Zinc in PDB 5i8r: Asmase with Zinc

All present enzymatic activity of Asmase with Zinc:
3.1.4.12;

The structure of Asmase with Zinc, PDB code: 5i8r 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)	44.13 / 3.65
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	191.020, 230.870, 252.320, 90.00, 90.00, 90.00
R / Rfree (%)	24.8 / 25.4

The binding sites of Zinc atom in the Asmase with Zinc (pdb code 5i8r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Asmase with Zinc, PDB code: 5i8r:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 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:Zn712 b:0.1 occ:1.00 ND1 A:HIS457 2.2 0.3 1.0 NE2 A:HIS425 2.3 0.4 1.0 OD1 A:ASN318 2.4 0.8 1.0 OD2 A:ASP278 2.6 0.4 1.0 CE1 A:HIS457 2.9 1.0 1.0 ZN A:ZN713 3.1 0.4 1.0 CE1 A:HIS425 3.3 0.6 1.0 CG A:ASN318 3.3 0.9 1.0 CD2 A:HIS425 3.3 0.0 1.0 CG A:HIS457 3.4 0.8 1.0 CG A:ASP278 3.4 1.0 1.0 ND2 A:ASN318 3.5 0.2 1.0 OD1 A:ASP278 3.6 0.4 1.0 CA A:HIS457 3.8 0.0 1.0 OD1 A:ASP206 3.8 0.4 1.0 CB A:HIS457 3.9 0.7 1.0 O A:HIS457 3.9 0.1 1.0 NE2 A:HIS457 4.1 0.4 1.0 CD2 A:HIS319 4.3 0.6 1.0 CD2 A:HIS457 4.4 0.5 1.0 C A:HIS457 4.4 0.4 1.0 ND1 A:HIS425 4.4 0.8 1.0 CG A:HIS425 4.5 0.7 1.0 CB A:ASN318 4.7 0.2 1.0 NE2 A:HIS459 4.7 0.4 1.0 CB A:ASP278 4.8 0.5 1.0 N A:ASN318 4.9 0.1 1.0 N A:HIS457 4.9 0.6 1.0 NE2 A:HIS319 5.0 0.1 1.0

Zinc binding site 2 out of 6 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:Zn713 b:0.4 occ:1.00 NE2 A:HIS459 2.0 0.4 1.0 OD2 A:ASP278 2.3 0.4 1.0 CE1 A:HIS208 2.4 0.7 1.0 CE1 A:HIS459 2.8 0.2 1.0 OD1 A:ASP206 2.8 0.4 1.0 NE2 A:HIS208 3.0 0.7 1.0 CD2 A:HIS459 3.1 0.3 1.0 ZN A:ZN712 3.1 0.1 1.0 CG A:ASP278 3.4 1.0 1.0 ND1 A:HIS208 3.6 0.2 1.0 CG A:ASP206 3.6 0.4 1.0 ND1 A:HIS459 3.9 0.8 1.0 CB A:ASP206 4.0 0.3 1.0 CE1 A:HIS282 4.1 0.7 1.0 CG A:HIS459 4.1 0.2 1.0 CB A:ASP278 4.2 0.5 1.0 O A:HIS457 4.2 0.1 1.0 CD2 A:HIS208 4.3 0.8 1.0 OD1 A:ASP278 4.4 0.4 1.0 NE2 A:HIS282 4.4 0.3 1.0 NE2 A:HIS425 4.6 0.4 1.0 CG A:HIS208 4.6 0.7 1.0 OD2 A:ASP206 4.6 0.2 1.0 CE1 A:HIS425 4.6 0.6 1.0 CD2 A:HIS319 4.7 0.6 1.0 CA A:HIS457 4.8 0.0 1.0 ND1 A:HIS457 4.8 0.3 1.0 CA A:ASP206 4.8 0.5 1.0 C A:HIS457 4.9 0.4 1.0

Zinc binding site 3 out of 6 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 3 of Asmase with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn713 b:0.2 occ:1.00 ND1 B:HIS457 2.2 0.8 1.0 NE2 B:HIS425 2.5 0.2 1.0 OD2 B:ASP278 2.6 0.8 1.0 OD1 B:ASN318 2.7 1.0 1.0 CE1 B:HIS457 3.0 0.3 1.0 ZN B:ZN714 3.0 0.5 1.0 CG B:HIS457 3.2 0.1 1.0 CE1 B:HIS425 3.3 0.3 1.0 CA B:HIS457 3.5 0.5 1.0 CD2 B:HIS425 3.5 0.2 1.0 CG B:ASN318 3.5 0.9 1.0 CG B:ASP278 3.6 0.7 1.0 O B:HIS457 3.6 0.6 1.0 OD1 B:ASP206 3.6 0.6 1.0 ND2 B:ASN318 3.7 0.6 1.0 CB B:HIS457 3.7 0.1 1.0 OD1 B:ASP278 3.9 0.8 1.0 C B:HIS457 4.0 0.3 1.0 NE2 B:HIS457 4.2 0.9 1.0 CD2 B:HIS457 4.3 0.3 1.0 CD2 B:HIS319 4.5 1.0 1.0 ND1 B:HIS425 4.5 0.4 1.0 NE2 B:HIS459 4.6 0.7 1.0 CG B:HIS425 4.6 1.0 1.0 N B:HIS457 4.6 1.0 1.0 CG B:ASP206 4.8 0.4 1.0 CB B:ASP278 4.9 0.5 1.0 CB B:ASN318 4.9 0.4 1.0 CD2 B:HIS459 5.0 0.6 1.0 NE2 B:HIS319 5.0 0.3 1.0

Zinc binding site 4 out of 6 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 4 of Asmase with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn714 b:0.5 occ:1.00 NE2 B:HIS459 2.2 0.7 1.0 CE1 B:HIS208 2.3 0.8 1.0 OD2 B:ASP278 2.3 0.8 1.0 NE2 B:HIS208 2.8 0.1 1.0 OD1 B:ASP206 2.8 0.6 1.0 CE1 B:HIS459 3.0 0.7 1.0 ZN B:ZN713 3.0 0.2 1.0 CD2 B:HIS459 3.3 0.6 1.0 CG B:ASP278 3.4 0.7 1.0 ND1 B:HIS208 3.5 0.9 1.0 CG B:ASP206 3.6 0.4 1.0 CE1 B:HIS282 3.9 0.9 1.0 CB B:ASP206 4.0 0.1 1.0 CB B:ASP278 4.0 0.5 1.0 CD2 B:HIS208 4.1 0.9 1.0 NE2 B:HIS282 4.2 0.5 1.0 ND1 B:HIS459 4.2 1.0 1.0 O B:HIS457 4.3 0.6 1.0 CG B:HIS459 4.3 1.0 1.0 OD1 B:ASP278 4.4 0.8 1.0 CG B:HIS208 4.4 0.9 1.0 CD2 B:HIS319 4.5 1.0 1.0 NE2 B:HIS425 4.6 0.2 1.0 OD2 B:ASP206 4.6 0.0 1.0 CE1 B:HIS425 4.6 0.3 1.0 CA B:ASP206 4.8 0.8 1.0 NE2 B:HIS319 4.8 0.3 1.0 OD1 B:ASN318 4.9 1.0 1.0 CA B:HIS457 4.9 0.5 1.0 C B:HIS457 5.0 0.3 1.0

Zinc binding site 5 out of 6 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 5 of Asmase with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn707 b:1.0 occ:1.00 ND1 C:HIS457 2.0 0.4 1.0 NE2 C:HIS425 2.2 0.8 1.0 OD1 C:ASN318 2.2 0.1 1.0 OD2 C:ASP278 2.6 0.1 1.0 CE1 C:HIS457 2.8 0.2 1.0 CG C:ASN318 3.1 0.7 1.0 CD2 C:HIS425 3.1 0.6 1.0 CE1 C:HIS425 3.1 0.6 1.0 CG C:HIS457 3.2 0.4 1.0 ZN C:ZN708 3.4 0.2 1.0 CG C:ASP278 3.4 0.8 1.0 ND2 C:ASN318 3.5 0.4 1.0 OD1 C:ASP278 3.6 0.6 1.0 CB C:HIS457 3.7 0.3 1.0 CA C:HIS457 3.8 0.1 1.0 OD1 C:ASP206 3.8 0.3 1.0 NE2 C:HIS457 4.0 0.1 1.0 O C:HIS457 4.1 0.1 1.0 CD2 C:HIS457 4.2 0.9 1.0 ND1 C:HIS425 4.2 0.1 1.0 CG C:HIS425 4.3 1.0 1.0 CD2 C:HIS319 4.3 0.1 1.0 CB C:ASN318 4.4 0.7 1.0 C C:HIS457 4.4 0.5 1.0 N C:ASN318 4.5 0.9 1.0 CB C:ASP278 4.7 1.0 1.0 N C:HIS457 4.9 0.8 1.0 NE2 C:HIS459 4.9 0.8 1.0 NE2 C:HIS319 5.0 0.1 1.0

Zinc binding site 6 out of 6 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 6 of Asmase with Zinc within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn708 b:0.2 occ:1.00 NE2 C:HIS459 2.0 0.8 1.0 OD2 C:ASP278 2.5 0.1 1.0 CE1 C:HIS208 2.6 0.5 1.0 CE1 C:HIS459 2.8 0.4 1.0 NE2 C:HIS208 3.0 0.3 1.0 OD1 C:ASP206 3.1 0.3 1.0 CD2 C:HIS459 3.2 0.3 1.0 ZN C:ZN707 3.4 1.0 1.0 CG C:ASP278 3.7 0.8 1.0 ND1 C:HIS208 3.8 0.1 1.0 CE1 C:HIS282 3.8 0.3 1.0 CG C:ASP206 3.9 0.7 1.0 ND1 C:HIS459 3.9 0.5 1.0 O C:HIS457 4.0 0.1 1.0 NE2 C:HIS282 4.1 0.6 1.0 CG C:HIS459 4.1 0.8 1.0 CB C:ASP206 4.3 0.7 1.0 CD2 C:HIS208 4.3 0.7 1.0 CB C:ASP278 4.4 1.0 1.0 CD2 C:HIS319 4.5 0.1 1.0 ND1 C:HIS457 4.6 0.4 1.0 NE2 C:HIS319 4.6 0.1 1.0 CG C:HIS208 4.7 0.9 1.0 OD1 C:ASP278 4.7 0.6 1.0 NE2 C:HIS425 4.8 0.8 1.0 C C:HIS457 4.8 0.5 1.0 CA C:HIS457 4.8 0.1 1.0 OD2 C:ASP206 4.8 0.5 1.0 CE1 C:HIS425 4.9 0.6 1.0 OD1 C:ASN318 4.9 0.1 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