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Sodium in PDB 1so8: Abeta-Bound Human Abad Structure [Also Known As 3-Hydroxyacyl-Coa Dehydrogenase Type II (Type II Hadh), Endoplasmic Reticulum- Associated Amyloid Beta-Peptide Binding Protein (Erab)]

Enzymatic activity of Abeta-Bound Human Abad Structure [Also Known As 3-Hydroxyacyl-Coa Dehydrogenase Type II (Type II Hadh), Endoplasmic Reticulum- Associated Amyloid Beta-Peptide Binding Protein (Erab)]

All present enzymatic activity of Abeta-Bound Human Abad Structure [Also Known As 3-Hydroxyacyl-Coa Dehydrogenase Type II (Type II Hadh), Endoplasmic Reticulum- Associated Amyloid Beta-Peptide Binding Protein (Erab)]:
1.1.1.35;

Protein crystallography data

The structure of Abeta-Bound Human Abad Structure [Also Known As 3-Hydroxyacyl-Coa Dehydrogenase Type II (Type II Hadh), Endoplasmic Reticulum- Associated Amyloid Beta-Peptide Binding Protein (Erab)], PDB code: 1so8 was solved by J.W.Lustbader, M.Cirilli, H.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.83 / 2.30
Space group P 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 130.000, 130.000, 130.000, 90.00, 90.00, 90.00
R / Rfree (%) 23.1 / 26.1

Other elements in 1so8:

The structure of Abeta-Bound Human Abad Structure [Also Known As 3-Hydroxyacyl-Coa Dehydrogenase Type II (Type II Hadh), Endoplasmic Reticulum- Associated Amyloid Beta-Peptide Binding Protein (Erab)] also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Abeta-Bound Human Abad Structure [Also Known As 3-Hydroxyacyl-Coa Dehydrogenase Type II (Type II Hadh), Endoplasmic Reticulum- Associated Amyloid Beta-Peptide Binding Protein (Erab)] (pdb code 1so8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Abeta-Bound Human Abad Structure [Also Known As 3-Hydroxyacyl-Coa Dehydrogenase Type II (Type II Hadh), Endoplasmic Reticulum- Associated Amyloid Beta-Peptide Binding Protein (Erab)], PDB code: 1so8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1so8

Go back to Sodium Binding Sites List in 1so8
Sodium binding site 1 out of 2 in the Abeta-Bound Human Abad Structure [Also Known As 3-Hydroxyacyl-Coa Dehydrogenase Type II (Type II Hadh), Endoplasmic Reticulum- Associated Amyloid Beta-Peptide Binding Protein (Erab)]


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Abeta-Bound Human Abad Structure [Also Known As 3-Hydroxyacyl-Coa Dehydrogenase Type II (Type II Hadh), Endoplasmic Reticulum- Associated Amyloid Beta-Peptide Binding Protein (Erab)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:4.0
occ:0.50
 OG A:SER67 3.1 23.1 1.0
N A:LYS69 3.3 23.2 1.0
N A:GLU68 3.4 23.0 1.0
CG A:LYS69 3.6 29.4 1.0
CB A:LYS69 3.8 28.4 1.0
C A:SER67 3.9 22.7 1.0
CA A:SER67 3.9 21.7 1.0
O A:HOH543 3.9 15.0 0.5
CB A:SER67 3.9 23.4 1.0
CA A:GLU68 4.1 26.0 1.0
CB A:GLU68 4.1 30.3 1.0
CD A:LYS69 4.2 32.9 1.0
CA A:LYS69 4.2 27.1 1.0
C A:GLU68 4.2 23.8 1.0
CE A:LYS69 4.6 33.9 1.0
O A:SER67 4.8 23.4 1.0
N A:ASP70 5.0 26.1 1.0

Sodium binding site 2 out of 2 in 1so8

Go back to Sodium Binding Sites List in 1so8
Sodium binding site 2 out of 2 in the Abeta-Bound Human Abad Structure [Also Known As 3-Hydroxyacyl-Coa Dehydrogenase Type II (Type II Hadh), Endoplasmic Reticulum- Associated Amyloid Beta-Peptide Binding Protein (Erab)]


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Abeta-Bound Human Abad Structure [Also Known As 3-Hydroxyacyl-Coa Dehydrogenase Type II (Type II Hadh), Endoplasmic Reticulum- Associated Amyloid Beta-Peptide Binding Protein (Erab)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:29.7
occ:1.00
 O A:GLY17 2.4 25.7 1.0
O A:HOH545 2.4 23.7 1.0
O A:HOH522 2.4 32.9 1.0
O A:SER20 2.4 29.6 1.0
O A:HOH560 2.5 48.0 1.0
O A:HOH602 3.0 47.1 1.0
C A:SER20 3.3 30.6 1.0
C A:GLY17 3.3 24.6 1.0
OG A:SER20 3.6 34.5 1.0
CA A:GLY17 3.6 22.4 1.0
N A:SER20 3.8 28.3 1.0
CA A:SER20 4.0 30.6 1.0
O A:CYS91 4.0 22.3 1.0
N A:GLY21 4.1 29.5 1.0
O A:HOH501 4.3 19.0 1.0
N A:GLY23 4.3 25.0 1.0
CA A:GLY21 4.3 29.3 1.0
CB A:SER20 4.4 32.6 1.0
N A:GLY18 4.5 24.9 1.0
OD2 A:ASP41 4.5 27.1 1.0
CA A:GLY23 4.6 25.0 1.0
C A:GLY21 4.7 28.5 1.0
N A:ALA19 4.8 25.8 1.0
N A:LEU22 4.8 26.2 1.0
O A:HOH546 4.9 15.0 1.0
CA A:GLY18 5.0 25.4 1.0

Reference:

J.W.Lustbader, M.Cirilli, C.Lin, H.W.Xu, K.Takuma, N.Wang, C.Caspersen, X.Chen, S.Pollak, M.Chaney, F.Trinchese, F.Gunn-Moore, L.F.Lue, D.G.Walker, P.Kuppusamy, Z.L.Zewier, O.Arancio, D.Stern, S.S.Yan, H.Wu. Abad Directly Links Abeta to Mitochondrial Toxicity in Alzheimer'S Disease. Science V. 304 448 2004.
ISSN: ISSN 0036-8075
PubMed: 15087549
DOI: 10.1126/SCIENCE.1091230
Page generated: Sun Aug 17 07:44:24 2025

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