdb code 8yk5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Glycerophosphoethanolamine Ethanolaminephosphodiesterase From Streptomyces Sanglieri, PDB code: 8yk5:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Glycerophosphoethanolamine Ethanolaminephosphodiesterase From Streptomyces Sanglieri


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Glycerophosphoethanolamine Ethanolaminephosphodiesterase From Streptomyces Sanglieri within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:39.9 occ:1.00 OD1 A:ASN16 2.1 40.0 1.0 OD2 A:ASP341 2.1 41.3 1.0 OE1 A:GLU15 2.2 40.8 1.0 OG1 A:THR139 2.3 35.5 1.0 O1 A:GOL702 2.3 51.1 1.0 CG A:ASP341 2.8 34.2 1.0 OD1 A:ASP341 2.8 29.5 1.0 CD A:GLU15 2.9 36.9 1.0 CG A:ASN16 3.2 42.6 1.0 OE2 A:GLU15 3.3 37.5 1.0 OE2 A:GLU342 3.4 52.7 1.0 CB A:THR139 3.4 35.1 1.0 C1 A:GOL702 3.7 50.8 1.0 CG2 A:THR139 3.8 33.7 1.0 ND2 A:ASN16 3.9 41.4 1.0 C3 A:GOL702 3.9 46.5 1.0 CG A:GLU342 3.9 39.7 1.0 CA A:THR139 3.9 34.2 1.0 CG A:GLU15 4.1 31.9 1.0 O2 A:GOL702 4.1 44.7 1.0 CD A:GLU342 4.2 49.0 1.0 CB A:GLU15 4.2 35.2 1.0 C2 A:GOL702 4.2 52.8 1.0 CD2 A:HIS304 4.2 35.4 1.0 CB A:ASP341 4.2 33.2 1.0 N A:ASN16 4.2 33.1 1.0 N A:THR139 4.3 34.0 1.0 CB A:ASN16 4.3 36.6 1.0 CA A:GLU15 4.4 31.5 1.0 NE2 A:HIS304 4.6 39.8 1.0 CA A:ASN16 4.6 35.8 1.0 C A:GLU15 4.7 29.0 1.0 O3 A:GOL702 4.8 53.0 1.0

Calcium binding site 2 out of 2 in the Structure of Glycerophosphoethanolamine Ethanolaminephosphodiesterase From Streptomyces Sanglieri


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Glycerophosphoethanolamine Ethanolaminephosphodiesterase From Streptomyces Sanglieri within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca701 b:31.6 occ:1.00 OD2 B:ASP341 2.0 30.4 1.0 OD1 B:ASN16 2.0 27.2 1.0 OG1 B:THR139 2.0 35.2 1.0 OE1 B:GLU342 2.2 43.7 1.0 OE2 B:GLU15 2.2 35.5 1.0 O1 B:GOL702 2.4 43.5 1.0 CG B:ASP341 2.8 31.2 1.0 OD1 B:ASP341 3.0 29.5 1.0 CD B:GLU15 3.1 32.4 1.0 CG B:ASN16 3.1 30.0 1.0 O2 B:GOL702 3.2 44.6 1.0 CB B:THR139 3.2 36.6 1.0 CD B:GLU342 3.3 41.9 1.0 OE1 B:GLU15 3.4 30.0 1.0 CA B:THR139 3.7 32.8 1.0 C1 B:GOL702 3.7 38.5 1.0 ND2 B:ASN16 3.7 32.6 1.0 CG2 B:THR139 3.8 28.1 1.0 CG B:GLU342 3.8 30.5 1.0 C2 B:GOL702 3.9 36.1 1.0 NH1 A:ARG436 4.0 42.2 1.0 N B:THR139 4.1 35.6 1.0 OE2 B:GLU342 4.2 50.7 1.0 C3 B:GOL702 4.2 41.1 1.0 CB B:ASP341 4.2 28.6 1.0 CG B:GLU15 4.3 28.4 1.0 N B:ASN16 4.3 27.8 1.0 CD2 B:HIS304 4.3 26.4 1.0 CB B:ASN16 4.3 29.0 1.0 CB B:GLU15 4.4 27.0 1.0 CA B:GLU15 4.6 26.0 1.0 CA B:ASN16 4.6 25.7 1.0 NE2 B:HIS304 4.8 32.5 1.0 C B:GLU15 4.8 25.3 1.0 CB B:GLU342 4.9 30.8 1.0 C B:SER138 4.9 32.8 1.0 N B:GLU342 5.0 24.3 1.0

K.Murayama, T.Hosaka, M.Shirouzu, D.Sugimori. Structure of A Phosphodiesterase From Streptomyces Sanglieri with A Novel C-Terminal Domain. Biochem.Biophys.Res.Commun. V. 708 49784 2024.
ISSN: ESSN 1090-2104
PubMed: 38503170
DOI: 10.1016/J.BBRC.2024.149784