Zinc in PDB 5i81: Asmase with Zinc

All present enzymatic activity of Asmase with Zinc:
3.1.4.12;

The structure of Asmase with Zinc, PDB code: 5i81 was solved by Y.F.Zhou, R.R.Wei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.81 / 2.25
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	132.629, 132.629, 189.565, 90.00, 90.00, 120.00
R / Rfree (%)	18.4 / 20.5

The binding sites of Zinc atom in the Asmase with Zinc (pdb code 5i81). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Asmase with Zinc, PDB code: 5i81:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Asmase with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Asmase with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn715 b:65.8 occ:1.00 O A:HOH891 1.9 39.0 1.0 NE2 A:HIS425 2.1 55.6 1.0 OD1 A:ASN318 2.2 62.2 1.0 ND1 A:HIS457 2.2 41.8 1.0 OD2 A:ASP278 2.4 44.5 1.0 CE1 A:HIS425 3.0 49.4 1.0 CE1 A:HIS457 3.0 38.4 1.0 CD2 A:HIS425 3.1 50.2 1.0 CG A:ASP278 3.1 50.5 1.0 CG A:ASN318 3.2 55.2 1.0 OD1 A:ASP278 3.3 47.9 1.0 ZN A:ZN716 3.3 66.1 1.0 CG A:HIS457 3.3 39.1 1.0 OD1 A:ASP206 3.6 47.7 1.0 ND2 A:ASN318 3.7 50.1 1.0 CA A:HIS457 3.7 44.0 1.0 CB A:HIS457 3.8 38.5 1.0 O A:HOH953 3.9 49.8 1.0 O A:HIS457 4.0 46.1 1.0 ND1 A:HIS425 4.2 50.2 1.0 O A:HOH944 4.2 60.1 1.0 NE2 A:HIS457 4.2 38.4 1.0 CG A:HIS425 4.2 48.6 1.0 CD2 A:HIS319 4.2 50.0 1.0 C A:HIS457 4.4 46.8 1.0 CD2 A:HIS457 4.4 38.3 1.0 CB A:ASP278 4.5 50.2 1.0 N A:ASN318 4.5 45.3 1.0 CB A:ASN318 4.5 50.6 1.0 N A:HIS457 4.8 45.0 1.0 CG A:ASP206 4.8 43.4 1.0 NE2 A:HIS459 4.9 54.6 1.0 CE1 A:HIS208 4.9 65.2 1.0 NE2 A:HIS319 5.0 49.4 1.0

Zinc binding site 2 out of 2 in the Asmase with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Asmase with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn716 b:66.1 occ:1.00 NE2 A:HIS459 2.0 54.6 1.0 CE1 A:HIS208 2.2 65.2 1.0 OD1 A:ASP206 2.2 47.7 1.0 OD2 A:ASP278 2.2 44.5 1.0 O A:HOH891 2.4 39.0 1.0 CE1 A:HIS459 3.0 50.2 1.0 CD2 A:HIS459 3.0 49.0 1.0 NE2 A:HIS208 3.0 58.2 1.0 CG A:ASP206 3.1 43.4 1.0 ND1 A:HIS208 3.2 59.9 1.0 O A:HOH953 3.3 49.8 1.0 ZN A:ZN715 3.3 65.8 1.0 CG A:ASP278 3.3 50.5 1.0 CB A:ASP206 3.4 40.0 1.0 CB A:ASP278 3.8 50.2 1.0 O A:HIS457 4.0 46.1 1.0 ND1 A:HIS459 4.1 48.5 1.0 CG A:HIS459 4.2 47.9 1.0 OD2 A:ASP206 4.2 48.2 1.0 CA A:ASP206 4.3 45.1 1.0 CD2 A:HIS208 4.3 60.4 1.0 CE1 A:HIS425 4.3 49.4 1.0 CG A:HIS208 4.3 58.7 1.0 NE2 A:HIS425 4.4 55.6 1.0 OD1 A:ASP278 4.4 47.9 1.0 NE2 A:HIS282 4.5 53.9 1.0 CA A:HIS457 4.6 44.0 1.0 CE1 A:HIS282 4.7 53.5 1.0 C A:HIS457 4.7 46.8 1.0 CD2 A:HIS319 4.8 50.0 1.0 O A:HOH958 4.9 64.6 1.0 ND1 A:HIS457 4.9 41.8 1.0

Y.F.Zhou, M.C.Metcalf, S.C.Garman, T.Edmunds, H.Qiu, R.R.Wei. Human Acid Sphingomyelinase Structures Provide Insight to Molecular Basis of Niemann-Pick Disease. Nat Commun V. 7 13082 2016.
ISSN: ESSN 2041-1723
PubMed: 27725636
DOI: 10.1038/NCOMMS13082