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

Protein crystallography data

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

Other elements in 3dh4:

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

Erbium Binding Sites:

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 3dh4

Go back to Erbium Binding Sites List in 3dh4
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 3dh4

Go back to Erbium Binding Sites List in 3dh4
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 3dh4

Go back to Erbium Binding Sites List in 3dh4
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 3dh4

Go back to Erbium Binding Sites List in 3dh4
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

Reference:

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
Page generated: Sun Dec 13 11:27:38 2020

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