Sodium in PDB 4afk: In Meso Structure of Alginate Transporter, Alge, From Pseudomonas Aeruginosa, PAO1

The structure of In Meso Structure of Alginate Transporter, Alge, From Pseudomonas Aeruginosa, PAO1, PDB code: 4afk was solved by J.Tan, V.E.Pye, D.Aragao, M.Caffrey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.77 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	57.253, 74.416, 115.529, 90.00, 101.56, 90.00
R / Rfree (%)	16.3 / 20.9

The structure of In Meso Structure of Alginate Transporter, Alge, From Pseudomonas Aeruginosa, PAO1 also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the In Meso Structure of Alginate Transporter, Alge, From Pseudomonas Aeruginosa, PAO1 (pdb code 4afk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the In Meso Structure of Alginate Transporter, Alge, From Pseudomonas Aeruginosa, PAO1, PDB code: 4afk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the In Meso Structure of Alginate Transporter, Alge, From Pseudomonas Aeruginosa, PAO1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of In Meso Structure of Alginate Transporter, Alge, From Pseudomonas Aeruginosa, PAO1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1507 b:21.7 occ:1.00 O A:ALA136 2.5 13.7 1.0 O A:GLU144 2.5 15.2 1.0 O A:TYR141 2.6 19.8 1.0 OE1 A:GLU144 2.7 17.3 1.0 O A:THR139 2.7 14.2 1.0 O A:HOH2064 2.7 29.4 1.0 C A:GLU144 3.5 13.5 1.0 C A:ALA136 3.5 15.6 1.0 CD A:GLU144 3.6 15.8 1.0 C A:TYR141 3.6 21.4 1.0 CB A:GLU144 3.7 12.2 1.0 C A:THR139 3.7 18.8 1.0 OG1 A:THR139 3.8 17.4 1.0 CA A:GLU144 3.9 15.6 1.0 CA A:ALA136 4.0 15.2 1.0 CB A:ALA136 4.0 12.3 1.0 N A:TYR141 4.1 17.2 1.0 N A:GLU144 4.1 13.6 1.0 N A:THR139 4.2 13.5 1.0 CG A:GLU144 4.2 11.1 1.0 CA A:TYR141 4.4 15.3 1.0 OE2 A:GLU144 4.4 16.3 1.0 C A:ALA140 4.4 25.8 1.0 CA A:THR139 4.4 15.5 1.0 O A:HOH2063 4.5 15.0 1.0 N A:PRO142 4.5 24.1 1.0 N A:GLY137 4.5 11.8 1.0 N A:HIS145 4.6 7.6 1.0 CA A:PRO142 4.6 22.0 1.0 N A:ALA140 4.6 18.2 1.0 CB A:THR139 4.7 19.6 1.0 CA A:ALA140 4.8 26.5 1.0 C A:PRO142 4.8 20.8 1.0 O A:PRO142 4.8 21.4 1.0 CA A:HIS145 4.9 11.7 1.0 CB A:TYR141 4.9 18.4 1.0 CA A:GLY137 4.9 14.3 1.0 N A:LEU138 4.9 11.7 1.0 O A:ALA140 4.9 27.1 1.0

Sodium binding site 2 out of 2 in the In Meso Structure of Alginate Transporter, Alge, From Pseudomonas Aeruginosa, PAO1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of In Meso Structure of Alginate Transporter, Alge, From Pseudomonas Aeruginosa, PAO1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1508 b:32.4 occ:1.00 NE A:ARG317 3.0 15.1 1.0 NZ A:LYS325 3.0 23.4 1.0 OD1 A:ASN319 3.0 22.6 1.0 OD1 A:ASN273 3.1 19.0 1.0 NH2 A:ARG317 3.1 17.7 1.0 O A:ASN265 3.2 20.1 1.0 CZ A:ARG317 3.4 15.3 1.0 CE A:LYS325 3.6 23.0 1.0 CD A:LYS325 3.6 20.1 1.0 CG A:ASN319 3.8 21.4 1.0 CA A:GLY358 3.8 10.9 1.0 ND2 A:ASN319 3.8 19.9 1.0 O A:GLY358 4.0 13.5 1.0 CD A:ARG317 4.0 18.0 1.0 CA A:TYR266 4.1 20.1 0.6 CA A:TYR266 4.1 20.1 0.5 O A:TYR266 4.1 18.6 0.6 CB A:SER268 4.2 13.1 1.0 C A:ASN265 4.2 19.7 1.0 C A:TYR266 4.2 19.9 0.6 CG A:ASN273 4.3 18.5 1.0 C A:TYR266 4.4 19.9 0.5 C A:GLY358 4.4 12.2 1.0 O A:TYR266 4.5 19.5 0.5 N A:SER268 4.6 23.7 1.0 N A:TYR266 4.6 19.5 0.6 N A:TYR266 4.6 19.5 0.5 NH1 A:ARG317 4.7 13.9 1.0 CG A:ARG317 4.9 10.7 1.0 CG A:LYS325 4.9 17.0 1.0

J.Tan, S.L.Rouse, D.Li, V.E.Pye, L.Vogeley, A.R.Brinth, T.El Arnaout, J.C.Whitney, P.L.Howell, M.S.P.Sansom, M.Caffrey. A Conformational Landscape For Alginate Secretion Across the Outer Membrane of Pseudomonas Aeruginosa. Acta Crystallogr.,Sect.D V. 70 2054 2014.
ISSN: ISSN 0907-4449
PubMed: 25084326
DOI: 10.1107/S1399004714001850