Zinc in PDB 8a28: Structure of the Astacin Zymogen of Last-Mam From Limulus Polyphemus

The structure of Structure of the Astacin Zymogen of Last-Mam From Limulus Polyphemus, PDB code: 8a28 was solved by T.Guevara, A.Rodriguez Banqueri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.73 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.83, 47.57, 236.4, 90, 102.91, 90
R / Rfree (%)	25.3 / 28.9

The structure of Structure of the Astacin Zymogen of Last-Mam From Limulus Polyphemus also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Structure of the Astacin Zymogen of Last-Mam From Limulus Polyphemus (pdb code 8a28). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of the Astacin Zymogen of Last-Mam From Limulus Polyphemus, PDB code: 8a28:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of the Astacin Zymogen of Last-Mam From Limulus Polyphemus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Astacin Zymogen of Last-Mam From Limulus Polyphemus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:44.9 occ:1.00 NE2 A:HIS143 2.1 40.9 1.0 NE2 A:HIS139 2.1 37.8 1.0 NE2 A:HIS149 2.1 49.9 1.0 OD1 A:ASP38 2.2 49.2 1.0 OD2 A:ASP38 2.4 57.9 1.0 CG A:ASP38 2.6 51.2 1.0 CE1 A:HIS149 2.6 50.0 1.0 CD2 A:HIS139 3.0 39.0 1.0 CE1 A:HIS143 3.0 40.7 1.0 CD2 A:HIS143 3.1 40.1 1.0 CE1 A:HIS139 3.2 39.0 1.0 OH A:TYR198 3.3 35.4 1.0 CD2 A:HIS149 3.4 49.8 1.0 ND1 A:HIS149 3.9 50.4 1.0 CZ A:TYR198 4.0 37.6 1.0 CE1 A:TYR198 4.0 37.9 1.0 CB A:ASP38 4.1 47.0 1.0 ND1 A:HIS143 4.2 42.5 1.0 CG A:HIS139 4.2 40.1 1.0 CG A:HIS143 4.2 41.1 1.0 CG A:HIS149 4.2 48.7 1.0 ND1 A:HIS139 4.3 40.0 1.0 CE A:MET196 4.7 34.9 1.0 CG1 A:ILE39 4.8 44.7 1.0 O A:GLU36 4.8 46.9 1.0 CD2 A:LEU29 4.9 39.8 1.0 CA A:ASP38 5.0 46.4 1.0

Zinc binding site 2 out of 2 in the Structure of the Astacin Zymogen of Last-Mam From Limulus Polyphemus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Astacin Zymogen of Last-Mam From Limulus Polyphemus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:51.3 occ:1.00 OD2 B:ASP38 2.1 55.9 1.0 NE2 B:HIS139 2.1 48.3 1.0 NE2 B:HIS149 2.1 56.2 1.0 NE2 B:HIS143 2.1 49.0 1.0 OD1 B:ASP38 2.2 56.4 1.0 CG B:ASP38 2.4 53.9 1.0 CE1 B:HIS149 2.7 57.4 1.0 CD2 B:HIS139 3.0 48.5 1.0 CE1 B:HIS143 3.1 47.8 1.0 CD2 B:HIS143 3.1 48.5 1.0 CE1 B:HIS139 3.2 47.2 1.0 OH B:TYR198 3.3 43.7 1.0 CD2 B:HIS149 3.3 55.1 1.0 ND1 B:HIS149 3.9 57.3 1.0 CE1 B:TYR198 3.9 42.3 1.0 CZ B:TYR198 4.0 42.4 1.0 CB B:ASP38 4.0 50.2 1.0 CG B:HIS139 4.2 47.4 1.0 CG B:HIS149 4.2 55.1 1.0 ND1 B:HIS143 4.2 47.2 1.0 CG B:HIS143 4.2 49.6 1.0 ND1 B:HIS139 4.3 46.7 1.0 CG1 B:ILE39 4.8 44.9 1.0 O B:GLU36 4.8 53.3 1.0 CD2 B:LEU29 4.9 46.7 1.0 CE B:MET196 4.9 44.2 1.0 CA B:ASP38 5.0 48.5 1.0

T.Guevara, A.Rodriguez-Banqueri, M.Ksiazek, J.Potempa, F.X.Gomis-Ruth. Structure-Based Mechanism of Cysteine-Switch Latency and of Catalysis By Pappalysin-Family Metallopeptidases Iucrj V. 7 18 2020.
ISSN: ESSN 2052-2525
DOI: 10.1107/S2059798322009688