Sodium 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:

Magnesium	(Mg)	2 atoms
Zinc	(Zn)	1 atom
Calcium	(Ca)	1 atom

The binding sites of Sodium 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 Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Human Alkaline Ceramidase 3 (ACER3) at 2.7 Angstrom Resolution, PDB code: 6g7o:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 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 Sodium with other atoms in the Na 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:Na408 b:93.6 occ:1.00 CE2 A:TRP219 3.6 97.5 1.0 NE1 A:TRP219 3.7 97.7 1.0 CD2 A:TRP219 3.8 90.9 1.0 CD1 A:TRP219 4.0 96.7 1.0 CE2 A:PHE188 4.0 97.0 1.0 CZ2 A:TRP219 4.0 97.5 1.0 CG A:TRP219 4.0 91.2 1.0 CZ A:PHE188 4.3 96.3 1.0 CE3 A:TRP219 4.3 90.2 1.0 CG2 A:THR213 4.5 0.3 1.0 CH2 A:TRP219 4.5 95.6 1.0 CZ3 A:TRP219 4.7 92.3 1.0 O A:THR213 4.7 0.3 1.0 CB A:THR213 4.8 0.6 1.0 CE1 A:PHE216 4.8 0.9 1.0 CD2 A:PHE188 4.9 93.6 1.0 CB A:TRP219 4.9 88.1 1.0

Sodium binding site 2 out of 3 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 Sodium with other atoms in the Na 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:Na409 b:55.2 occ:1.00 OD2 A:ASP246 2.5 57.2 1.0 O A:HOH526 2.8 50.8 1.0 CG A:ASP246 3.2 49.9 1.0 OD1 A:ASP246 3.3 50.0 1.0 CB A:GLU248 3.9 39.0 1.0 CD A:GLU248 4.3 77.6 1.0 OE2 A:GLU248 4.3 73.1 1.0 CG A:GLU248 4.5 52.5 1.0 OD2 A:ASP249 4.5 57.3 1.0 OE1 A:GLU248 4.6 75.7 1.0 OD1 A:ASP249 4.6 51.5 1.0 CB A:ASP246 4.7 38.9 1.0 CG A:ASP249 4.7 50.2 1.0 O A:HOH534 4.8 40.5 1.0

Sodium binding site 3 out of 3 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 Sodium with other atoms in the Na binding site number 3 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:Na410 b:76.3 occ:1.00 OD2 A:ASP19 3.1 0.7 1.0 OG1 A:THR14 3.6 0.1 1.0 CG A:ASP19 3.7 0.8 1.0 ND2 A:ASN24 3.7 0.9 1.0 CB A:ASP19 4.0 0.3 1.0 O A:HOH569 4.1 61.9 1.0 CG2 A:THR14 4.4 0.4 1.0 CB A:THR14 4.5 0.9 1.0 OD1 A:ASP19 4.5 0.2 1.0 CG A:ASN24 4.8 0.8 1.0 CG A:ARG7 5.0 0.2 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