Sodium in PDB 4ma6: Crystal Structure of Ara H 8 with Epicatechin Bound

The structure of Crystal Structure of Ara H 8 with Epicatechin Bound, PDB code: 4ma6 was solved by L.R.Offermann, B.K.Hurlburt, K.A.Majorek, J.K.Mcbride, S.J.Maleki, M.Chruszcz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.80 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.647, 88.957, 42.657, 90.00, 96.58, 90.00
R / Rfree (%)	19.2 / 24.8

The binding sites of Sodium atom in the Crystal Structure of Ara H 8 with Epicatechin Bound (pdb code 4ma6). 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 Ara H 8 with Epicatechin Bound, PDB code: 4ma6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Ara H 8 with Epicatechin Bound


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 Ara H 8 with Epicatechin Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:36.6 occ:1.00 O A:HOH354 2.3 46.6 1.0 O A:PRO31 2.4 32.7 1.0 O A:VAL37 2.5 27.0 1.0 O A:HOH307 2.5 45.6 1.0 O A:ILE34 2.6 28.6 1.0 O A:ASP35 3.1 34.0 1.0 C A:PRO31 3.5 31.7 1.0 C A:VAL37 3.6 27.1 1.0 C A:ILE34 3.6 28.7 1.0 C A:ASP35 3.6 32.9 1.0 CA A:ASP35 3.7 33.6 1.0 CA A:PRO31 4.0 29.7 1.0 N A:ASP35 4.1 30.7 1.0 N A:VAL37 4.1 29.6 1.0 CD A:LYS38 4.2 30.4 1.0 NZ A:LYS38 4.3 34.2 1.0 CA A:VAL37 4.4 27.0 1.0 N A:LYS38 4.5 26.4 1.0 CA A:LYS38 4.5 27.1 1.0 O A:LYS32 4.5 34.2 1.0 N A:LYS32 4.6 32.0 1.0 N A:ASP36 4.6 32.1 1.0 C A:LYS32 4.7 32.2 1.0 O A:HOH320 4.7 39.5 1.0 CB A:PRO31 4.7 29.8 1.0 N A:ILE34 4.8 27.1 1.0 OD2 A:ASP35 4.8 43.6 1.0 CA A:ILE34 4.8 27.1 1.0 C A:ASP36 4.9 31.6 1.0 CB A:VAL37 4.9 26.3 1.0 O A:THR30 4.9 29.1 1.0 CE A:LYS38 4.9 33.1 1.0 CA A:LYS32 4.9 33.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Ara H 8 with Epicatechin Bound


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 Ara H 8 with Epicatechin Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:28.2 occ:1.00 O B:PRO31 2.2 29.4 1.0 O B:HOH314 2.3 34.0 1.0 O B:ILE34 2.4 28.4 1.0 O B:VAL37 2.4 27.8 1.0 O B:HOH307 2.5 25.3 1.0 O B:ASP35 2.7 29.3 1.0 C B:PRO31 3.3 29.0 1.0 C B:ASP35 3.4 29.5 1.0 C B:ILE34 3.4 30.2 1.0 C B:VAL37 3.6 27.6 1.0 CA B:ASP35 3.6 31.1 1.0 CA B:PRO31 3.8 29.1 1.0 N B:ASP35 4.0 29.9 1.0 N B:VAL37 4.0 28.1 1.0 CA B:VAL37 4.3 26.9 1.0 N B:ASP36 4.4 28.0 1.0 N B:LYS32 4.4 28.9 1.0 CD B:LYS38 4.5 30.8 1.0 N B:LYS38 4.5 27.1 1.0 CB B:PRO31 4.5 28.9 1.0 NZ B:LYS38 4.5 34.3 1.0 N B:ILE34 4.6 29.9 1.0 O B:THR30 4.6 25.9 1.0 CA B:LYS38 4.6 27.0 1.0 CA B:ILE34 4.6 31.1 1.0 O B:HOH315 4.7 37.0 1.0 C B:LYS32 4.7 29.6 1.0 C B:ASP36 4.7 28.1 1.0 CB B:VAL37 4.7 26.6 1.0 CA B:LYS32 4.7 29.6 1.0 O B:LYS32 4.9 29.7 1.0 OD2 B:ASP35 4.9 43.4 1.0

B.K.Hurlburt, L.R.Offermann, J.K.Mcbride, K.A.Majorek, S.J.Maleki, M.Chruszcz. Structure and Function of the Peanut Panallergen Ara H 8. J.Biol.Chem. V. 288 36890 2013.
ISSN: ISSN 0021-9258
PubMed: 24253038
DOI: 10.1074/JBC.M113.517797