Magnesium in PDB 8p6f: Crystal Structure of Porx-Fj

The structure of Crystal Structure of Porx-Fj, PDB code: 8p6f was solved by P.Leone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.16 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	84.609, 97.483, 131.103, 90, 90, 90
R / Rfree (%)	21.6 / 25.5

The structure of Crystal Structure of Porx-Fj also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of Porx-Fj (pdb code 8p6f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Porx-Fj, PDB code: 8p6f:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Porx-Fj


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Porx-Fj within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:37.5 occ:1.00 O A:ASN56 2.2 56.7 1.0 O A:HOH896 2.2 44.4 1.0 OD2 A:ASP54 2.3 53.5 1.0 OD1 A:ASP11 2.3 49.1 1.0 O A:HOH785 2.4 42.9 1.0 O A:HOH862 3.0 60.5 1.0 CG A:ASP11 3.2 50.2 1.0 CG A:ASP54 3.4 49.1 1.0 OD2 A:ASP11 3.4 51.7 1.0 C A:ASN56 3.4 56.3 1.0 OD1 A:ASP54 3.8 49.0 1.0 O A:HOH774 4.0 56.2 1.0 OD1 A:ASP10 4.3 49.2 1.0 N A:MET57 4.3 55.8 1.0 CA A:ASN56 4.4 56.0 1.0 CA A:MET57 4.4 55.8 1.0 OE2 A:GLU12 4.4 62.3 1.0 CG A:MET57 4.4 54.5 1.0 CB A:ASN56 4.5 59.6 1.0 CB A:ASP11 4.6 48.4 1.0 CB A:ASP54 4.6 46.5 1.0 ND2 A:ASN56 4.7 70.3 1.0 N A:ASN56 4.8 54.1 1.0 N A:ASP11 4.8 46.7 1.0 NZ A:LYS104 4.9 54.0 1.0 CD A:GLU12 5.0 59.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Porx-Fj


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Porx-Fj within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:40.5 occ:1.00 OD2 B:ASP54 2.0 58.7 1.0 O B:ASN56 2.1 55.6 1.0 O B:HOH770 2.3 43.6 1.0 OD1 B:ASP11 2.4 61.6 1.0 O B:HOH897 2.5 52.4 1.0 CG B:ASP54 3.0 54.5 1.0 O B:HOH832 3.2 52.1 1.0 C B:ASN56 3.3 54.7 1.0 OD1 B:ASP54 3.3 54.5 1.0 CG B:ASP11 3.4 60.5 1.0 OD2 B:ASP11 3.6 63.8 1.0 CA B:ASN56 4.2 55.0 1.0 OD1 B:ASP10 4.2 57.6 1.0 N B:MET57 4.3 53.5 1.0 CB B:ASN56 4.3 57.5 1.0 ND2 B:ASN56 4.3 66.1 1.0 CB B:ASP54 4.4 48.6 1.0 CA B:MET57 4.4 52.9 1.0 N B:ASN56 4.5 53.8 1.0 CG B:MET57 4.5 53.2 1.0 NZ B:LYS83 4.7 71.9 1.0 CG B:ASN56 4.7 63.9 1.0 CB B:ASP11 4.7 55.8 1.0 NZ B:LYS104 4.8 60.6 1.0 N B:ASP11 4.8 52.5 1.0 CG B:ASP10 4.9 55.4 1.0 OE1 B:GLU12 5.0 68.9 1.0

M.Zammit, J.Bartoli, C.Kellenberger, P.Melani, A.Roussel, E.Cascales, P.Leone. Structure-Function Analysis of Porx Fj , the Porx Homolog From Flavobacterium Johnsioniae, Suggests A Role of the Chey-Like Domain in Type IX Secretion Motor Activity. Sci Rep V. 14 6577 2024.
ISSN: ESSN 2045-2322
PubMed: 38503809
DOI: 10.1038/S41598-024-57089-9