Sodium in PDB 3tsj: Crystal Structure of Phl P 4, A Grass Pollen Allergen with Glucose Dehydrogenase Activity

The structure of Crystal Structure of Phl P 4, A Grass Pollen Allergen with Glucose Dehydrogenase Activity, PDB code: 3tsj was solved by D.Zafred, A.Nandy, W.Keller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.94 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	75.774, 153.437, 177.631, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 20.7

The binding sites of Sodium atom in the Crystal Structure of Phl P 4, A Grass Pollen Allergen with Glucose Dehydrogenase Activity (pdb code 3tsj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Phl P 4, A Grass Pollen Allergen with Glucose Dehydrogenase Activity, PDB code: 3tsj:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Phl P 4, A Grass Pollen Allergen with Glucose Dehydrogenase Activity


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 Phl P 4, A Grass Pollen Allergen with Glucose Dehydrogenase Activity within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:23.0 occ:1.00 O A:HOH702 2.2 18.6 1.0 O A:HOH704 2.3 18.3 1.0 OE1 A:GLU338 2.3 25.9 1.0 O A:HOH705 2.4 25.2 1.0 OE2 A:GLU89 2.5 20.1 1.0 O A:HOH701 2.5 21.1 1.0 CD A:GLU89 3.2 19.4 1.0 CD A:GLU338 3.3 23.6 1.0 OE1 A:GLU89 3.5 18.5 1.0 OE2 A:GLU338 3.6 26.9 1.0 NH1 A:ARG44 4.1 17.1 1.0 O A:HOH1131 4.3 33.8 1.0 O A:TYR339 4.3 14.4 1.0 O A:HOH951 4.3 30.3 1.0 N A:TYR339 4.3 15.1 1.0 O A:ARG440 4.4 12.3 1.0 OD1 A:ASP441 4.4 19.2 1.0 CG A:GLU89 4.5 16.4 1.0 N A:ILE442 4.6 13.8 1.0 CA A:ASP441 4.6 13.5 1.0 CG A:GLU338 4.6 18.1 1.0 CA A:GLU338 4.7 15.6 1.0 O A:TYR88 4.7 14.3 1.0 CG2 A:ILE442 5.0 15.5 1.0 CZ A:ARG44 5.0 18.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Phl P 4, A Grass Pollen Allergen with Glucose Dehydrogenase Activity


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 Phl P 4, A Grass Pollen Allergen with Glucose Dehydrogenase Activity within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:24.5 occ:1.00 O B:HOH709 2.3 34.0 1.0 OE2 B:GLU89 2.4 20.3 1.0 O B:HOH708 2.4 22.6 1.0 OE1 B:GLU338 2.4 25.0 1.0 O B:HOH705 2.4 19.4 1.0 O B:HOH712 2.8 24.3 1.0 CD B:GLU89 3.1 18.7 1.0 OE1 B:GLU89 3.3 18.7 1.0 CD B:GLU338 3.4 24.9 1.0 OE2 B:GLU338 3.7 28.0 1.0 NH1 B:ARG44 4.2 20.4 1.0 O B:TYR339 4.3 16.3 1.0 O B:HOH1113 4.4 28.4 1.0 CG B:GLU89 4.4 16.7 1.0 O B:HOH1048 4.4 39.2 1.0 O B:ARG440 4.4 12.8 1.0 OD1 B:ASP441 4.5 18.6 1.0 CA B:ASP441 4.5 14.8 1.0 N B:TYR339 4.5 16.4 1.0 N B:ILE442 4.5 15.8 1.0 O B:TYR88 4.7 13.7 1.0 CG B:GLU338 4.7 18.7 1.0 CA B:GLU338 4.8 16.7 1.0

D.Zafred, A.Nandy, L.Pump, H.Kahlert, W.Keller. Crystal Structure and Immunologic Characterization of the Major Grass Pollen Allergen Phl P 4. J. Allergy Clin. Immunol. V. 132 696 2013.
ISSN: ESSN 1097-6825
PubMed: 23683465
DOI: 10.1016/J.JACI.2013.03.021