Magnesium in PDB 6g7o: Crystal Structure of Human Alkaline Ceramidase 3 (ACER3) at 2.7 Angstrom Resolution

The structure of Crystal Structure of Human Alkaline Ceramidase 3 (ACER3) at 2.7 Angstrom Resolution, PDB code: 6g7o was solved by C.Leyrat, I.Vasiliauskaite-Brooks, R.D.Healey, R.Sounier, C.Grison, F.Hoh, S.Basu, S.Granier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.60 / 2.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	60.880, 68.830, 257.520, 90.00, 90.00, 90.00
R / Rfree (%)	24.8 / 27

The structure of Crystal Structure of Human Alkaline Ceramidase 3 (ACER3) at 2.7 Angstrom Resolution also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Calcium	(Ca)	1 atom
Sodium	(Na)	3 atoms

The binding sites of Magnesium atom in the Crystal Structure of Human Alkaline Ceramidase 3 (ACER3) at 2.7 Angstrom Resolution (pdb code 6g7o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human Alkaline Ceramidase 3 (ACER3) at 2.7 Angstrom Resolution, PDB code: 6g7o:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Alkaline Ceramidase 3 (ACER3) at 2.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Alkaline Ceramidase 3 (ACER3) at 2.7 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg413 b:0.7 occ:0.50 O A:HOH509 2.5 62.8 1.0 O A:HOH571 3.1 60.2 1.0 O3 A:SO4407 3.7 0.7 1.0 O3 A:SO4406 4.3 0.7 1.0 O A:HOH593 4.3 0.2 0.5 O A:HOH532 4.7 90.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Alkaline Ceramidase 3 (ACER3) at 2.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Alkaline Ceramidase 3 (ACER3) at 2.7 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg414 b:51.0 occ:1.00 OE1 A:GLU60 2.5 61.5 1.0 N A:ASN115 2.6 41.4 1.0 O1 A:SO4402 2.8 72.2 1.0 CA A:ASN115 3.2 42.3 1.0 CD A:GLU60 3.4 72.0 1.0 CG A:GLU60 3.5 58.2 1.0 O2 A:SO4402 3.6 72.2 1.0 C A:LYS114 3.7 44.7 1.0 S A:SO4402 3.8 71.9 1.0 CG A:ASN115 3.8 62.5 1.0 CA A:LYS114 3.9 40.3 1.0 OD1 A:ASN115 3.9 56.0 1.0 CB A:ASN115 4.1 42.4 1.0 ND2 A:ASN115 4.1 54.3 1.0 CG A:LYS114 4.2 55.7 1.0 CB A:LYS114 4.3 42.1 1.0 C A:ASN115 4.4 47.5 1.0 N A:SER116 4.4 44.5 1.0 CE A:LYS114 4.5 78.7 1.0 CB A:GLU60 4.6 50.3 1.0 OE2 A:GLU60 4.6 63.3 1.0 NH2 A:ARG239 4.6 52.2 1.0 O3 A:SO4402 4.7 72.2 1.0 O A:LYS114 4.8 44.7 1.0 O4 A:SO4402 4.9 71.4 1.0 O A:HOH513 4.9 53.8 1.0 NH1 A:ARG62 5.0 70.0 1.0

I.Vasiliauskaite-Brooks, R.D.Healey, P.Rochaix, J.Saint-Paul, R.Sounier, C.Grison, T.Waltrich-Augusto, M.Fortier, F.Hoh, E.M.Saied, C.Arenz, S.Basu, C.Leyrat, S.Granier. Structure of A Human Intramembrane Ceramidase Explains Enzymatic Dysfunction Found in Leukodystrophy. Nat Commun V. 9 5437 2018.
ISSN: ESSN 2041-1723
PubMed: 30575723
DOI: 10.1038/S41467-018-07864-W