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

Protein crystallography data

The structure of Crystal Structure of Phl P 4, A Grass Pollen Allergen with Glucose Dehydrogenase Activity, PDB code: 3tsh 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) 19.50 / 1.90
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 117.077, 117.077, 202.090, 90.00, 90.00, 120.00
R / Rfree (%) 16.2 / 19

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Phl P 4, A Grass Pollen Allergen with Glucose Dehydrogenase Activity (pdb code 3tsh). 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: 3tsh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3tsh

Go back to Sodium Binding Sites List in 3tsh
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:23.9
occ:1.00
OE1 A:GLU338 2.3 24.1 1.0
O A:HOH719 2.3 20.2 1.0
OE2 A:GLU89 2.3 21.2 1.0
O A:HOH720 2.4 28.3 1.0
O A:HOH718 2.5 26.3 1.0
O A:HOH717 2.5 24.1 1.0
CD A:GLU89 3.1 23.3 1.0
CD A:GLU338 3.3 25.9 1.0
OE1 A:GLU89 3.4 20.2 1.0
OE2 A:GLU338 3.5 28.6 1.0
NH1 A:ARG44 4.1 23.9 1.0
O A:TYR339 4.3 18.9 1.0
O A:HOH1111 4.3 47.7 1.0
OD1 A:ASP441 4.4 19.7 1.0
O A:HOH1068 4.4 36.3 1.0
CG A:GLU89 4.4 18.4 1.0
O A:ARG440 4.5 13.6 1.0
CA A:ASP441 4.5 16.9 1.0
N A:ILE442 4.5 17.4 1.0
N A:TYR339 4.5 19.1 1.0
CG A:GLU338 4.6 22.1 1.0
CA A:GLU338 4.9 20.9 1.0
CG2 A:ILE442 4.9 20.8 1.0
O A:TYR88 4.9 18.3 1.0
CZ A:ARG44 5.0 25.6 1.0

Sodium binding site 2 out of 2 in 3tsh

Go back to Sodium Binding Sites List in 3tsh
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
A:Na604

b:30.6
occ:1.00
O A:LYS430 2.2 24.2 1.0
O1 A:FMT603 2.3 31.0 1.0
O A:HOH722 2.4 19.0 1.0
O A:HOH721 2.4 40.0 1.0
O2 A:FMT603 2.4 35.7 1.0
O A:HOH723 2.5 39.0 1.0
C A:FMT603 2.7 34.6 1.0
C A:LYS430 3.4 22.6 1.0
O A:ASN431 3.7 22.9 1.0
NZ A:LYS468 3.8 22.4 0.5
N A:LYS430 3.8 21.7 1.0
C A:ASN431 4.1 23.1 1.0
O A:PRO432 4.2 17.9 1.0
CA A:LYS430 4.2 23.4 1.0
N A:ASN431 4.4 23.5 1.0
N A:PRO432 4.5 22.1 1.0
CA A:ASN431 4.6 24.0 1.0
CB A:ASN431 4.7 25.1 1.0
OE1 A:GLN434 4.8 21.0 1.0
O A:HOH1165 4.8 47.7 1.0
CD A:PRO432 4.8 22.9 1.0
CG A:LYS430 4.9 28.0 1.0
C A:SER429 4.9 20.3 1.0
CB A:SER429 5.0 18.8 1.0

Reference:

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
Page generated: Tue Dec 15 06:26:36 2020

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