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

Protein crystallography data

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

Other elements in 8a28:

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

Magnesium (Mg) 1 atom

Zinc Binding Sites:

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 8a28

Go back to Zinc Binding Sites List in 8a28
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 8a28

Go back to Zinc Binding Sites List in 8a28
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

Reference:

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
Page generated: Sat Apr 8 07:28:57 2023

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