Sodium in PDB 5o65: Crystal Structure of the Pseudomonas Functional Amyloid Secretion Protein Fapf

The structure of Crystal Structure of the Pseudomonas Functional Amyloid Secretion Protein Fapf, PDB code: 5o65 was solved by S.L.Rouse, S.Hare, S.Lambert, R.M.L.Morgan, W.J.Hawthorne, J.Berry, S.J.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	2.64 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	143.260, 124.731, 80.359, 90.00, 96.29, 90.00
R / Rfree (%)	22.2 / 25.9

The binding sites of Sodium atom in the Crystal Structure of the Pseudomonas Functional Amyloid Secretion Protein Fapf (pdb code 5o65). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Pseudomonas Functional Amyloid Secretion Protein Fapf, PDB code: 5o65:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the Pseudomonas Functional Amyloid Secretion Protein Fapf


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Pseudomonas Functional Amyloid Secretion Protein Fapf within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:55.7 occ:1.00 OD2 A:ASP395 2.5 36.5 1.0 N C:ASP391 3.0 35.6 1.0 OD1 A:ASP395 3.1 40.5 1.0 CG A:ASP395 3.1 36.8 1.0 CB A:ASP120 3.2 60.4 1.0 CG C:ASP391 3.4 43.9 1.0 OD2 C:ASP391 3.5 49.4 1.0 CA C:THR390 3.7 29.5 1.0 OD1 C:ASP391 3.7 48.9 1.0 CB C:ASP391 3.7 40.0 1.0 C C:THR390 3.8 32.4 1.0 CA C:ASP391 3.9 36.9 1.0 CB C:THR390 4.0 27.8 1.0 OD2 A:ASP120 4.0 65.5 1.0 CG A:ASP120 4.0 62.5 1.0 O A:HOH626 4.1 44.0 1.0 CA A:ASP120 4.2 52.0 1.0 O A:HOH645 4.2 53.0 1.0 C A:ASP120 4.3 48.7 1.0 N A:ASP120 4.3 46.3 1.0 CB A:ASP395 4.5 35.2 1.0 CG2 C:THR390 4.6 27.1 1.0 O C:MSE389 4.7 36.7 1.0 O A:ASP120 4.8 56.9 1.0 N C:THR390 4.9 30.0 1.0 O C:THR390 4.9 34.8 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the Pseudomonas Functional Amyloid Secretion Protein Fapf


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Pseudomonas Functional Amyloid Secretion Protein Fapf within 5.0Å range: probe atom residue distance (Å) B Occ B:Na503 b:38.2 occ:1.00 OD2 B:ASP395 2.6 39.9 1.0 N A:ASP391 2.9 38.9 1.0 OD1 B:ASP395 3.1 37.8 1.0 CG B:ASP395 3.1 34.7 1.0 CG A:ASP391 3.2 42.2 1.0 CB B:ASP120 3.3 50.9 1.0 OD2 A:ASP391 3.4 46.4 1.0 CB A:ASP391 3.5 40.1 1.0 CG2 A:THR390 3.6 52.5 1.0 OD1 A:ASP391 3.6 46.5 1.0 CA A:THR390 3.7 39.4 1.0 C A:THR390 3.8 37.2 1.0 CA A:ASP391 3.8 38.9 1.0 CG B:ASP120 3.9 59.9 1.0 O A:HOH649 4.1 49.2 1.0 OD2 B:ASP120 4.1 53.0 1.0 CB A:THR390 4.3 41.6 1.0 CA B:ASP120 4.5 47.3 1.0 CB B:ASP395 4.5 31.8 1.0 OD1 B:ASP120 4.6 67.7 1.0 N B:ASP120 4.6 41.4 1.0 O A:MSE389 4.9 40.3 1.0 O A:THR390 4.9 38.1 1.0 O B:ASP120 4.9 58.4 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the Pseudomonas Functional Amyloid Secretion Protein Fapf


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Pseudomonas Functional Amyloid Secretion Protein Fapf within 5.0Å range: probe atom residue distance (Å) B Occ B:Na504 b:56.5 occ:1.00 OD2 C:ASP395 2.7 43.1 1.0 N B:ASP391 3.1 34.8 1.0 CG B:ASP391 3.1 53.4 1.0 OD1 C:ASP395 3.2 46.4 1.0 OD2 B:ASP391 3.2 61.7 1.0 CB C:ASP120 3.3 57.7 1.0 CG C:ASP395 3.3 37.0 1.0 OD1 B:ASP391 3.5 66.1 1.0 CB B:ASP391 3.5 44.8 1.0 CG C:ASP120 3.8 64.3 1.0 CA B:ASP391 3.9 38.4 1.0 CA B:THR390 3.9 33.2 1.0 C B:THR390 3.9 35.5 1.0 O C:HOH653 4.0 47.6 1.0 OD2 C:ASP120 4.0 65.6 1.0 CB B:THR390 4.3 34.9 1.0 O B:HOH661 4.3 43.6 1.0 OD1 C:ASP120 4.4 84.2 1.0 CA C:ASP120 4.5 56.2 1.0 O C:ASP120 4.7 64.5 1.0 CB C:ASP395 4.7 37.4 1.0 N C:ASP120 4.7 50.8 1.0 CG2 B:THR390 4.9 36.7 1.0

S.L.Rouse, W.J.Hawthorne, J.L.Berry, D.S.Chorev, S.A.Ionescu, S.Lambert, F.Stylianou, W.Ewert, U.Mackie, R.M.L.Morgan, D.Otzen, F.A.Herbst, P.H.Nielsen, M.Dueholm, H.Bayley, C.V.Robinson, S.Hare, S.Matthews. A New Class of Hybrid Secretion System Is Employed in Pseudomonas Amyloid Biogenesis. Nat Commun V. 8 263 2017.
ISSN: ESSN 2041-1723
PubMed: 28811582
DOI: 10.1038/S41467-017-00361-6