Zinc 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:

Calcium	(Ca)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Human Neutral Ceramidase with Zn-Bound Phosphate, PDB code: 4wgk:
Jump to Zinc binding site number: 1; 2;

Zinc 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 Zinc with other atoms in the Zn 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:Zn801 b:21.8 occ:1.00 O2 A:PO4810 2.0 35.2 1.0 OE1 A:GLU540 2.1 24.1 1.0 NE2 A:HIS194 2.1 13.3 1.0 NE2 A:HIS303 2.1 16.3 1.0 OH A:TYR579 2.4 17.1 1.0 OE2 A:GLU540 2.6 25.5 1.0 CD A:GLU540 2.6 25.8 1.0 CD2 A:HIS303 3.0 16.1 1.0 CE1 A:HIS303 3.0 19.8 1.0 CE1 A:HIS194 3.1 17.5 1.0 CD2 A:HIS194 3.1 12.2 1.0 CZ A:TYR579 3.2 16.5 1.0 P A:PO4810 3.4 39.7 1.0 O1 A:PO4810 3.7 39.2 1.0 CE2 A:TYR579 3.8 17.3 1.0 CG A:GLU540 4.1 24.0 1.0 CE1 A:TYR579 4.1 17.3 1.0 ND1 A:HIS303 4.1 19.5 1.0 CG A:HIS303 4.1 18.3 1.0 CE1 A:HIS196 4.1 17.7 1.0 ND1 A:HIS194 4.2 13.3 1.0 O3 A:PO4810 4.2 35.9 1.0 CG A:HIS194 4.2 13.1 1.0 NE2 A:HIS196 4.2 19.5 1.0 NH2 A:ARG257 4.2 19.3 1.0 O4 A:PO4810 4.4 42.3 1.0 CD1 A:LEU350 4.7 12.8 1.0 O A:HOH1082 4.8 21.5 1.0 CB A:GLU540 4.8 21.8 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn801 b:29.0 occ:1.00 NE2 B:HIS303 2.0 13.1 1.0 OE1 B:GLU540 2.1 37.0 1.0 O4 B:PO4808 2.1 37.3 1.0 NE2 B:HIS194 2.2 19.1 1.0 OH B:TYR579 2.3 17.6 1.0 CD B:GLU540 2.7 30.7 1.0 OE2 B:GLU540 2.7 32.3 1.0 CD2 B:HIS303 2.9 11.3 1.0 CE1 B:HIS303 3.0 12.9 1.0 CD2 B:HIS194 3.1 18.4 1.0 CE1 B:HIS194 3.2 19.6 1.0 CZ B:TYR579 3.3 18.5 1.0 P B:PO4808 3.4 35.7 1.0 O2 B:PO4808 3.8 37.2 1.0 CE2 B:TYR579 3.8 16.6 1.0 ND1 B:HIS303 4.1 13.0 1.0 CG B:HIS303 4.1 13.3 1.0 CE1 B:HIS196 4.1 20.5 1.0 NH2 B:ARG257 4.1 17.0 1.0 O B:HOH1027 4.1 21.6 1.0 O1 B:PO4808 4.2 25.9 1.0 CG B:GLU540 4.2 19.3 1.0 CE1 B:TYR579 4.2 21.2 1.0 NE2 B:HIS196 4.2 20.2 1.0 CG B:HIS194 4.2 19.8 1.0 ND1 B:HIS194 4.3 18.9 1.0 O3 B:PO4808 4.5 37.1 1.0 CD1 B:LEU350 4.7 11.0 1.0 CB B:GLU540 4.9 18.4 1.0 NH1 B:ARG257 4.9 16.2 1.0 CZ B:ARG257 4.9 19.2 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