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

Go back to Sodium Binding Sites List in 6v8j
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

Go back to Sodium Binding Sites List in 6v8j
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: Thu Dec 17 13:13:18 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