Sodium in PDB 3dh4: Crystal Structure of Sodium/Sugar Symporter with Bound Galactose From Vibrio Parahaemolyticus

The structure of Crystal Structure of Sodium/Sugar Symporter with Bound Galactose From Vibrio Parahaemolyticus, PDB code: 3dh4 was solved by J.Abramson, S.Faham, D.Cascio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	83.280, 109.210, 127.580, 109.70, 92.02, 102.11
R / Rfree (%)	27 / 28.7

The structure of Crystal Structure of Sodium/Sugar Symporter with Bound Galactose From Vibrio Parahaemolyticus also contains other interesting chemical elements:

Erbium

(Er)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Sodium/Sugar Symporter with Bound Galactose From Vibrio Parahaemolyticus (pdb code 3dh4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Sodium/Sugar Symporter with Bound Galactose From Vibrio Parahaemolyticus, PDB code: 3dh4:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Sodium/Sugar Symporter with Bound Galactose From Vibrio Parahaemolyticus


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 Sodium/Sugar Symporter with Bound Galactose From Vibrio Parahaemolyticus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na801 b:42.6 occ:1.00 OG A:SER364 3.1 56.6 1.0 O A:ALA361 3.2 52.2 1.0 O A:ILE65 3.3 53.7 1.0 O A:ALA62 3.6 49.7 1.0 OG A:SER365 3.7 56.4 1.0 CB A:SER364 4.0 56.1 1.0 C A:ALA361 4.1 52.7 1.0 CA A:ALA361 4.1 52.2 1.0 CB A:ALA361 4.4 52.1 1.0 OD1 A:ASP189 4.4 70.6 1.0 C A:ILE65 4.4 54.0 1.0 N A:SER365 4.6 55.5 1.0 C A:ALA62 4.7 49.5 1.0 CB A:SER365 4.8 55.6 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Sodium/Sugar Symporter with Bound Galactose From Vibrio Parahaemolyticus


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 Sodium/Sugar Symporter with Bound Galactose From Vibrio Parahaemolyticus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na801 b:41.9 occ:1.00 OG B:SER364 3.1 57.1 1.0 O B:ALA361 3.1 53.2 1.0 O B:ILE65 3.2 54.8 1.0 OG B:SER365 3.5 56.6 1.0 O B:ALA62 3.7 50.3 1.0 CB B:SER364 4.0 56.8 1.0 C B:ALA361 4.0 53.6 1.0 CA B:ALA361 4.1 53.1 1.0 C B:ILE65 4.3 55.2 1.0 CB B:ALA361 4.4 53.0 1.0 N B:SER365 4.5 56.0 1.0 OD1 B:ASP189 4.6 71.3 1.0 CB B:SER365 4.6 55.9 1.0 C B:ALA62 4.8 50.3 1.0 CA B:SER365 4.9 55.7 1.0 CA B:SER66 5.0 55.8 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Sodium/Sugar Symporter with Bound Galactose From Vibrio Parahaemolyticus


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 Sodium/Sugar Symporter with Bound Galactose From Vibrio Parahaemolyticus within 5.0Å range: probe atom residue distance (Å) B Occ C:Na801 b:43.2 occ:1.00 O C:ALA361 3.1 52.6 1.0 OG C:SER364 3.1 56.9 1.0 O C:ILE65 3.2 54.5 1.0 OG C:SER365 3.6 56.6 1.0 O C:ALA62 3.8 50.2 1.0 C C:ALA361 3.9 53.0 1.0 CB C:SER364 3.9 56.5 1.0 CA C:ALA361 4.0 52.6 1.0 CB C:ALA361 4.3 52.4 1.0 C C:ILE65 4.4 54.9 1.0 N C:SER365 4.5 55.8 1.0 OD1 C:ASP189 4.6 71.1 1.0 CB C:SER365 4.7 55.8 1.0 C C:ALA62 4.9 50.2 1.0 CA C:SER365 4.9 55.6 1.0 CA C:SER66 5.0 55.6 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Sodium/Sugar Symporter with Bound Galactose From Vibrio Parahaemolyticus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Sodium/Sugar Symporter with Bound Galactose From Vibrio Parahaemolyticus within 5.0Å range: probe atom residue distance (Å) B Occ D:Na801 b:42.4 occ:1.00 O D:ALA361 3.0 52.8 1.0 OG D:SER364 3.1 56.8 1.0 O D:ILE65 3.2 54.0 1.0 OG D:SER365 3.6 56.4 1.0 O D:ALA62 3.8 49.8 1.0 C D:ALA361 3.9 53.2 1.0 CB D:SER364 3.9 56.4 1.0 CA D:ALA361 4.0 52.9 1.0 CB D:ALA361 4.3 52.7 1.0 C D:ILE65 4.4 54.4 1.0 N D:SER365 4.5 55.7 1.0 OD1 D:ASP189 4.6 70.8 1.0 CB D:SER365 4.7 55.7 1.0 C D:ALA62 4.9 49.6 1.0 CA D:SER66 5.0 55.3 1.0 CA D:SER365 5.0 55.5 1.0

S.Faham, A.Watanabe, G.M.Besserer, D.Cascio, A.Specht, B.A.Hirayama, E.M.Wright, J.Abramson. The Crystal Structure of A Sodium Galactose Transporter Reveals Mechanistic Insights Into Na+/Sugar Symport. Science V. 321 810 2008.
ISSN: ISSN 0036-8075
PubMed: 18599740
DOI: 10.1126/SCIENCE.1160406