Erbium 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:

Sodium

(Na)

4 atoms

The binding sites of Erbium 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 Erbium atom.
In total 4 binding sites of Erbium where determined in the Crystal Structure of Sodium/Sugar Symporter with Bound Galactose From Vibrio Parahaemolyticus, PDB code: 3dh4:
Jump to Erbium binding site number: 1; 2; 3; 4;

Erbium 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 Erbium with other atoms in the Er 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:Er702 b:54.5 occ:1.00 OD2 A:ASP481 2.8 12.3 1.0 OD1 A:ASP481 2.9 13.2 1.0 CG A:ASP481 3.1 9.9 1.0 OD1 B:ASP481 3.3 13.2 1.0 OD2 B:ASP481 3.3 11.9 1.0 CG B:ASP481 3.6 9.8 1.0 CB A:ASP481 4.4 9.0 1.0 CB B:ASP481 4.8 9.1 1.0

Erbium 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 Erbium with other atoms in the Er 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 A:Er704 b:93.2 occ:1.00 OE1 A:GLU155 3.0 58.6 1.0 OE2 A:GLU155 3.1 58.5 1.0 CD A:GLU155 3.3 56.8 1.0 CG A:GLU155 4.5 55.9 1.0 O A:ILE160 5.0 63.6 1.0 CA A:PRO161 5.0 64.4 1.0

Erbium 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 Erbium with other atoms in the Er 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 D:Er703 b:53.2 occ:1.00 OD1 D:ASP481 3.0 13.2 1.0 OD2 D:ASP481 3.1 12.1 1.0 OD1 C:ASP481 3.3 13.1 1.0 CG D:ASP481 3.3 9.8 1.0 OD2 C:ASP481 3.4 12.0 1.0 CG C:ASP481 3.6 9.8 1.0 CB D:ASP481 4.5 9.0 1.0 CB C:ASP481 4.8 9.0 1.0

Erbium 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 Erbium with other atoms in the Er 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:Er705 b:99.3 occ:1.00 OE1 D:GLU155 2.9 59.3 1.0 OE2 D:GLU155 3.0 59.3 1.0 CD D:GLU155 3.2 57.3 1.0 CG D:GLU155 4.4 56.3 1.0 CA D:PRO161 4.9 64.2 1.0 O D:ILE160 4.9 63.3 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