Zinc in PDB 6lz1: Structure of S.Pombe Alpha-Mannosidase AMS1

All present enzymatic activity of Structure of S.Pombe Alpha-Mannosidase AMS1:
3.2.1.24;

The binding sites of Zinc atom in the Structure of S.Pombe Alpha-Mannosidase AMS1 (pdb code 6lz1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of S.Pombe Alpha-Mannosidase AMS1, PDB code: 6lz1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of S.Pombe Alpha-Mannosidase AMS1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of S.Pombe Alpha-Mannosidase AMS1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1201 b:62.1 occ:1.00 OD2 A:ASP402 2.1 38.0 1.0 OD2 A:ASP292 2.1 43.1 1.0 OD1 A:ASP292 2.3 43.1 1.0 CG A:ASP292 2.5 43.1 1.0 NE2 A:HIS615 2.9 35.6 1.0 OD2 A:ASP616 3.0 38.8 1.0 NE2 A:HIS290 3.2 38.0 1.0 CG A:ASP402 3.2 38.0 1.0 CD2 A:HIS615 3.7 35.6 1.0 CD2 A:HIS290 3.9 38.0 1.0 OD1 A:ASP402 3.9 38.0 1.0 CB A:ASP292 3.9 43.1 1.0 CE1 A:HIS615 4.0 35.6 1.0 CG A:ASP616 4.1 38.8 1.0 CB A:ASP402 4.2 38.0 1.0 CE1 A:HIS290 4.3 38.0 1.0 OH A:TYR460 4.3 36.2 1.0 OD1 A:ASP493 4.4 45.4 1.0 OD1 A:ASP616 4.4 38.8 1.0 CE3 A:TRP295 4.7 44.8 1.0 CA A:ASP493 4.8 45.4 1.0 CA A:ASP292 4.8 43.1 1.0 CD2 A:TRP295 4.9 44.8 1.0 CG A:ASP493 4.9 45.4 1.0 CB A:ASP493 5.0 45.4 1.0 CG A:HIS615 5.0 35.6 1.0

Zinc binding site 2 out of 4 in the Structure of S.Pombe Alpha-Mannosidase AMS1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of S.Pombe Alpha-Mannosidase AMS1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1201 b:62.1 occ:1.00 OD2 B:ASP402 2.1 38.0 1.0 OD2 B:ASP292 2.1 43.1 1.0 OD1 B:ASP292 2.3 43.1 1.0 CG B:ASP292 2.5 43.1 1.0 NE2 B:HIS615 2.9 35.6 1.0 OD2 B:ASP616 3.0 38.8 1.0 NE2 B:HIS290 3.2 38.0 1.0 CG B:ASP402 3.2 38.0 1.0 CD2 B:HIS615 3.7 35.6 1.0 CD2 B:HIS290 3.9 38.0 1.0 OD1 B:ASP402 3.9 38.0 1.0 CB B:ASP292 3.9 43.1 1.0 CE1 B:HIS615 4.0 35.6 1.0 CG B:ASP616 4.1 38.8 1.0 CB B:ASP402 4.2 38.0 1.0 CE1 B:HIS290 4.3 38.0 1.0 OH B:TYR460 4.3 36.2 1.0 OD1 B:ASP493 4.4 45.4 1.0 OD1 B:ASP616 4.4 38.8 1.0 CE3 B:TRP295 4.7 44.8 1.0 CA B:ASP493 4.8 45.4 1.0 CA B:ASP292 4.8 43.1 1.0 CD2 B:TRP295 4.9 44.8 1.0 CG B:ASP493 4.9 45.4 1.0 CB B:ASP493 5.0 45.4 1.0 CG B:HIS615 5.0 35.6 1.0

Zinc binding site 3 out of 4 in the Structure of S.Pombe Alpha-Mannosidase AMS1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of S.Pombe Alpha-Mannosidase AMS1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1201 b:62.1 occ:1.00 OD2 C:ASP402 2.1 38.0 1.0 OD2 C:ASP292 2.1 43.1 1.0 OD1 C:ASP292 2.3 43.1 1.0 CG C:ASP292 2.5 43.1 1.0 NE2 C:HIS615 2.9 35.6 1.0 OD2 C:ASP616 3.0 38.8 1.0 NE2 C:HIS290 3.2 38.0 1.0 CG C:ASP402 3.2 38.0 1.0 CD2 C:HIS615 3.7 35.6 1.0 CD2 C:HIS290 3.9 38.0 1.0 OD1 C:ASP402 3.9 38.0 1.0 CB C:ASP292 3.9 43.1 1.0 CE1 C:HIS615 4.0 35.6 1.0 CG C:ASP616 4.1 38.8 1.0 CB C:ASP402 4.2 38.0 1.0 CE1 C:HIS290 4.3 38.0 1.0 OH C:TYR460 4.3 36.2 1.0 OD1 C:ASP493 4.4 45.4 1.0 OD1 C:ASP616 4.4 38.8 1.0 CE3 C:TRP295 4.7 44.8 1.0 CA C:ASP493 4.8 45.4 1.0 CA C:ASP292 4.8 43.1 1.0 CD2 C:TRP295 4.9 44.8 1.0 CG C:ASP493 4.9 45.4 1.0 CB C:ASP493 5.0 45.4 1.0 CG C:HIS615 5.0 35.6 1.0

Zinc binding site 4 out of 4 in the Structure of S.Pombe Alpha-Mannosidase AMS1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of S.Pombe Alpha-Mannosidase AMS1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1201 b:62.1 occ:1.00 OD2 D:ASP402 2.1 38.0 1.0 OD2 D:ASP292 2.1 43.1 1.0 OD1 D:ASP292 2.3 43.1 1.0 CG D:ASP292 2.5 43.1 1.0 NE2 D:HIS615 2.9 35.6 1.0 OD2 D:ASP616 3.0 38.8 1.0 NE2 D:HIS290 3.2 38.0 1.0 CG D:ASP402 3.2 38.0 1.0 CD2 D:HIS615 3.7 35.6 1.0 CD2 D:HIS290 3.9 38.0 1.0 OD1 D:ASP402 3.9 38.0 1.0 CB D:ASP292 3.9 43.1 1.0 CE1 D:HIS615 4.0 35.6 1.0 CG D:ASP616 4.1 38.8 1.0 CB D:ASP402 4.2 38.0 1.0 CE1 D:HIS290 4.3 38.0 1.0 OH D:TYR460 4.3 36.2 1.0 OD1 D:ASP493 4.4 45.4 1.0 OD1 D:ASP616 4.4 38.8 1.0 CE3 D:TRP295 4.7 44.8 1.0 CA D:ASP493 4.8 45.4 1.0 CA D:ASP292 4.8 43.1 1.0 CD2 D:TRP295 4.9 44.8 1.0 CG D:ASP493 4.9 45.4 1.0 CB D:ASP493 5.0 45.4 1.0 CG D:HIS615 5.0 35.6 1.0

J.Zhang, Y.Y.Wang, L.L.Du, K.Ye. Cryo-Em Structure of Fission Yeast Tetrameric Alpha-Mannosidase AMS1. Febs Open Bio 2020.
ISSN: ESSN 2211-5463
PubMed: 32981237
DOI: 10.1002/2211-5463.12988