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Sodium in PDB 6v8j: Crystal Structure of Ara H 8.0201

Protein crystallography data

The structure of Crystal Structure of Ara H 8.0201, PDB code: 6v8j was solved by L.R.Offermann, S.Pote, B.K.Hurlburt, J.K.Mcbride, M.Chruszcz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.96 / 1.95
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 38.406, 59.209, 67.078, 89.96, 89.99, 71.02
R / Rfree (%) 17.3 / 21.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Ara H 8.0201 (pdb code 6v8j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Ara H 8.0201, PDB code: 6v8j:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6v8j

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Sodium binding site 1 out of 4 in the Crystal Structure of Ara H 8.0201


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 8.0201 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:25.6
occ:1.00
 O A:PRO32 2.2 31.1 1.0
O A:ILE35 2.5 32.6 1.0
O A:ILE38 2.6 30.3 1.0
O A:PRO36 3.2 32.9 1.0
C A:PRO32 3.2 30.9 1.0
C A:ILE38 3.5 31.6 1.0
C A:ILE35 3.6 31.3 1.0
C A:PRO36 3.6 32.9 1.0
CA A:PRO32 3.7 30.4 1.0
CA A:PRO36 3.9 33.0 1.0
N A:ILE38 4.0 33.4 1.0
N A:PRO36 4.1 32.3 1.0
CA A:ILE38 4.3 32.4 1.0
N A:GLN39 4.3 30.4 1.0
CB A:PRO32 4.4 30.6 1.0
N A:LYS33 4.4 31.1 1.0
CA A:GLN39 4.5 30.3 1.0
N A:ALA37 4.6 34.0 1.0
N A:ILE35 4.7 29.3 1.0
CA A:ILE35 4.7 29.9 1.0
O A:THR31 4.7 30.2 1.0
CB A:ILE38 4.8 32.1 1.0
C A:ALA37 4.8 34.4 1.0
O A:GLN39 4.9 29.2 1.0
C A:GLN39 4.9 29.5 1.0
C A:LYS33 4.9 30.8 1.0
CA A:LYS33 4.9 31.9 1.0

Sodium binding site 2 out of 4 in 6v8j

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Sodium binding site 2 out of 4 in the Crystal Structure of Ara H 8.0201


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 8.0201 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:37.5
occ:1.00
 O B:PRO32 2.2 33.8 1.0
O B:ILE35 2.2 34.5 1.0
O B:HOH336 2.4 22.2 1.0
O B:ILE38 2.6 28.8 1.0
C B:ILE35 3.2 33.4 1.0
C B:PRO32 3.2 33.5 1.0
O B:PRO36 3.4 33.9 1.0
O B:HOH305 3.5 31.4 1.0
C B:PRO36 3.6 33.9 1.0
C B:ILE38 3.6 30.4 1.0
CA B:PRO36 3.7 34.9 1.0
CA B:PRO32 3.8 32.7 1.0
N B:PRO36 3.9 34.5 1.0
N B:ILE38 4.1 32.4 1.0
N B:ILE35 4.3 33.0 1.0
CA B:ILE35 4.3 32.5 1.0
N B:LYS33 4.3 33.8 1.0
CA B:ILE38 4.4 30.7 1.0
O B:LYS33 4.5 37.2 1.0
N B:ALA37 4.5 33.7 1.0
N B:GLN39 4.5 29.4 1.0
O B:THR31 4.6 31.5 1.0
CB B:PRO32 4.6 32.8 1.0
C B:LYS33 4.6 35.5 1.0
CA B:LYS33 4.7 35.6 1.0
CA B:GLN39 4.8 30.1 1.0
CB B:ILE38 4.8 30.8 1.0
C B:ALA37 4.9 33.0 1.0
CB B:ILE35 5.0 31.1 1.0

Sodium binding site 3 out of 4 in 6v8j

Go back to Sodium Binding Sites List in 6v8j
Sodium binding site 3 out of 4 in the Crystal Structure of Ara H 8.0201


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Ara H 8.0201 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na201

b:32.5
occ:1.00
 O C:PRO32 2.1 38.1 1.0
O C:HOH338 2.1 18.1 1.0
O C:HOH332 2.4 33.8 1.0
O C:ILE35 2.6 36.1 1.0
O C:ILE38 2.6 31.8 1.0
O C:PRO36 3.2 38.1 1.0
C C:PRO32 3.3 36.4 1.0
C C:ILE35 3.5 36.6 1.0
C C:PRO36 3.7 37.3 1.0
CA C:PRO36 3.7 37.6 1.0
C C:ILE38 3.8 32.1 1.0
CA C:PRO32 3.9 35.1 1.0
N C:PRO36 4.0 37.5 1.0
N C:LYS33 4.4 36.4 1.0
N C:ILE38 4.4 34.1 1.0
N C:ILE35 4.5 37.4 1.0
CA C:ILE35 4.6 36.4 1.0
C C:LYS33 4.6 38.8 1.0
N C:ALA37 4.6 37.7 1.0
CA C:ILE38 4.6 32.8 1.0
O C:LYS33 4.7 40.6 1.0
CB C:PRO32 4.7 35.2 1.0
CA C:LYS33 4.7 38.1 1.0
N C:GLN39 4.7 30.2 1.0
O C:THR31 4.8 33.5 1.0
CA C:GLN39 4.8 30.3 1.0
NE2 C:GLN39 4.8 32.1 1.0

Sodium binding site 4 out of 4 in 6v8j

Go back to Sodium Binding Sites List in 6v8j
Sodium binding site 4 out of 4 in the Crystal Structure of Ara H 8.0201


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Ara H 8.0201 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na201

b:23.2
occ:1.00
 O D:ILE38 2.1 27.1 1.0
O D:PRO32 2.3 34.8 1.0
O D:ILE35 2.5 31.5 1.0
C D:PRO32 3.3 33.1 1.0
O D:PRO36 3.3 31.9 1.0
C D:ILE38 3.3 27.7 1.0
C D:ILE35 3.5 32.3 1.0
CA D:PRO32 3.6 31.3 1.0
C D:PRO36 3.7 32.2 1.0
CA D:PRO36 3.8 32.6 1.0
N D:ILE38 4.1 28.6 1.0
N D:PRO36 4.1 32.6 1.0
CA D:ILE38 4.2 27.6 1.0
N D:GLN39 4.2 26.6 1.0
CB D:PRO32 4.4 31.2 1.0
CA D:GLN39 4.4 27.6 1.0
N D:LYS33 4.5 35.0 1.0
N D:ALA37 4.6 31.4 1.0
N D:ILE35 4.6 34.0 1.0
CA D:ILE35 4.6 32.4 1.0
CB D:ILE38 4.6 27.2 1.0
O D:THR31 4.7 28.4 1.0
C D:ALA37 4.9 30.1 1.0
N D:PRO32 4.9 29.9 1.0
C D:LYS33 4.9 37.6 1.0
C D:GLN39 5.0 27.4 1.0
O D:GLN39 5.0 26.8 1.0
CA D:LYS33 5.0 37.6 1.0

Reference:

L.R.Offermann, S.Pote, B.K.Hurlburt, J.K.Mcbride, M.Chruszcz. Crystal Structure of Ara H 8.0201 To Be Published.
Page generated: Tue Oct 8 14:17:48 2024

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