Zinc 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:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Porx-Fj (pdb code 8p6f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Porx-Fj, PDB code: 8p6f:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Porx-Fj


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Porx-Fj within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:41.6 occ:1.00 NE2 A:HIS415 2.0 36.2 1.0 OD2 A:ASP414 2.1 35.0 1.0 OG1 A:THR271 2.1 46.5 1.0 OD1 A:ASP237 2.2 42.9 1.0 OD2 A:ASP237 2.3 42.6 1.0 CG A:ASP237 2.5 41.2 1.0 CG A:ASP414 2.8 35.3 1.0 CD2 A:HIS415 2.9 35.4 1.0 OD1 A:ASP414 2.9 33.3 1.0 CE1 A:HIS415 3.0 35.0 1.0 CB A:THR271 3.1 44.8 1.0 CG2 A:THR271 3.5 44.2 1.0 CA A:THR271 3.5 43.8 1.0 N A:THR271 3.8 43.4 1.0 CG A:HIS415 4.0 34.3 1.0 CB A:ASP237 4.0 39.8 1.0 ND1 A:HIS415 4.0 35.0 1.0 N A:ASN238 4.1 37.6 1.0 CB A:ASP414 4.3 35.1 1.0 O A:HOH886 4.3 56.6 1.0 CA A:ASP237 4.5 38.1 1.0 C A:ALA270 4.7 43.4 1.0 C A:ASP237 4.7 38.8 1.0 CE1 A:HIS499 4.7 36.0 1.0 NH1 A:ARG275 4.8 39.5 1.0 CB A:ASN238 4.8 37.7 1.0 CA A:ASN238 4.9 37.0 1.0 O A:HOH901 4.9 44.5 1.0 C A:THR271 4.9 44.5 1.0 CD A:ARG275 4.9 40.0 1.0 OD1 A:ASP360 5.0 41.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Porx-Fj


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Porx-Fj within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:41.1 occ:1.00 OD1 A:ASP360 1.9 41.5 1.0 NE2 A:HIS499 2.0 36.3 1.0 NE2 A:HIS364 2.0 36.7 1.0 O A:HOH935 2.4 49.4 1.0 CG A:ASP360 2.8 41.2 1.0 CE1 A:HIS499 2.9 36.0 1.0 CD2 A:HIS364 3.0 36.4 1.0 OD2 A:ASP360 3.1 43.8 1.0 CE1 A:HIS364 3.1 38.0 1.0 CD2 A:HIS499 3.1 36.0 1.0 ND2 A:ASN238 4.1 40.0 1.0 O A:HOH901 4.1 44.5 1.0 ND1 A:HIS499 4.1 36.0 1.0 CG A:HIS364 4.1 37.3 1.0 CG A:HIS499 4.2 35.3 1.0 ND1 A:HIS364 4.2 38.6 1.0 O A:HOH930 4.2 65.7 1.0 CB A:ASP360 4.2 35.9 1.0 O A:HOH788 4.3 35.3 1.0 O A:HOH912 4.3 42.6 1.0 O A:ASP360 4.6 35.5 1.0 CE1 A:HIS415 4.8 35.0 1.0 OG A:SER363 4.8 39.5 1.0 CA A:ASP360 4.8 35.7 1.0 OG1 A:THR271 4.9 46.5 1.0 CG A:ASN238 4.9 41.0 1.0 OD1 A:ASP237 4.9 42.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Porx-Fj


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Porx-Fj within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:44.3 occ:1.00 OG1 B:THR271 2.0 45.0 1.0 OD2 B:ASP414 2.0 46.7 1.0 NE2 B:HIS415 2.0 38.8 1.0 OD2 B:ASP237 2.1 42.2 1.0 OD1 B:ASP237 2.4 38.7 1.0 CG B:ASP237 2.5 39.5 1.0 CG B:ASP414 2.8 43.5 1.0 CD2 B:HIS415 2.9 37.4 1.0 OD1 B:ASP414 2.9 40.1 1.0 CB B:THR271 3.0 44.0 1.0 CE1 B:HIS415 3.0 38.2 1.0 CA B:THR271 3.4 43.0 1.0 CG2 B:THR271 3.5 44.0 1.0 N B:THR271 3.7 44.0 1.0 CG B:HIS415 4.0 37.6 1.0 CB B:ASP237 4.0 37.5 1.0 ND1 B:HIS415 4.0 38.3 1.0 N B:ASN238 4.2 36.6 1.0 CB B:ASP414 4.2 38.3 1.0 O B:HOH862 4.3 60.9 1.0 CA B:ASP237 4.5 36.5 1.0 O B:HOH882 4.5 44.6 1.0 C B:ALA270 4.6 44.9 1.0 C B:ASP237 4.7 36.1 1.0 CE1 B:HIS499 4.7 39.2 1.0 NH1 B:ARG275 4.8 40.5 1.0 CB B:ASN238 4.9 39.7 1.0 C B:THR271 4.9 42.4 1.0 CA B:ASN238 4.9 37.8 1.0 CD B:ARG275 4.9 43.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Porx-Fj


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Porx-Fj within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:45.8 occ:1.00 OD1 B:ASP360 1.9 51.8 1.0 NE2 B:HIS499 2.0 39.5 1.0 NE2 B:HIS364 2.1 49.3 1.0 O B:HOH882 2.6 44.6 1.0 CG B:ASP360 2.8 50.2 1.0 CE1 B:HIS499 2.9 39.2 1.0 CD2 B:HIS364 3.0 47.4 1.0 OD2 B:ASP360 3.1 54.1 1.0 CE1 B:HIS364 3.1 48.6 1.0 CD2 B:HIS499 3.1 38.9 1.0 O B:HOH909 3.9 53.5 1.0 ND2 B:ASN238 4.1 44.7 1.0 ND1 B:HIS499 4.1 39.1 1.0 CG B:HIS364 4.1 45.0 1.0 CG B:HIS499 4.2 38.1 1.0 ND1 B:HIS364 4.2 47.6 1.0 CB B:ASP360 4.2 43.7 1.0 O B:HOH905 4.4 41.5 1.0 O B:HOH890 4.4 44.5 1.0 O B:HOH767 4.4 40.4 1.0 O B:HOH900 4.5 66.7 1.0 O B:ASP360 4.7 42.3 1.0 CE1 B:HIS415 4.8 38.2 1.0 OG B:SER363 4.8 40.3 1.0 O B:HOH862 4.8 60.9 1.0 CA B:ASP360 4.9 41.2 1.0 CG B:ASN238 4.9 44.9 1.0 OG1 B:THR271 4.9 45.0 1.0 OD1 B:ASP237 5.0 38.7 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