Sodium in PDB 6awv: Ara H 8.01 in Complex with Epicatechin

The structure of Ara H 8.01 in Complex with Epicatechin, PDB code: 6awv 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 / 2.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	177.519, 52.232, 56.449, 90.00, 96.87, 90.00
R / Rfree (%)	21.9 / 26.2

The binding sites of Sodium atom in the Ara H 8.01 in Complex with Epicatechin (pdb code 6awv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Ara H 8.01 in Complex with Epicatechin, PDB code: 6awv:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Ara H 8.01 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 Ara H 8.01 in Complex with Epicatechin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:74.0 occ:1.00 O B:PRO31 2.3 56.3 1.0 O B:VAL37 2.7 56.7 1.0 O B:ILE34 2.7 65.2 1.0 O B:ASP35 2.9 71.3 1.0 O B:HOH303 3.0 63.0 1.0 C B:PRO31 3.4 57.6 1.0 C B:ASP35 3.5 72.0 1.0 C B:VAL37 3.7 56.8 1.0 CA B:ASP35 3.7 72.6 1.0 C B:ILE34 3.8 66.1 1.0 CA B:PRO31 4.0 56.7 1.0 N B:ASP35 4.2 69.7 1.0 O B:HOH312 4.2 58.9 1.0 NZ B:LYS38 4.3 68.6 1.0 N B:VAL37 4.3 62.2 1.0 CD B:LYS38 4.4 65.3 1.0 CA B:VAL37 4.5 58.5 1.0 N B:LYS38 4.5 57.4 1.0 N B:LYS32 4.6 61.3 1.0 CB B:PRO31 4.6 57.0 1.0 N B:ASP36 4.6 70.0 1.0 CA B:LYS38 4.7 58.0 1.0 O B:LYS32 4.8 68.6 1.0 C B:ASP36 4.9 67.0 1.0 CA B:LYS32 4.9 67.7 1.0 CE B:LYS38 5.0 67.8 1.0 C B:LYS32 5.0 69.1 1.0 O B:THR30 5.0 54.2 1.0

Sodium binding site 2 out of 2 in the Ara H 8.01 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 Ara H 8.01 in Complex with Epicatechin within 5.0Å range: probe atom residue distance (Å) B Occ C:Na201 b:70.9 occ:1.00 O C:HOH301 2.3 72.1 1.0 O C:PRO31 2.4 66.6 1.0 O C:VAL37 2.5 64.4 1.0 O C:ILE34 2.7 67.6 1.0 O C:ASP35 3.0 76.9 1.0 C C:PRO31 3.5 66.7 1.0 C C:ASP35 3.6 73.1 1.0 C C:VAL37 3.6 61.0 1.0 C C:ILE34 3.8 66.8 1.0 CA C:ASP35 3.9 71.9 1.0 CA C:PRO31 4.0 65.1 1.0 NZ C:LYS38 4.2 79.1 1.0 CD C:LYS38 4.3 76.4 1.0 N C:VAL37 4.3 58.9 1.0 N C:ASP35 4.3 66.2 1.0 N C:LYS38 4.5 64.4 1.0 CA C:VAL37 4.5 58.2 1.0 CA C:LYS38 4.6 68.1 1.0 OD1 C:ASP35 4.6 97.7 1.0 N C:ASP36 4.6 69.2 1.0 CB C:PRO31 4.7 66.4 1.0 N C:LYS32 4.7 69.2 1.0 O C:LYS32 4.7 64.6 1.0 C C:ASP36 4.7 65.3 1.0 CE C:LYS38 4.9 78.4 1.0 C C:LYS32 4.9 67.5 1.0 O C:THR30 4.9 58.1 1.0 N C:ILE34 4.9 68.3 1.0 CA C:LYS32 5.0 70.6 1.0 CB C:VAL37 5.0 56.3 1.0 CA C:ILE34 5.0 65.2 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.