Sodium in PDB 6awt: Structure of Pr 10 Allergen in Complex with Epicatechin

The structure of Structure of Pr 10 Allergen in Complex with Epicatechin, PDB code: 6awt was solved by L.R.Offermann, M.Perdue, J.Mcbride, B.K.Hurlburt, S.J.Maleki, S.S.Pote, M.Chruszcz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.451, 62.507, 186.585, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 25.2

The binding sites of Sodium atom in the Structure of Pr 10 Allergen in Complex with Epicatechin (pdb code 6awt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of Pr 10 Allergen in Complex with Epicatechin, PDB code: 6awt:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structure of Pr 10 Allergen in Complex with Epicatechin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Pr 10 Allergen in Complex with Epicatechin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:52.4 occ:1.00 O A:PRO31 2.2 55.5 1.0 O A:HOH722 2.2 53.4 1.0 O A:VAL37 2.4 52.4 1.0 O A:ILE34 2.5 48.7 1.0 O A:HOH710 2.5 44.3 1.0 O A:ASP35 3.2 66.6 1.0 C A:PRO31 3.3 54.9 1.0 C A:ILE34 3.5 52.2 1.0 C A:VAL37 3.5 52.0 1.0 C A:ASP35 3.6 59.4 1.0 CA A:ASP35 3.7 58.4 1.0 CA A:PRO31 3.9 54.4 1.0 N A:ASP35 4.0 53.3 1.0 N A:VAL37 4.1 49.8 1.0 CA A:VAL37 4.3 50.1 1.0 O A:HOH713 4.4 61.0 1.0 N A:LYS32 4.4 56.3 1.0 NZ A:LYS38 4.4 60.4 1.0 CD A:LYS38 4.4 57.0 1.0 O A:THR30 4.4 50.9 1.0 N A:LYS38 4.5 50.6 1.0 CA A:LYS38 4.6 50.6 1.0 C A:LYS32 4.6 60.1 1.0 O A:LYS32 4.6 63.3 1.0 N A:ASP36 4.6 54.0 1.0 O A:HOH730 4.6 64.7 1.0 N A:ILE34 4.7 54.3 1.0 CB A:VAL37 4.7 50.6 1.0 CA A:ILE34 4.7 52.4 1.0 CA A:LYS32 4.7 61.5 1.0 CB A:PRO31 4.8 55.8 1.0 C A:ASP36 4.8 51.3 1.0 CE A:LYS38 4.9 59.5 1.0

Sodium binding site 2 out of 3 in the Structure of Pr 10 Allergen in Complex with Epicatechin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Pr 10 Allergen in Complex with Epicatechin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:61.1 occ:1.00 O B:PRO31 2.2 54.0 1.0 O B:VAL37 2.3 51.5 1.0 O B:ILE34 2.3 55.2 1.0 O B:HOH327 2.4 56.5 1.0 O B:HOH319 2.6 63.6 1.0 O B:ASP35 3.0 67.6 1.0 C B:PRO31 3.3 52.6 1.0 C B:ILE34 3.4 54.3 1.0 C B:ASP35 3.4 65.1 1.0 C B:VAL37 3.5 53.7 1.0 CA B:ASP35 3.6 64.3 1.0 N B:VAL37 3.9 53.0 1.0 CA B:PRO31 3.9 50.6 1.0 N B:ASP35 4.0 56.8 1.0 CA B:VAL37 4.2 51.2 1.0 O B:THR30 4.3 45.9 1.0 NZ B:LYS38 4.3 73.5 1.0 N B:LYS32 4.4 52.3 1.0 N B:ASP36 4.4 65.2 1.0 CD B:LYS38 4.4 68.3 1.0 N B:LYS38 4.5 54.2 1.0 N B:ILE34 4.5 50.0 1.0 CA B:ILE34 4.6 52.9 1.0 CB B:VAL37 4.6 48.0 1.0 C B:LYS32 4.6 56.9 1.0 O B:LYS32 4.6 61.2 1.0 C B:ASP36 4.6 60.7 1.0 CA B:LYS38 4.6 58.2 1.0 CA B:LYS32 4.8 55.6 1.0 CE B:LYS38 4.8 71.7 1.0 CB B:PRO31 4.9 52.0 1.0 OD1 B:ASP35 5.0 80.1 1.0 CB B:ASP35 5.0 69.3 1.0

Sodium binding site 3 out of 3 in the Structure of Pr 10 Allergen in Complex with Epicatechin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Pr 10 Allergen in Complex with Epicatechin within 5.0Å range: probe atom residue distance (Å) B Occ C:Na203 b:45.2 occ:1.00 O C:HOH327 2.2 49.5 1.0 O C:PRO31 2.2 49.2 1.0 O C:ILE34 2.3 43.2 1.0 O C:VAL37 2.3 40.7 1.0 O C:HOH315 2.7 43.2 1.0 O C:ASP35 3.2 48.2 1.0 C C:PRO31 3.3 49.5 1.0 C C:ILE34 3.3 45.5 1.0 C C:VAL37 3.4 41.4 1.0 C C:ASP35 3.5 48.8 1.0 CA C:ASP35 3.6 50.6 1.0 CA C:PRO31 3.8 47.4 1.0 N C:VAL37 3.9 40.6 1.0 N C:ASP35 3.9 45.8 1.0 CA C:VAL37 4.1 40.7 1.0 O C:THR30 4.3 46.6 1.0 NZ C:LYS38 4.4 54.0 1.0 N C:LYS32 4.4 50.5 1.0 N C:LYS38 4.4 43.8 1.0 N C:ASP36 4.4 47.2 1.0 N C:ILE34 4.4 47.1 1.0 CB C:VAL37 4.4 41.0 1.0 CA C:ILE34 4.5 46.6 1.0 CD C:LYS38 4.5 49.9 1.0 C C:ASP36 4.6 44.0 1.0 C C:LYS32 4.6 52.4 1.0 CA C:LYS38 4.7 44.3 1.0 O C:LYS32 4.7 49.0 1.0 CB C:PRO31 4.7 46.9 1.0 CA C:LYS32 4.8 54.6 1.0 CE C:LYS38 4.9 52.7 1.0 OD1 C:ASP35 4.9 66.5 1.0

L.R.Offermann, J.Yarbrough, J.Mcbride, B.K.Hurlburt, S.J.Maleki, S.S.Pote, M.Chruszcz. Structure of Pr-10 Allergen Ara H 8.01. To Be Published.