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Sodium in PDB 1oa8: Axh Domain of Human Spinocerebellar Ataxin-1

Protein crystallography data

The structure of Axh Domain of Human Spinocerebellar Ataxin-1, PDB code: 1oa8 was solved by M.D.Allen, Y.W.Chen, M.Bycroft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.71 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.783, 82.441, 137.781, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 25.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Axh Domain of Human Spinocerebellar Ataxin-1 (pdb code 1oa8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Axh Domain of Human Spinocerebellar Ataxin-1, PDB code: 1oa8:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 1oa8

Go back to Sodium Binding Sites List in 1oa8
Sodium binding site 1 out of 3 in the Axh Domain of Human Spinocerebellar Ataxin-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Axh Domain of Human Spinocerebellar Ataxin-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1690

b:43.4
occ:1.00
O A:HOH2096 2.1 38.5 1.0
O A:ALA603 2.4 38.5 1.0
O A:SER606 2.6 43.2 1.0
O A:LEU609 2.6 32.4 1.0
C A:ALA603 3.4 38.8 1.0
NZ A:LYS689 3.5 51.4 1.0
C A:SER606 3.7 43.0 1.0
C A:LEU609 3.8 32.0 1.0
O A:GLU604 3.9 41.8 1.0
C A:GLU604 4.1 42.0 1.0
N A:GLU604 4.2 40.1 1.0
CA A:GLU604 4.2 41.4 1.0
CE A:LYS689 4.2 48.6 1.0
CB A:SER606 4.4 41.8 1.0
CA A:ALA603 4.4 37.4 1.0
CA A:SER606 4.4 42.7 1.0
N A:SER606 4.5 42.9 1.0
CA A:LYS610 4.5 29.1 1.0
O A:HOH2033 4.5 32.6 1.0
CD A:LYS689 4.5 46.8 1.0
N A:LYS610 4.6 30.0 1.0
N A:LEU609 4.7 35.0 1.0
N A:ASN607 4.7 42.9 1.0
N A:ILE605 4.8 42.1 1.0
CA A:LEU609 4.8 32.9 1.0
CB A:LYS610 4.9 28.2 1.0
CA A:ASN607 4.9 43.4 1.0
CB A:ALA603 4.9 36.8 1.0
C A:ILE605 4.9 43.3 1.0

Sodium binding site 2 out of 3 in 1oa8

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Sodium binding site 2 out of 3 in the Axh Domain of Human Spinocerebellar Ataxin-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Axh Domain of Human Spinocerebellar Ataxin-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1691

b:23.9
occ:1.00
O C:ALA603 2.1 19.1 1.0
O C:LEU609 2.3 20.2 1.0
O C:SER606 2.3 29.7 1.0
O B:HOH2049 2.4 24.0 1.0
O B:HOH2056 2.7 35.7 1.0
C C:ALA603 3.3 18.8 1.0
C C:LEU609 3.5 21.2 1.0
C C:SER606 3.5 31.0 1.0
O B:HOH2048 3.9 25.2 1.0
CA C:ALA603 4.1 18.2 1.0
N C:GLU604 4.3 19.1 1.0
CA C:LYS610 4.3 19.5 1.0
N C:LEU609 4.3 25.1 1.0
N C:LYS610 4.4 19.8 1.0
N C:SER606 4.4 29.3 1.0
CA C:SER606 4.4 29.3 1.0
N C:ASN607 4.5 32.2 1.0
CA C:ASN607 4.5 33.5 1.0
CA C:LEU609 4.5 22.5 1.0
CA C:GLU604 4.5 20.9 1.0
O C:GLU604 4.5 23.0 1.0
OG C:SER606 4.5 32.4 1.0
O B:GLY655 4.5 20.4 1.0
O B:HOH2057 4.6 35.3 1.0
C C:GLU604 4.6 22.6 1.0
CB C:ALA603 4.6 16.4 1.0
C C:ASN607 4.7 32.5 1.0
CB C:SER606 4.7 29.9 1.0
NE2 B:GLN656 4.7 26.5 1.0
CB C:LYS610 4.8 19.8 1.0
CB C:LYS689 4.8 31.2 1.0
O C:ASN607 4.9 32.4 1.0
CG B:GLN656 5.0 19.3 1.0

Sodium binding site 3 out of 3 in 1oa8

Go back to Sodium Binding Sites List in 1oa8
Sodium binding site 3 out of 3 in the Axh Domain of Human Spinocerebellar Ataxin-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Axh Domain of Human Spinocerebellar Ataxin-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1695

b:20.2
occ:1.00
O D:LEU609 2.2 25.1 1.0
O D:ALA603 2.3 19.1 1.0
O D:SER606 2.3 30.7 1.0
O D:HOH2115 2.3 30.1 1.0
CE D:LYS689 3.4 36.3 1.0
C D:ALA603 3.4 21.9 1.0
C D:LEU609 3.5 23.3 1.0
C D:SER606 3.5 29.8 1.0
NZ D:LYS689 3.7 38.5 1.0
N D:LEU609 4.2 23.9 1.0
CA D:ALA603 4.2 21.5 1.0
N D:SER606 4.2 29.3 1.0
CA D:SER606 4.3 30.2 1.0
CA D:LEU609 4.4 22.9 1.0
N D:LYS610 4.4 21.6 1.0
CA D:LYS610 4.4 22.2 1.0
N D:GLU604 4.4 22.4 1.0
O D:GLU604 4.4 26.6 1.0
OG D:SER606 4.5 36.9 1.0
N D:ASN607 4.5 30.3 1.0
C D:GLU604 4.5 26.1 1.0
CA D:GLU604 4.6 24.6 1.0
C D:ASN607 4.6 30.9 1.0
CA D:ASN607 4.7 31.6 1.0
CB D:SER606 4.7 29.9 1.0
O D:ASN607 4.8 32.4 1.0
CB D:ALA603 4.8 22.1 1.0
CD D:LYS689 4.9 34.6 1.0
CB D:LEU609 4.9 22.1 1.0
CB D:LYS610 5.0 21.9 1.0

Reference:

Y.W.Chen, M.D.Allen, D.B.Veprintsev, J.Lowe, M.Bycroft. The Structure of the Axh Domain of Spinocerebellar Ataxin-1. J. Biol. Chem. V. 279 3758 2004.
ISSN: ISSN 0021-9258
PubMed: 14583607
DOI: 10.1074/JBC.M309817200
Page generated: Tue Dec 15 05:32:10 2020

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