Sodium in PDB 6fue: Periplasmic Coiled Coil Domain of the Fapf Amyloid Transporter

The structure of Periplasmic Coiled Coil Domain of the Fapf Amyloid Transporter, PDB code: 6fue was solved by S.L.Rouse, F.Stylianou, R.M.L.Morgan, S.J.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.01 / 1.78
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	37.590, 37.700, 57.340, 90.24, 108.95, 119.89
R / Rfree (%)	20.7 / 24.8

The structure of Periplasmic Coiled Coil Domain of the Fapf Amyloid Transporter also contains other interesting chemical elements:

Zinc

(Zn)

11 atoms

The binding sites of Sodium atom in the Periplasmic Coiled Coil Domain of the Fapf Amyloid Transporter (pdb code 6fue). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Periplasmic Coiled Coil Domain of the Fapf Amyloid Transporter, PDB code: 6fue:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Periplasmic Coiled Coil Domain of the Fapf Amyloid Transporter


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Periplasmic Coiled Coil Domain of the Fapf Amyloid Transporter within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:71.1 occ:1.00 O A:HOH240 4.1 92.6 1.0

Sodium binding site 2 out of 6 in the Periplasmic Coiled Coil Domain of the Fapf Amyloid Transporter


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Periplasmic Coiled Coil Domain of the Fapf Amyloid Transporter within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:35.5 occ:1.00 OD1 B:ASP37 2.0 52.5 1.0 O B:HOH215 2.2 61.3 1.0 CG B:ASP37 3.2 60.3 1.0 OD2 B:ASP37 3.7 59.2 1.0 OE1 B:GLU36 4.1 72.8 1.0 CB B:ASP37 4.4 64.8 1.0 CB B:GLU36 4.4 54.9 1.0 CA B:ASP37 4.6 69.2 1.0 N B:ASP37 4.7 65.2 1.0 C B:GLU36 4.8 61.8 1.0 O B:GLU36 4.9 73.3 1.0

Sodium binding site 3 out of 6 in the Periplasmic Coiled Coil Domain of the Fapf Amyloid Transporter


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Periplasmic Coiled Coil Domain of the Fapf Amyloid Transporter within 5.0Å range: probe atom residue distance (Å) B Occ B:Na103 b:62.6 occ:1.00 NA B:NA105 2.4 95.4 1.0 O B:HOH202 4.4 46.5 1.0

Sodium binding site 4 out of 6 in the Periplasmic Coiled Coil Domain of the Fapf Amyloid Transporter


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Periplasmic Coiled Coil Domain of the Fapf Amyloid Transporter within 5.0Å range: probe atom residue distance (Å) B Occ B:Na104 b:51.0 occ:1.00 O B:HOH236 2.8 38.6 1.0 O B:ALA26 3.0 26.1 1.0 OE1 B:GLN30 3.1 44.2 1.0 OE2 B:GLU29 3.2 35.5 1.0 CG B:GLN30 3.5 39.1 1.0 CD B:GLN30 3.7 45.4 1.0 C B:ALA26 3.7 27.8 1.0 CD B:GLU29 3.7 29.0 1.0 CA B:ALA26 3.7 25.1 1.0 CB B:ALA26 3.7 27.4 1.0 CB B:GLU29 4.0 25.6 1.0 CG B:GLU29 4.1 29.4 1.0 O B:HOH202 4.1 46.5 1.0 OE1 B:GLU29 4.3 32.5 1.0 N B:GLN30 4.3 28.9 1.0 O B:HOH227 4.4 38.0 1.0 NA B:NA105 4.5 95.4 1.0 CB B:GLN30 4.6 33.8 1.0 C B:GLU29 4.9 27.0 1.0 N B:VAL27 4.9 27.1 1.0 CA B:GLN30 4.9 29.7 1.0 CA B:GLU29 4.9 25.8 1.0 NE2 B:GLN30 5.0 46.6 1.0 O B:HOH221 5.0 59.3 1.0

Sodium binding site 5 out of 6 in the Periplasmic Coiled Coil Domain of the Fapf Amyloid Transporter


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Periplasmic Coiled Coil Domain of the Fapf Amyloid Transporter within 5.0Å range: probe atom residue distance (Å) B Occ B:Na105 b:95.4 occ:1.00 NA B:NA103 2.4 62.6 1.0 O B:HOH202 2.4 46.5 1.0 OE2 B:GLU29 3.4 35.5 1.0 CD B:GLU29 4.2 29.0 1.0 OE1 B:GLU29 4.3 32.5 1.0 NA B:NA104 4.5 51.0 1.0 O B:HOH218 4.8 43.5 1.0

Sodium binding site 6 out of 6 in the Periplasmic Coiled Coil Domain of the Fapf Amyloid Transporter


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Periplasmic Coiled Coil Domain of the Fapf Amyloid Transporter within 5.0Å range: probe atom residue distance (Å) B Occ D:Na102 b:46.2 occ:1.00 O D:HOH232 2.6 40.7 1.0 O D:GLU10 2.8 26.2 1.0 OE1 D:GLU10 2.9 32.5 1.0 NZ F:LYS15 3.4 49.4 1.0 CE F:LYS15 3.5 50.0 1.0 CB D:GLU13 3.6 27.5 1.0 N D:LEU14 3.7 26.2 1.0 C D:GLU10 3.7 28.5 1.0 CA D:GLU10 3.8 25.8 1.0 CD D:GLU10 4.0 28.4 1.0 CB D:GLU10 4.0 25.3 1.0 OE1 D:GLU13 4.0 33.0 1.0 CB D:LEU14 4.0 34.0 1.0 C D:GLU13 4.2 27.2 1.0 CD F:LYS15 4.2 39.5 1.0 CA D:LEU14 4.2 28.1 1.0 ZN D:ZN101 4.3 0.7 1.0 CA D:GLU13 4.4 28.1 1.0 CG F:LYS15 4.4 37.7 1.0 CD D:GLU13 4.5 33.9 1.0 CG D:GLU10 4.5 26.1 1.0 CG D:GLU13 4.7 32.4 1.0 O D:HOH219 4.8 43.6 1.0 OE2 D:GLU10 4.8 30.1 1.0 CD1 D:LEU14 4.8 36.0 1.0 CG D:LEU14 4.9 39.2 1.0 N D:LEU11 4.9 24.2 1.0 N D:GLU13 4.9 25.3 1.0 O D:GLU13 5.0 27.9 1.0

S.L.Rouse, F.Stylianou, H.Y.G.Wu, J.L.Berry, L.Sewell, R.M.L.Morgan, A.C.Sauerwein, S.Matthews. The Fapf Amyloid Secretion Transporter Possesses An Atypical Asymmetric Coiled Coil. J. Mol. Biol. V. 430 3863 2018.
ISSN: ESSN 1089-8638
PubMed: 29886016
DOI: 10.1016/J.JMB.2018.06.007