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

The binding sites of Zinc 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 Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Human Alkaline Ceramidase 3 (ACER3) at 2.7 Angstrom Resolution, PDB code: 6g7o:

Zinc binding site 1 out of 1 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 Zinc with other atoms in the Zn 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:Zn401 b:86.0 occ:1.00 O A:HOH505 2.2 0.8 1.0 NE2 A:HIS221 2.4 88.0 1.0 NE2 A:HIS217 2.4 93.4 1.0 NE2 A:HIS81 2.4 87.0 1.0 CE1 A:HIS81 3.1 88.7 1.0 CE1 A:HIS221 3.3 89.4 1.0 CE1 A:HIS217 3.3 92.5 1.0 CD2 A:HIS217 3.4 95.2 1.0 CD2 A:HIS221 3.4 86.5 1.0 C4 A:OLB411 3.4 89.0 1.0 CD2 A:HIS81 3.6 87.8 1.0 C3 A:OLB411 3.7 89.6 1.0 OG A:SER77 3.9 86.3 1.0 C5 A:OLB411 3.9 88.4 1.0 NE1 A:TRP220 4.0 83.0 1.0 C2 A:OLB411 4.2 90.0 1.0 CD1 A:TRP220 4.3 84.8 1.0 NE1 A:TRP20 4.4 95.0 1.0 ND1 A:HIS81 4.4 91.0 1.0 C6 A:OLB411 4.4 87.8 1.0 ND1 A:HIS217 4.4 94.3 1.0 CG A:HIS217 4.4 94.0 1.0 ND1 A:HIS221 4.4 89.6 1.0 CE2 A:PHE80 4.5 90.6 1.0 CE2 A:TRP20 4.5 95.8 1.0 CZ2 A:TRP20 4.5 93.3 1.0 CG A:HIS221 4.5 85.5 1.0 CG A:HIS81 4.6 88.4 1.0 CD2 A:PHE80 4.8 87.0 1.0 OD2 A:ASP92 4.9 0.5 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