Calcium in PDB 4wgk: Crystal Structure of Human Neutral Ceramidase with Zn-Bound Phosphate

All present enzymatic activity of Crystal Structure of Human Neutral Ceramidase with Zn-Bound Phosphate:
3.5.1.23;

The structure of Crystal Structure of Human Neutral Ceramidase with Zn-Bound Phosphate, PDB code: 4wgk was solved by M.V.Airola, M.J.Pulkoski-Gross, L.M.Obeid, Y.A.Hannun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.65 / 2.58
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.480, 156.630, 80.330, 90.00, 108.04, 90.00
R / Rfree (%)	17.8 / 22.3

The structure of Crystal Structure of Human Neutral Ceramidase with Zn-Bound Phosphate also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Crystal Structure of Human Neutral Ceramidase with Zn-Bound Phosphate (pdb code 4wgk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Human Neutral Ceramidase with Zn-Bound Phosphate, PDB code: 4wgk:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Human Neutral Ceramidase with Zn-Bound Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human Neutral Ceramidase with Zn-Bound Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:68.8 occ:1.00 O A:HOH977 2.2 26.0 1.0 O A:SER714 2.3 14.8 1.0 O A:LEU134 2.4 17.8 1.0 O A:THR717 2.4 18.5 1.0 O A:ASP712 2.4 29.6 1.0 OG1 A:THR717 2.7 14.9 1.0 C A:ASP712 3.1 24.3 1.0 C A:THR717 3.2 17.6 1.0 C A:LEU134 3.4 18.5 1.0 C A:SER714 3.4 15.1 1.0 CA A:ASP712 3.7 18.9 1.0 CB A:THR717 3.8 16.2 1.0 CA A:THR717 3.8 15.7 1.0 N A:SER714 3.9 15.2 1.0 N A:THR717 4.0 18.3 1.0 C A:ALA713 4.0 15.5 1.0 N A:ALA713 4.0 18.7 1.0 O A:ASN711 4.0 15.9 1.0 CA A:LEU134 4.2 19.0 1.0 CA A:SER714 4.2 16.8 1.0 N A:ARG718 4.2 18.8 1.0 N A:THR135 4.3 17.6 1.0 CA A:ALA713 4.3 18.6 1.0 N A:TRP715 4.4 23.0 1.0 O A:ALA713 4.4 15.9 1.0 CA A:THR135 4.4 17.7 1.0 O A:ILE133 4.5 19.0 1.0 CA A:TRP715 4.5 24.5 1.0 CA A:ARG718 4.5 20.9 1.0 CB A:ASP712 4.6 16.5 1.0 C A:TRP715 4.7 23.2 1.0 CB A:SER714 4.8 16.2 1.0 CD1 A:LEU134 4.8 21.7 1.0 N A:ASP712 4.8 16.4 1.0 C A:ASN711 4.8 17.0 1.0 CG2 A:THR717 5.0 13.8 1.0 N A:LEU134 5.0 20.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Human Neutral Ceramidase with Zn-Bound Phosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human Neutral Ceramidase with Zn-Bound Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:74.6 occ:1.00 O B:THR717 2.4 22.1 1.0 O B:ASP712 2.4 24.4 1.0 O B:LEU134 2.5 27.0 1.0 OG1 B:THR717 2.6 24.6 1.0 O B:SER714 2.6 15.9 1.0 C B:ASP712 3.1 21.0 1.0 C B:THR717 3.1 23.3 1.0 C B:LEU134 3.4 24.1 1.0 CA B:ASP712 3.5 19.8 1.0 CB B:THR717 3.6 24.6 1.0 C B:SER714 3.8 17.6 1.0 CA B:THR717 3.8 23.8 1.0 N B:ARG718 4.0 23.5 1.0 O B:ASN711 4.0 16.4 1.0 CA B:LEU134 4.0 18.2 1.0 N B:ALA713 4.1 19.5 1.0 N B:THR717 4.1 23.6 1.0 O B:ILE133 4.1 20.2 1.0 N B:SER714 4.2 17.2 1.0 CA B:ARG718 4.2 23.1 1.0 CB B:ASP712 4.3 20.2 1.0 C B:ALA713 4.3 22.6 1.0 N B:THR135 4.4 24.0 1.0 CA B:SER714 4.5 18.1 1.0 CA B:ALA713 4.6 20.6 1.0 CA B:THR135 4.6 21.4 1.0 N B:ASP712 4.6 16.6 1.0 N B:TRP715 4.8 19.4 1.0 CD1 B:LEU134 4.8 12.8 1.0 C B:ASN711 4.8 20.1 1.0 C B:ILE133 4.8 18.8 1.0 O B:ALA713 4.8 17.0 1.0 N B:LEU134 4.8 17.4 1.0 CD2 B:LEU694 4.9 15.6 1.0 CA B:TRP715 4.9 22.9 1.0 CG2 B:THR717 4.9 26.8 1.0 C B:ARG718 5.0 20.7 1.0

M.V.Airola, W.J.Allen, M.J.Pulkoski-Gross, L.M.Obeid, R.C.Rizzo, Y.A.Hannun. Structural Basis For Ceramide Recognition and Hydrolysis By Human Neutral Ceramidase. Structure V. 23 1482 2015.
ISSN: ISSN 0969-2126
PubMed: 26190575
DOI: 10.1016/J.STR.2015.06.013