Zinc in PDB 5i85: Asmase with Zinc and Phosphocholine

All present enzymatic activity of Asmase with Zinc and Phosphocholine:
3.1.4.12;

The structure of Asmase with Zinc and Phosphocholine, PDB code: 5i85 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)	31.18 / 2.50
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	131.601, 131.601, 188.573, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 22.2

The binding sites of Zinc atom in the Asmase with Zinc and Phosphocholine (pdb code 5i85). 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 and Phosphocholine, PDB code: 5i85:
Jump to Zinc binding site number: 1; 2;

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


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 and Phosphocholine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn714 b:25.8 occ:1.00 NE2 A:HIS425 2.0 37.5 1.0 OD1 A:ASN318 2.1 38.3 1.0 O4 A:PC727 2.1 35.3 1.0 ND1 A:HIS457 2.2 34.4 1.0 OD2 A:ASP278 2.4 39.6 1.0 CE1 A:HIS425 2.9 36.3 1.0 CE1 A:HIS457 3.0 32.5 1.0 O3 A:PC727 3.0 46.1 1.0 CG A:ASP278 3.1 37.5 1.0 CG A:ASN318 3.1 34.0 1.0 CD2 A:HIS425 3.1 36.3 1.0 P1 A:PC727 3.2 45.9 1.0 OD1 A:ASP278 3.2 38.0 1.0 CG A:HIS457 3.3 31.4 1.0 ZN A:ZN715 3.4 24.5 1.0 ND2 A:ASN318 3.5 32.3 1.0 OD1 A:ASP206 3.7 40.2 1.0 CB A:HIS457 3.8 28.9 1.0 O1 A:PC727 3.8 50.6 1.0 CA A:HIS457 3.9 27.8 1.0 ND1 A:HIS425 4.1 36.1 1.0 NE2 A:HIS457 4.1 32.1 1.0 O A:HIS457 4.2 29.8 1.0 CD2 A:HIS319 4.2 29.1 1.0 CG A:HIS425 4.2 35.5 1.0 CD2 A:HIS457 4.3 31.9 1.0 CB A:ASP278 4.4 35.3 1.0 CB A:ASN318 4.4 32.6 1.0 N A:ASN318 4.4 29.2 1.0 C A:HIS457 4.5 28.3 1.0 O2 A:PC727 4.6 49.6 1.0 NE2 A:HIS319 4.9 28.9 1.0 CG A:ASP206 4.9 36.5 1.0 CA A:ASN318 5.0 31.4 1.0 N A:HIS457 5.0 26.4 1.0 NE2 A:HIS208 5.0 26.3 1.0

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


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 and Phosphocholine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn715 b:24.5 occ:1.00 NE2 A:HIS459 2.1 34.9 1.0 OD1 A:ASP206 2.1 40.2 1.0 OD2 A:ASP278 2.1 39.6 1.0 NE2 A:HIS208 2.2 26.3 1.0 O4 A:PC727 2.5 35.3 1.0 O1 A:PC727 2.5 50.6 1.0 CE1 A:HIS459 3.0 34.1 1.0 CD2 A:HIS459 3.1 32.7 1.0 CG A:ASP206 3.1 36.5 1.0 P1 A:PC727 3.1 45.9 1.0 CD2 A:HIS208 3.2 26.3 1.0 CG A:ASP278 3.2 37.5 1.0 CE1 A:HIS208 3.2 26.7 1.0 ZN A:ZN714 3.4 25.8 1.0 CB A:ASP206 3.5 31.9 1.0 CB A:ASP278 3.6 35.3 1.0 O3 A:PC727 4.0 46.1 1.0 OD2 A:ASP206 4.1 37.8 1.0 ND1 A:HIS459 4.2 33.7 1.0 CG A:HIS459 4.2 32.7 1.0 O A:HIS457 4.2 29.8 1.0 O2 A:PC727 4.3 49.6 1.0 OD1 A:ASP278 4.3 38.0 1.0 CA A:ASP206 4.3 28.2 1.0 CE1 A:HIS425 4.3 36.3 1.0 ND1 A:HIS208 4.3 27.8 1.0 CG A:HIS208 4.3 27.9 1.0 NE2 A:HIS282 4.4 24.1 1.0 C1 A:PC727 4.4 52.0 1.0 NE2 A:HIS425 4.5 37.5 1.0 CD2 A:HIS319 4.6 29.1 1.0 CE1 A:HIS282 4.7 22.7 1.0 CA A:HIS457 4.7 27.8 1.0 C A:HIS457 4.9 28.3 1.0 ND1 A:HIS457 4.9 34.4 1.0 NE2 A:HIS319 5.0 28.9 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