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Sodium in PDB 4m9b: Crystal Structure of Apo Ara H 8

Protein crystallography data

The structure of Crystal Structure of Apo Ara H 8, PDB code: 4m9b 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) 29.52 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.939, 87.965, 42.898, 90.00, 96.78, 90.00
R / Rfree (%) 18 / 22.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Apo Ara H 8 (pdb code 4m9b). 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 Apo Ara H 8, PDB code: 4m9b:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4m9b

Go back to Sodium Binding Sites List in 4m9b
Sodium binding site 1 out of 2 in the Crystal Structure of Apo Ara H 8


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 Apo Ara H 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:27.8
occ:1.00
O A:HOH340 2.2 34.6 1.0
O A:VAL37 2.4 18.5 1.0
O A:PRO31 2.4 25.3 1.0
O A:HOH458 2.5 29.4 0.5
O A:ILE34 2.5 21.3 1.0
O A:ASP35 2.9 27.9 1.0
C A:ASP35 3.4 24.1 1.0
C A:PRO31 3.5 22.6 1.0
C A:VAL37 3.5 19.9 1.0
O A:HOH336 3.5 37.6 1.0
C A:ILE34 3.6 22.4 1.0
CA A:ASP35 3.6 24.5 1.0
CA A:PRO31 3.9 23.2 1.0
N A:VAL37 4.0 20.0 1.0
N A:ASP35 4.0 22.2 1.0
O A:HOH404 4.2 27.2 0.5
O A:HOH467 4.3 49.5 1.0
CA A:VAL37 4.3 17.9 1.0
CD A:LYS38 4.3 26.6 1.0
N A:ASP36 4.4 24.3 1.0
NZ A:LYS38 4.4 31.6 1.0
N A:LYS38 4.5 18.8 1.0
CA A:LYS38 4.5 19.7 1.0
N A:LYS32 4.6 20.2 1.0
C A:ASP36 4.6 22.9 1.0
O A:THR30 4.6 22.6 1.0
O A:LYS32 4.7 21.3 1.0
CB A:PRO31 4.7 24.3 1.0
N A:ILE34 4.7 20.7 1.0
O A:HOH359 4.7 34.6 1.0
O A:HOH413 4.7 43.6 1.0
C A:LYS32 4.8 19.7 1.0
CA A:ILE34 4.8 19.9 1.0
CB A:VAL37 4.8 17.4 1.0
CA A:LYS32 5.0 20.2 1.0

Sodium binding site 2 out of 2 in 4m9b

Go back to Sodium Binding Sites List in 4m9b
Sodium binding site 2 out of 2 in the Crystal Structure of Apo Ara H 8


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 Apo Ara H 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:23.6
occ:1.00
O B:PRO31 2.2 22.9 1.0
O B:HOH322 2.3 25.2 1.0
O B:VAL37 2.4 19.5 1.0
O B:ILE34 2.4 21.6 1.0
O B:HOH304 2.5 25.8 1.0
O B:ASP35 2.7 24.2 1.0
C B:ASP35 3.3 24.5 1.0
C B:PRO31 3.3 20.7 1.0
C B:ILE34 3.4 21.9 1.0
C B:VAL37 3.5 20.8 1.0
CA B:ASP35 3.5 24.2 1.0
CA B:PRO31 3.8 20.4 1.0
N B:ASP35 3.9 22.3 1.0
O B:HOH379 3.9 37.9 1.0
N B:VAL37 4.0 20.9 1.0
CA B:VAL37 4.3 20.5 1.0
N B:ASP36 4.3 23.5 1.0
N B:LYS38 4.4 20.0 1.0
CD B:LYS38 4.5 26.5 1.0
N B:LYS32 4.5 22.2 1.0
CB B:PRO31 4.5 20.2 1.0
NZ B:LYS38 4.5 26.5 1.0
C B:ASP36 4.6 22.8 1.0
CA B:LYS38 4.6 20.6 1.0
CA B:ILE34 4.6 24.3 1.0
O B:HOH330 4.7 32.5 1.0
O B:HOH446 4.7 42.4 1.0
N B:ILE34 4.7 23.5 1.0
CB B:VAL37 4.7 22.0 1.0
O B:THR30 4.7 22.0 1.0
O B:HOH308 4.8 27.3 1.0
OD2 B:ASP35 4.8 38.9 1.0
C B:LYS32 4.8 24.8 1.0
CA B:LYS32 4.9 24.7 1.0
CA B:ASP36 4.9 26.1 1.0
CB B:ASP35 4.9 27.5 1.0
O B:LYS32 5.0 30.8 1.0

Reference:

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
Page generated: Tue Dec 15 06:53:35 2020

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