Atomistry » Sodium » PDB 4m04-4mfa » 4m9b
Atomistry »
  Sodium »
    PDB 4m04-4mfa »
      4m9b »

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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy