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Sodium in PDB 3inl: Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Agonist Alda-1

Enzymatic activity of Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Agonist Alda-1

All present enzymatic activity of Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Agonist Alda-1:
1.2.1.3;

Protein crystallography data

The structure of Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Agonist Alda-1, PDB code: 3inl was solved by S.Perez-Miller, T.D.Hurley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.00 / 1.86
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 102.121, 176.900, 102.323, 90.00, 94.57, 90.00
R / Rfree (%) 13.6 / 16.8

Other elements in 3inl:

The structure of Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Agonist Alda-1 also contains other interesting chemical elements:

Chlorine (Cl) 16 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Agonist Alda-1 (pdb code 3inl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Agonist Alda-1, PDB code: 3inl:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 3inl

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Sodium binding site 1 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Agonist Alda-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Agonist Alda-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:33.9
occ:1.00
 O A:GLN196 2.4 32.5 1.0
OD1 A:ASP109 2.4 31.3 1.0
O A:VAL40 2.4 34.1 1.0
O A:ASP109 2.5 29.9 1.0
O A:HOH501 2.7 33.0 1.0
OG1 A:THR39 3.0 35.2 1.0
CG A:ASP109 3.4 31.6 1.0
C A:ASP109 3.4 29.6 1.0
C A:VAL40 3.5 34.5 1.0
C A:GLN196 3.5 32.5 1.0
N A:VAL40 3.6 35.7 1.0
CA A:ASP109 3.7 29.5 1.0
CB A:ASP109 4.1 30.2 1.0
CA A:VAL40 4.1 35.6 1.0
OD2 A:ASP109 4.2 31.6 1.0
CB A:THR39 4.3 36.2 1.0
C A:THR39 4.3 36.7 1.0
CA A:GLN196 4.3 33.7 1.0
CD A:PRO42 4.4 31.4 1.0
CG2 A:THR197 4.5 30.8 1.0
N A:THR197 4.5 32.4 1.0
CD1 A:ILE48 4.6 33.8 1.0
N A:ASN41 4.6 34.5 1.0
CA A:THR39 4.7 37.8 1.0
N A:ASN110 4.7 29.6 1.0
CA A:THR197 4.7 31.0 1.0
CB A:GLN196 4.8 32.3 1.0
CB A:VAL40 4.9 36.1 1.0
CG2 A:THR39 5.0 35.9 1.0
CA A:ASN41 5.0 33.4 1.0

Sodium binding site 2 out of 8 in 3inl

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Sodium binding site 2 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Agonist Alda-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Agonist Alda-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na601

b:27.9
occ:1.00
 O B:GLN196 2.4 27.6 1.0
OD1 B:ASP109 2.4 29.2 1.0
O B:ASP109 2.4 26.4 1.0
O B:VAL40 2.5 28.2 1.0
O B:HOH3389 2.6 39.5 1.0
OG1 B:THR39 3.0 30.1 1.0
CG B:ASP109 3.3 28.5 1.0
O B:HOH2051 3.3 30.5 1.0
C B:ASP109 3.4 26.8 1.0
C B:VAL40 3.6 28.8 1.0
C B:GLN196 3.6 29.3 1.0
CA B:ASP109 3.7 27.5 1.0
N B:VAL40 3.7 28.2 1.0
CB B:ASP109 4.0 27.5 1.0
OD2 B:ASP109 4.2 27.6 1.0
CA B:VAL40 4.2 28.8 1.0
CA B:GLN196 4.3 29.0 1.0
CB B:THR39 4.4 29.3 1.0
CD B:PRO42 4.4 26.5 1.0
C B:THR39 4.5 29.4 1.0
CD1 B:ILE48 4.5 27.1 1.0
N B:THR197 4.6 28.6 1.0
N B:ASN41 4.6 26.8 1.0
N B:ASN110 4.6 25.6 1.0
CG2 B:THR197 4.6 27.0 1.0
CA B:THR197 4.7 27.1 1.0
O B:HOH2164 4.7 27.8 1.0
CA B:THR39 4.8 28.6 1.0
CB B:GLN196 4.9 28.7 1.0
CA B:ASN41 5.0 28.4 1.0

Sodium binding site 3 out of 8 in 3inl

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Sodium binding site 3 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Agonist Alda-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Agonist Alda-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na601

b:31.0
occ:1.00
 OD1 C:ASP109 2.4 32.1 1.0
O C:GLN196 2.4 32.6 1.0
O C:VAL40 2.4 32.7 1.0
O C:ASP109 2.5 31.0 1.0
O C:HOH501 2.7 33.7 1.0
OG1 C:THR39 3.0 33.5 1.0
CG C:ASP109 3.2 31.9 1.0
C C:ASP109 3.4 30.0 1.0
O C:HOH1853 3.5 34.7 1.0
C C:VAL40 3.5 33.2 1.0
C C:GLN196 3.6 32.8 1.0
N C:VAL40 3.6 34.5 1.0
CA C:ASP109 3.7 30.5 1.0
CB C:ASP109 4.0 30.5 1.0
OD2 C:ASP109 4.0 31.2 1.0
CA C:VAL40 4.1 34.6 1.0
CB C:THR39 4.3 34.7 1.0
C C:THR39 4.3 34.8 1.0
CA C:GLN196 4.4 33.8 1.0
N C:THR197 4.5 32.1 1.0
CG2 C:THR197 4.6 30.0 1.0
CD1 C:ILE48 4.6 33.0 1.0
CA C:THR197 4.6 32.0 1.0
CA C:THR39 4.6 34.9 1.0
N C:ASN41 4.6 32.9 1.0
N C:ASN110 4.6 28.8 1.0
CD C:PRO42 4.7 31.5 1.0
CB C:VAL40 4.9 34.5 1.0
CB C:GLN196 5.0 33.3 1.0

Sodium binding site 4 out of 8 in 3inl

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Sodium binding site 4 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Agonist Alda-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Agonist Alda-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na601

b:34.3
occ:1.00
 O D:GLN196 2.4 34.9 1.0
OD1 D:ASP109 2.4 33.5 1.0
O D:VAL40 2.4 38.2 1.0
O D:ASP109 2.4 32.7 1.0
O D:HOH501 2.8 35.9 1.0
OG1 D:THR39 3.0 37.1 1.0
O D:HOH2497 3.1 38.3 1.0
CG D:ASP109 3.3 33.2 1.0
C D:ASP109 3.4 32.6 1.0
C D:VAL40 3.5 38.0 1.0
C D:GLN196 3.5 35.2 1.0
N D:VAL40 3.6 38.1 1.0
CA D:ASP109 3.7 32.2 1.0
CB D:ASP109 4.1 32.0 1.0
CA D:VAL40 4.1 38.9 1.0
OD2 D:ASP109 4.2 33.0 1.0
O D:HOH3166 4.2 40.2 1.0
CA D:GLN196 4.3 35.9 1.0
CB D:THR39 4.3 37.1 1.0
CD D:PRO42 4.4 35.9 1.0
C D:THR39 4.4 37.9 1.0
N D:THR197 4.6 33.5 1.0
N D:ASN41 4.6 37.2 1.0
CD1 D:ILE48 4.6 34.8 1.0
CG2 D:THR197 4.6 32.5 1.0
N D:ASN110 4.7 31.8 1.0
CA D:THR197 4.7 33.5 1.0
CA D:THR39 4.8 38.5 1.0
CB D:GLN196 4.8 35.4 1.0
CG2 D:THR39 4.9 36.2 1.0
CB D:VAL40 4.9 39.9 1.0
CA D:ASN41 5.0 37.8 1.0

Sodium binding site 5 out of 8 in 3inl

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Sodium binding site 5 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Agonist Alda-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Agonist Alda-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na601

b:32.7
occ:1.00
 O E:GLN196 2.4 32.6 1.0
OD1 E:ASP109 2.4 31.6 1.0
O E:VAL40 2.4 33.2 1.0
O E:ASP109 2.4 31.5 1.0
O E:HOH503 2.6 35.0 1.0
OG1 E:THR39 3.0 32.4 1.0
O E:HOH502 3.2 35.5 1.0
CG E:ASP109 3.2 30.1 1.0
C E:ASP109 3.4 31.0 1.0
C E:VAL40 3.5 34.4 1.0
C E:GLN196 3.5 33.1 1.0
N E:VAL40 3.6 34.6 1.0
CA E:ASP109 3.7 30.0 1.0
CB E:ASP109 4.0 30.4 1.0
OD2 E:ASP109 4.0 31.0 1.0
CA E:VAL40 4.1 34.1 1.0
CA E:GLN196 4.3 32.9 1.0
CB E:THR39 4.3 33.6 1.0
C E:THR39 4.4 34.2 1.0
CD E:PRO42 4.4 33.5 1.0
N E:THR197 4.5 30.9 1.0
N E:ASN41 4.6 33.4 1.0
N E:ASN110 4.6 29.6 1.0
CA E:THR39 4.7 34.2 1.0
CA E:THR197 4.7 30.1 1.0
CD1 E:ILE48 4.7 33.4 1.0
CG2 E:THR197 4.8 29.3 1.0
CB E:GLN196 4.8 33.3 1.0
CB E:VAL40 4.9 35.7 1.0
CA E:ASN41 5.0 34.7 1.0

Sodium binding site 6 out of 8 in 3inl

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Sodium binding site 6 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Agonist Alda-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Agonist Alda-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na601

b:29.7
occ:1.00
 O F:GLN196 2.3 31.1 1.0
OD1 F:ASP109 2.4 31.0 1.0
O F:VAL40 2.4 32.0 1.0
O F:ASP109 2.5 30.2 1.0
O F:HOH502 2.7 32.1 1.0
OG1 F:THR39 3.0 33.5 1.0
CG F:ASP109 3.3 31.0 1.0
C F:ASP109 3.4 29.0 1.0
C F:GLN196 3.5 31.9 1.0
C F:VAL40 3.5 33.2 1.0
N F:VAL40 3.6 33.1 1.0
CA F:ASP109 3.7 29.1 1.0
O F:HOH2883 4.0 34.7 1.0
CB F:ASP109 4.1 29.1 1.0
OD2 F:ASP109 4.1 31.4 1.0
CA F:VAL40 4.1 34.4 1.0
CA F:GLN196 4.3 33.9 1.0
CB F:THR39 4.4 34.1 1.0
CD F:PRO42 4.4 30.5 1.0
C F:THR39 4.4 34.3 1.0
N F:THR197 4.5 30.5 1.0
CD1 F:ILE48 4.6 31.6 1.0
N F:ASN41 4.6 32.2 1.0
CG2 F:THR197 4.6 28.9 1.0
CA F:THR197 4.7 30.8 1.0
N F:ASN110 4.7 27.6 1.0
O F:HOH2493 4.7 32.2 1.0
CA F:THR39 4.7 34.5 1.0
CB F:GLN196 4.9 33.6 1.0
CB F:VAL40 5.0 34.5 1.0
CA F:ASN41 5.0 31.6 1.0

Sodium binding site 7 out of 8 in 3inl

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Sodium binding site 7 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Agonist Alda-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Agonist Alda-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na601

b:30.7
occ:1.00
 O G:GLN196 2.3 28.4 1.0
O G:VAL40 2.4 28.3 1.0
OD1 G:ASP109 2.4 27.5 1.0
O G:ASP109 2.4 27.7 1.0
O G:HOH503 2.6 30.3 1.0
OG1 G:THR39 3.0 29.9 1.0
CG G:ASP109 3.3 27.2 1.0
O G:HOH1923 3.3 31.8 1.0
C G:ASP109 3.4 26.4 1.0
C G:VAL40 3.5 28.5 1.0
C G:GLN196 3.5 29.0 1.0
CA G:ASP109 3.6 27.8 1.0
N G:VAL40 3.7 29.4 1.0
CB G:ASP109 4.0 26.7 1.0
OD2 G:ASP109 4.1 28.3 1.0
CA G:VAL40 4.2 29.8 1.0
CA G:GLN196 4.3 29.0 1.0
CD G:PRO42 4.4 26.9 1.0
CB G:THR39 4.4 30.4 1.0
O G:HOH1500 4.5 29.7 1.0
C G:THR39 4.5 30.6 1.0
N G:THR197 4.5 28.6 1.0
N G:ASN41 4.6 28.1 1.0
N G:ASN110 4.6 25.8 1.0
CD1 G:ILE48 4.6 29.0 1.0
CA G:THR197 4.7 27.2 1.0
CG2 G:THR197 4.8 27.1 1.0
CA G:THR39 4.8 29.6 1.0
CB G:GLN196 4.8 29.1 1.0
CB G:VAL40 4.9 29.7 1.0
CA G:ASN41 4.9 27.9 1.0
N G:ASP109 5.0 25.8 1.0

Sodium binding site 8 out of 8 in 3inl

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Sodium binding site 8 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Agonist Alda-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Agonist Alda-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na601

b:33.9
occ:1.00
 O H:GLN196 2.4 33.7 1.0
OD1 H:ASP109 2.4 33.8 1.0
O H:VAL40 2.4 36.9 1.0
O H:ASP109 2.5 32.3 1.0
O H:HOH501 2.8 33.4 1.0
OG1 H:THR39 3.0 36.4 1.0
O H:HOH3081 3.2 36.5 1.0
CG H:ASP109 3.2 32.7 1.0
C H:ASP109 3.4 30.9 1.0
C H:GLN196 3.5 34.6 1.0
C H:VAL40 3.5 37.0 1.0
N H:VAL40 3.6 36.9 1.0
CA H:ASP109 3.7 31.5 1.0
OD2 H:ASP109 4.0 33.2 1.0
CB H:ASP109 4.0 31.7 1.0
CA H:VAL40 4.1 37.7 1.0
CD H:PRO42 4.2 34.0 1.0
C H:THR39 4.3 37.7 1.0
CB H:THR39 4.3 36.5 1.0
CA H:GLN196 4.3 34.3 1.0
N H:THR197 4.5 34.4 1.0
CA H:THR197 4.6 33.6 1.0
CG2 H:THR197 4.6 32.0 1.0
N H:ASN41 4.6 36.6 1.0
CA H:THR39 4.6 37.6 1.0
N H:ASN110 4.7 30.9 1.0
CD1 H:ILE48 4.7 36.0 1.0
CG2 H:THR39 4.9 35.8 1.0
CB H:GLN196 5.0 34.2 1.0
CA H:ASN41 5.0 36.1 1.0
CB H:VAL40 5.0 37.9 1.0

Reference:

S.Perez-Miller, H.Younus, R.Vanam, C.H.Chen, D.Mochly-Rosen, T.D.Hurley. Alda-1 Is An Agonist and Chemical Chaperone For the Common Human Aldehyde Dehydrogenase 2 Variant. Nat.Struct.Mol.Biol. V. 17 159 2010.
ISSN: ISSN 1545-9993
PubMed: 20062057
DOI: 10.1038/NSMB.1737
Page generated: Mon Oct 7 10:59:54 2024

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