Magnesium in PDB 2zxc: Ceramidase Complexed with C2

All present enzymatic activity of Ceramidase Complexed with C2:
3.5.1.23;

The structure of Ceramidase Complexed with C2, PDB code: 2zxc was solved by H.Okano, T.Inoue, N.Okino, Y.Kakuta, H.Matsumura, M.Ito, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.97 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.741, 65.800, 340.339, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 22.8

The structure of Ceramidase Complexed with C2 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Ceramidase Complexed with C2 (pdb code 2zxc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ceramidase Complexed with C2, PDB code: 2zxc:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Ceramidase Complexed with C2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ceramidase Complexed with C2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg652 b:28.4 occ:1.00 O A:HIS37 2.1 21.2 1.0 O A:HOH653 2.2 14.9 1.0 O A:ASP579 2.3 20.6 1.0 OG1 A:THR584 2.5 22.0 1.0 O A:ASP581 2.6 22.4 1.0 O A:THR584 2.7 21.9 1.0 C A:ASP579 2.9 21.1 1.0 C A:HIS37 3.2 17.7 1.0 C A:THR584 3.2 22.3 1.0 CA A:ASP579 3.6 22.7 1.0 CB A:THR584 3.6 20.3 1.0 N A:ASP581 3.6 23.3 1.0 C A:ASP581 3.6 23.4 1.0 N A:ASN580 3.7 21.6 1.0 C A:ASN580 3.8 23.1 1.0 O A:THR578 3.8 22.4 1.0 CA A:THR584 3.8 21.4 1.0 N A:GLN585 4.0 23.0 1.0 CA A:HIS37 4.1 18.3 1.0 CA A:ASN580 4.1 22.3 1.0 N A:THR584 4.1 21.6 1.0 CA A:ASP581 4.1 23.6 1.0 N A:MET38 4.2 18.9 1.0 O A:ASN580 4.2 22.4 1.0 O A:ILE36 4.3 16.1 1.0 CA A:GLN585 4.3 23.6 1.0 CA A:MET38 4.4 19.6 1.0 CD2 A:HIS37 4.4 18.1 1.0 CB A:ASP579 4.5 19.9 1.0 C A:THR578 4.7 22.7 1.0 N A:ASP579 4.7 20.6 1.0 N A:TRP582 4.8 23.3 1.0 CG A:MET38 4.8 25.8 1.0 N A:HIS37 4.8 18.0 1.0 C A:ILE36 4.8 17.2 1.0 CB A:ASP581 4.9 24.6 1.0 CG2 A:THR584 4.9 17.8 1.0

Magnesium binding site 2 out of 2 in the Ceramidase Complexed with C2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ceramidase Complexed with C2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg654 b:29.8 occ:1.00 O B:HIS37 2.1 20.3 1.0 O B:HOH704 2.3 12.8 1.0 O B:ASP579 2.4 21.0 1.0 OG1 B:THR584 2.5 21.8 1.0 O B:ASP581 2.5 24.0 1.0 O B:THR584 2.7 23.7 1.0 C B:ASP579 3.0 21.0 1.0 C B:THR584 3.2 23.6 1.0 C B:HIS37 3.3 17.5 1.0 CA B:ASP579 3.6 22.5 1.0 N B:ASP581 3.6 23.5 1.0 C B:ASP581 3.6 23.5 1.0 CB B:THR584 3.6 21.1 1.0 N B:ASN580 3.8 21.3 1.0 C B:ASN580 3.8 22.7 1.0 O B:THR578 3.8 23.1 1.0 CA B:THR584 3.8 22.6 1.0 N B:GLN585 4.0 23.7 1.0 N B:THR584 4.1 22.7 1.0 CA B:HIS37 4.1 18.8 1.0 CA B:ASP581 4.1 24.0 1.0 CA B:ASN580 4.1 21.5 1.0 O B:ASN580 4.2 22.9 1.0 N B:MET38 4.2 18.6 1.0 CA B:GLN585 4.3 24.9 1.0 O B:ILE36 4.4 19.1 1.0 CD2 B:HIS37 4.4 17.2 1.0 CA B:MET38 4.4 20.1 1.0 CB B:ASP579 4.5 19.3 1.0 C B:THR578 4.7 23.6 1.0 N B:ASP579 4.7 21.1 1.0 N B:TRP582 4.8 23.3 1.0 CG B:MET38 4.8 24.1 1.0 CB B:ASP581 4.8 24.4 1.0 N B:HIS37 4.8 19.1 1.0 CG2 B:THR584 4.9 18.4 1.0 C B:ILE36 4.9 18.6 1.0

T.Inoue, N.Okino, Y.Kakuta, A.Hijikata, H.Okano, H.M.Goda, M.Tani, N.Sueyoshi, K.Kambayashi, H.Matsumura, Y.Kai, M.Ito. Mechanistic Insights Into the Hydrolysis and Synthesis of Ceramide By Neutral Ceramidase. J.Biol.Chem. V. 284 9566 2009.
ISSN: ISSN 0021-9258
PubMed: 19088069
DOI: 10.1074/JBC.M808232200