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Sodium in PDB 6aww: Structure of Pr 10 Allergen Ara H 8.01 in Complex with 3-Hydroxy-2- Naphthoic Acid

Protein crystallography data

The structure of Structure of Pr 10 Allergen Ara H 8.01 in Complex with 3-Hydroxy-2- Naphthoic Acid, PDB code: 6aww was solved by L.R.Offermann, J.Yarbrough, 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 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 44.567, 130.513, 140.883, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 26

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Pr 10 Allergen Ara H 8.01 in Complex with 3-Hydroxy-2- Naphthoic Acid (pdb code 6aww). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Structure of Pr 10 Allergen Ara H 8.01 in Complex with 3-Hydroxy-2- Naphthoic Acid, PDB code: 6aww:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6aww

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Sodium binding site 1 out of 5 in the Structure of Pr 10 Allergen Ara H 8.01 in Complex with 3-Hydroxy-2- Naphthoic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Pr 10 Allergen Ara H 8.01 in Complex with 3-Hydroxy-2- Naphthoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:48.6
occ:1.00
 O A:PRO31 2.1 42.8 1.0
O A:HOH340 2.2 53.3 1.0
O A:VAL37 2.5 47.8 1.0
O A:ILE34 2.6 38.5 1.0
O A:HOH313 2.8 54.5 1.0
O A:ASP35 2.9 47.2 1.0
C A:PRO31 3.2 41.8 1.0
C A:ASP35 3.6 48.4 1.0
C A:VAL37 3.6 45.0 1.0
C A:ILE34 3.7 38.0 1.0
CA A:ASP35 3.8 43.9 1.0
CA A:PRO31 3.9 41.5 1.0
O A:HOH335 4.0 54.2 1.0
N A:VAL37 4.2 45.6 1.0
N A:ASP35 4.2 37.5 1.0
N A:LYS32 4.3 43.4 1.0
CD A:LYS38 4.4 53.9 1.0
CA A:VAL37 4.4 43.3 1.0
NZ A:LYS38 4.5 55.3 1.0
N A:LYS38 4.5 48.1 1.0
N A:ASP36 4.6 47.4 1.0
CB A:PRO31 4.6 43.6 1.0
O A:LYS32 4.6 41.9 1.0
CA A:LYS38 4.6 47.6 1.0
CA A:LYS32 4.7 45.3 1.0
C A:LYS32 4.7 42.4 1.0
C A:ASP36 4.7 49.8 1.0
O A:THR30 4.8 37.4 1.0
N A:ILE34 4.8 38.4 1.0
CB A:VAL37 4.9 39.4 1.0
CA A:ILE34 4.9 36.5 1.0
OD1 A:ASP35 4.9 61.5 1.0
CE A:LYS38 5.0 54.9 1.0

Sodium binding site 2 out of 5 in 6aww

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Sodium binding site 2 out of 5 in the Structure of Pr 10 Allergen Ara H 8.01 in Complex with 3-Hydroxy-2- Naphthoic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Pr 10 Allergen Ara H 8.01 in Complex with 3-Hydroxy-2- Naphthoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:47.1
occ:1.00
 O B:PRO31 2.3 40.4 1.0
O B:HOH353 2.3 47.1 1.0
O B:ILE34 2.4 41.1 1.0
O B:VAL37 2.4 42.9 1.0
O B:ASP35 2.8 46.3 1.0
C B:ASP35 3.3 46.7 1.0
C B:PRO31 3.4 40.2 1.0
C B:ILE34 3.4 40.5 1.0
C B:VAL37 3.5 40.4 1.0
CA B:ASP35 3.6 45.7 1.0
CA B:PRO31 3.9 38.7 1.0
N B:VAL37 4.0 41.3 1.0
N B:ASP35 4.0 41.9 1.0
CA B:VAL37 4.2 39.7 1.0
N B:ASP36 4.3 45.1 1.0
CD B:LYS38 4.4 50.2 1.0
O B:HOH341 4.4 51.0 1.0
NZ B:LYS38 4.4 52.2 1.0
N B:LYS38 4.4 40.9 1.0
N B:LYS32 4.5 40.3 1.0
CA B:LYS38 4.6 42.6 1.0
C B:ASP36 4.6 44.5 1.0
O B:THR30 4.6 37.9 1.0
CA B:ILE34 4.6 39.7 1.0
N B:ILE34 4.7 39.0 1.0
CB B:VAL37 4.7 37.4 1.0
CB B:PRO31 4.7 39.2 1.0
O B:HOH352 4.7 56.9 1.0
O B:LYS32 4.8 39.4 1.0
C B:LYS32 4.8 40.3 1.0
CA B:LYS32 4.9 41.3 1.0
CE B:LYS38 4.9 52.1 1.0
CA B:ASP36 5.0 47.8 1.0

Sodium binding site 3 out of 5 in 6aww

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Sodium binding site 3 out of 5 in the Structure of Pr 10 Allergen Ara H 8.01 in Complex with 3-Hydroxy-2- Naphthoic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Pr 10 Allergen Ara H 8.01 in Complex with 3-Hydroxy-2- Naphthoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na204

b:62.5
occ:1.00
 O C:HOH334 2.0 56.9 1.0
O C:PRO31 2.2 55.3 1.0
O C:VAL37 2.4 61.9 1.0
O C:ILE34 2.5 53.5 1.0
O C:ASP35 2.9 65.1 1.0
C C:PRO31 3.3 57.0 1.0
C C:ASP35 3.5 64.0 1.0
C C:VAL37 3.6 60.2 1.0
C C:ILE34 3.7 54.5 1.0
CA C:ASP35 3.7 63.9 1.0
O C:HOH333 3.9 53.3 1.0
CA C:PRO31 3.9 52.1 1.0
N C:ASP35 4.2 58.9 1.0
N C:VAL37 4.2 59.8 1.0
CD C:LYS38 4.2 71.5 1.0
NZ C:LYS38 4.3 75.7 1.0
CA C:VAL37 4.4 58.7 1.0
N C:LYS38 4.4 61.8 1.0
N C:LYS32 4.5 58.7 1.0
CA C:LYS38 4.5 64.0 1.0
N C:ASP36 4.5 64.5 1.0
O C:LYS32 4.6 63.4 1.0
CB C:PRO31 4.6 53.5 1.0
C C:LYS32 4.7 62.3 1.0
CA C:LYS32 4.8 62.6 1.0
C C:ASP36 4.8 63.6 1.0
OD1 C:ASP35 4.8 84.0 1.0
O C:THR30 4.8 48.9 1.0
CB C:VAL37 4.8 57.2 1.0
CE C:LYS38 4.9 73.7 1.0
N C:ILE34 4.9 52.2 1.0
CA C:ILE34 4.9 52.1 1.0

Sodium binding site 4 out of 5 in 6aww

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Sodium binding site 4 out of 5 in the Structure of Pr 10 Allergen Ara H 8.01 in Complex with 3-Hydroxy-2- Naphthoic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Pr 10 Allergen Ara H 8.01 in Complex with 3-Hydroxy-2- Naphthoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na201

b:89.7
occ:1.00
 O D:HOH330 2.1 75.1 1.0
O D:PRO31 2.3 90.0 1.0
O D:VAL37 2.8 80.9 1.0
O D:ILE34 2.8 84.5 1.0
O D:ASP35 3.0 87.9 1.0
C D:PRO31 3.4 84.7 1.0
C D:ASP35 3.7 92.4 1.0
C D:ILE34 3.9 87.3 1.0
C D:VAL37 3.9 80.7 1.0
CA D:ASP35 3.9 94.0 1.0
CA D:PRO31 4.1 80.2 1.0
N D:ASP35 4.4 90.8 1.0
N D:LYS32 4.5 87.0 1.0
O D:LYS32 4.6 97.5 1.0
CA D:LYS38 4.6 81.6 1.0
CA D:LYS32 4.6 91.6 1.0
N D:VAL37 4.7 89.3 1.0
CB D:PRO31 4.7 79.4 1.0
N D:LYS38 4.7 81.6 1.0
C D:LYS32 4.7 91.4 1.0
N D:ASP36 4.8 94.7 1.0
CA D:VAL37 4.9 82.0 1.0

Sodium binding site 5 out of 5 in 6aww

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Sodium binding site 5 out of 5 in the Structure of Pr 10 Allergen Ara H 8.01 in Complex with 3-Hydroxy-2- Naphthoic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Pr 10 Allergen Ara H 8.01 in Complex with 3-Hydroxy-2- Naphthoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na201

b:62.6
occ:1.00
 O E:PRO31 2.2 52.1 1.0
O E:HOH313 2.3 64.6 1.0
O E:VAL37 2.4 56.4 1.0
O E:ILE34 2.6 52.1 1.0
O E:ASP35 3.0 62.8 1.0
C E:PRO31 3.4 53.0 1.0
C E:VAL37 3.6 53.4 1.0
C E:ASP35 3.6 62.5 1.0
C E:ILE34 3.6 54.2 1.0
CA E:ASP35 3.7 63.2 1.0
CA E:PRO31 3.9 51.6 1.0
N E:ASP35 4.1 60.6 1.0
N E:VAL37 4.3 53.3 1.0
CA E:VAL37 4.4 50.6 1.0
N E:LYS38 4.5 53.7 1.0
CA E:LYS38 4.5 56.2 1.0
N E:LYS32 4.5 53.2 1.0
CB E:PRO31 4.6 54.5 1.0
N E:ASP36 4.6 58.5 1.0
O E:THR30 4.8 45.9 1.0
N E:ILE34 4.8 55.0 1.0
O E:LYS32 4.8 60.1 1.0
CA E:ILE34 4.8 53.6 1.0
CB E:VAL37 4.8 48.2 1.0
C E:LYS32 4.8 57.9 1.0
CA E:LYS32 4.9 59.1 1.0
C E:ASP36 4.9 58.7 1.0
O E:HOH314 5.0 76.7 1.0

Reference:

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.
Page generated: Tue Oct 8 01:56:25 2024

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