Sodium in PDB 4m9w: Crystal Structure of Ara H 8 with Mes Bound

The structure of Crystal Structure of Ara H 8 with Mes Bound, PDB code: 4m9w 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)	40.01 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.183, 87.488, 42.290, 90.00, 95.84, 90.00
R / Rfree (%)	20.5 / 24.8

The binding sites of Sodium atom in the Crystal Structure of Ara H 8 with Mes Bound (pdb code 4m9w). 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 Mes Bound, PDB code: 4m9w:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Ara H 8 with Mes 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 Mes Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na200 b:36.9 occ:1.00 O A:HOH323 2.2 48.8 1.0 O A:ILE34 2.2 35.8 1.0 O A:VAL37 2.3 34.1 1.0 O A:PRO31 2.5 34.0 1.0 O A:HOH351 2.6 44.4 1.0 O A:ASP35 2.9 41.0 1.0 C A:ASP35 3.3 38.0 1.0 C A:ILE34 3.3 39.2 1.0 C A:VAL37 3.4 33.1 1.0 C A:PRO31 3.4 35.7 1.0 CA A:ASP35 3.5 39.9 1.0 N A:VAL37 3.8 34.8 1.0 CA A:PRO31 3.8 32.8 1.0 N A:ASP35 3.8 35.5 1.0 CA A:VAL37 4.1 32.8 1.0 N A:ASP36 4.2 38.7 1.0 N A:LYS38 4.4 32.8 1.0 CD A:LYS38 4.5 42.4 1.0 C A:ASP36 4.5 36.9 1.0 N A:ILE34 4.5 36.4 1.0 CA A:ILE34 4.5 36.2 1.0 O A:LYS32 4.5 35.8 1.0 CA A:LYS38 4.6 35.6 1.0 CB A:VAL37 4.6 31.6 1.0 N A:LYS32 4.6 35.3 1.0 O A:THR30 4.6 36.4 1.0 CB A:PRO31 4.6 34.7 1.0 NZ A:LYS38 4.6 47.0 1.0 C A:LYS32 4.7 37.2 1.0 OD1 A:ASP35 4.9 45.5 1.0 CA A:ASP36 4.9 40.3 1.0 CA A:LYS32 4.9 36.5 1.0 CB A:ASP35 5.0 43.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Ara H 8 with Mes 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 Mes Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:33.6 occ:1.00 O B:VAL37 2.3 28.2 1.0 O B:ILE34 2.3 32.2 1.0 O B:PRO31 2.3 32.4 1.0 O B:HOH309 2.4 29.5 1.0 O B:HOH304 2.7 35.9 1.0 O B:ASP35 2.8 29.1 1.0 C B:ASP35 3.3 30.5 1.0 C B:PRO31 3.3 34.3 1.0 C B:VAL37 3.4 26.9 1.0 C B:ILE34 3.4 34.1 1.0 CA B:ASP35 3.6 32.4 1.0 CA B:PRO31 3.7 34.0 1.0 O B:HOH346 3.9 41.4 1.0 N B:VAL37 3.9 28.3 1.0 N B:ASP35 3.9 31.6 1.0 CA B:VAL37 4.1 27.0 1.0 N B:ASP36 4.2 29.1 1.0 N B:LYS38 4.3 27.9 1.0 CB B:PRO31 4.4 34.2 1.0 O B:HOH318 4.4 42.4 1.0 CD B:LYS38 4.4 32.3 1.0 C B:ASP36 4.5 28.5 1.0 N B:LYS32 4.5 34.8 1.0 CA B:LYS38 4.5 29.0 1.0 NZ B:LYS38 4.5 35.8 1.0 CB B:VAL37 4.6 28.7 1.0 N B:ILE34 4.6 33.8 1.0 CA B:ILE34 4.6 35.6 1.0 O B:HOH308 4.7 34.7 1.0 O B:THR30 4.8 32.8 1.0 CA B:ASP36 4.8 29.8 1.0 C B:LYS32 4.9 36.8 1.0 OD1 B:ASP35 4.9 41.5 1.0 CA B:LYS32 4.9 35.6 1.0 CB B:ASP35 5.0 34.4 1.0 CE B:LYS38 5.0 35.0 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