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Sodium in PDB 1zum: Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Apo Form

Enzymatic activity of Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Apo Form

All present enzymatic activity of Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Apo Form:
1.2.1.3;

Protein crystallography data

The structure of Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Apo Form, PDB code: 1zum was solved by H.N.Larson, H.Weiner, T.D.Hurley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.63 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 95.873, 105.261, 162.672, 78.81, 81.95, 88.04
R / Rfree (%) 20.4 / 23.8

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Apo Form (pdb code 1zum). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Apo Form, PDB code: 1zum:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in 1zum

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Sodium binding site 1 out of 12 in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Apo Form


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, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3701

b:57.0
occ:1.00
 O A:GLN196 2.3 47.4 1.0
O A:VAL40 2.5 51.5 1.0
OD1 A:ASP109 2.6 55.5 1.0
O A:ASP109 2.7 48.8 1.0
O A:HOH3851 2.7 48.7 1.0
OG1 A:THR39 2.8 44.4 1.0
CG A:ASP109 3.4 56.0 1.0
C A:GLN196 3.4 47.2 1.0
C A:VAL40 3.6 50.2 1.0
N A:VAL40 3.6 46.8 1.0
C A:ASP109 3.7 49.5 1.0
CA A:ASP109 3.9 51.0 1.0
OD2 A:ASP109 4.1 55.0 1.0
CA A:VAL40 4.1 48.1 1.0
CA A:GLN196 4.1 43.6 1.0
CB A:THR39 4.1 43.5 1.0
CB A:ASP109 4.2 53.2 1.0
C A:THR39 4.2 45.5 1.0
CD A:PRO42 4.4 56.9 1.0
N A:THR197 4.4 48.4 1.0
CA A:THR39 4.5 46.4 1.0
CD1 A:ILE48 4.7 54.4 1.0
CA A:THR197 4.7 47.8 1.0
N A:ASN41 4.7 50.0 1.0
CB A:GLN196 4.7 46.3 1.0
CG2 A:THR197 4.9 44.6 1.0
CB A:VAL40 4.9 48.1 1.0
N A:ASN110 4.9 46.7 1.0
CG2 A:THR39 4.9 42.8 1.0

Sodium binding site 2 out of 12 in 1zum

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Sodium binding site 2 out of 12 in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Apo Form


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, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3702

b:30.4
occ:1.00
 O B:GLN196 2.3 19.0 1.0
O B:VAL40 2.4 22.1 1.0
O B:HOH3783 2.5 30.5 1.0
OD1 B:ASP109 2.5 21.8 1.0
O B:ASP109 2.6 18.4 1.0
OG1 B:THR39 3.2 30.1 1.0
C B:GLN196 3.4 21.8 1.0
CG B:ASP109 3.4 25.4 1.0
C B:VAL40 3.5 26.2 1.0
C B:ASP109 3.6 19.5 1.0
N B:VAL40 3.7 25.7 1.0
CA B:ASP109 3.9 18.1 1.0
O B:HOH3821 4.0 41.7 1.0
CA B:GLN196 4.1 22.8 1.0
CA B:VAL40 4.1 26.0 1.0
CD B:PRO42 4.2 19.6 1.0
OD2 B:ASP109 4.2 24.3 1.0
CB B:ASP109 4.2 21.5 1.0
C B:THR39 4.4 26.5 1.0
CB B:THR39 4.5 28.2 1.0
N B:THR197 4.5 21.0 1.0
CB B:GLN196 4.6 25.9 1.0
N B:ASN41 4.6 24.6 1.0
CA B:THR39 4.7 27.1 1.0
CG2 B:THR197 4.8 17.7 1.0
CD1 B:ILE48 4.8 26.1 1.0
CA B:THR197 4.8 19.8 1.0
N B:ASN110 4.8 19.7 1.0
CB B:VAL40 4.8 30.2 1.0
CA B:ASN41 5.0 24.7 1.0
O B:VAL345 5.0 20.6 1.0

Sodium binding site 3 out of 12 in 1zum

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Sodium binding site 3 out of 12 in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Apo Form


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, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na3703

b:34.8
occ:1.00
 O C:GLN196 2.3 19.9 1.0
O C:VAL40 2.4 28.2 1.0
O C:HOH3903 2.5 29.6 1.0
OD1 C:ASP109 2.6 29.1 1.0
O C:ASP109 2.7 24.3 1.0
O C:HOH3902 2.9 24.5 1.0
OG1 C:THR39 3.1 29.9 1.0
C C:GLN196 3.4 22.1 1.0
C C:VAL40 3.5 24.6 1.0
N C:VAL40 3.6 23.3 1.0
CG C:ASP109 3.6 28.4 1.0
C C:ASP109 3.7 25.1 1.0
CA C:VAL40 4.0 24.9 1.0
CA C:ASP109 4.0 24.8 1.0
CA C:GLN196 4.1 21.6 1.0
CD C:PRO42 4.3 21.5 1.0
CB C:ASP109 4.4 24.1 1.0
C C:THR39 4.4 25.1 1.0
OD2 C:ASP109 4.4 26.4 1.0
CB C:THR39 4.4 30.0 1.0
O C:HOH3863 4.4 38.2 1.0
N C:THR197 4.5 18.8 1.0
CB C:GLN196 4.6 26.1 1.0
N C:ASN41 4.6 23.1 1.0
CB C:VAL40 4.7 22.7 1.0
CA C:THR39 4.7 25.2 1.0
CD1 C:ILE48 4.7 23.8 1.0
CA C:THR197 4.8 20.0 1.0
CG2 C:THR197 4.8 16.6 1.0
N C:ASN110 4.9 24.8 1.0
O C:VAL345 5.0 20.2 1.0

Sodium binding site 4 out of 12 in 1zum

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Sodium binding site 4 out of 12 in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Apo Form


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, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na3704

b:55.6
occ:1.00
 O D:VAL40 2.4 51.6 1.0
O D:GLN196 2.4 50.0 1.0
O D:ASP109 2.5 35.9 1.0
OD1 D:ASP109 2.5 45.1 1.0
O D:HOH3840 2.6 59.8 1.0
O D:HOH3796 3.0 56.5 1.0
CG D:ASP109 3.4 48.3 1.0
OG1 D:THR39 3.4 50.4 1.0
C D:ASP109 3.5 40.2 1.0
C D:VAL40 3.5 50.2 1.0
C D:GLN196 3.6 49.0 1.0
N D:VAL40 3.8 50.7 1.0
CA D:ASP109 3.9 42.5 1.0
CD D:PRO42 4.1 57.5 1.0
CA D:VAL40 4.2 50.9 1.0
OD2 D:ASP109 4.2 47.5 1.0
CA D:GLN196 4.2 48.3 1.0
CG D:PRO42 4.2 58.0 1.0
CB D:ASP109 4.2 43.3 1.0
C D:THR39 4.5 50.3 1.0
N D:ASN41 4.6 50.0 1.0
N D:THR197 4.6 46.7 1.0
N D:ASN110 4.7 38.7 1.0
CB D:GLN196 4.7 48.7 1.0
CB D:THR39 4.7 50.3 1.0
CG2 D:THR197 4.8 46.3 1.0
O D:VAL345 4.8 50.5 1.0
CA D:THR39 4.9 51.2 1.0
CA D:THR197 4.9 47.4 1.0
CD1 D:ILE48 4.9 55.2 1.0
CB D:VAL40 4.9 51.9 1.0
CA D:ASN41 4.9 50.6 1.0

Sodium binding site 5 out of 12 in 1zum

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Sodium binding site 5 out of 12 in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Apo Form


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, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na3705

b:28.5
occ:1.00
 O E:GLN196 2.4 24.7 1.0
O E:HOH3904 2.4 34.2 1.0
O E:VAL40 2.4 27.6 1.0
O E:ASP109 2.4 24.9 1.0
OD1 E:ASP109 2.5 28.1 1.0
OG1 E:THR39 3.2 35.1 1.0
O E:HOH3835 3.2 39.3 1.0
C E:ASP109 3.4 20.9 1.0
CG E:ASP109 3.4 28.7 1.0
C E:VAL40 3.5 30.9 1.0
C E:GLN196 3.5 26.2 1.0
CA E:ASP109 3.7 21.6 1.0
N E:VAL40 3.7 29.6 1.0
CB E:ASP109 4.1 24.1 1.0
CA E:VAL40 4.1 29.0 1.0
OD2 E:ASP109 4.2 26.9 1.0
CA E:GLN196 4.2 23.7 1.0
CD E:PRO42 4.2 28.6 1.0
C E:THR39 4.4 28.7 1.0
CB E:THR39 4.5 30.9 1.0
N E:ASN41 4.5 27.3 1.0
N E:THR197 4.6 22.6 1.0
N E:ASN110 4.6 21.9 1.0
CD1 E:ILE48 4.6 26.7 1.0
CG2 E:THR197 4.7 18.7 1.0
CA E:THR197 4.7 24.3 1.0
CB E:GLN196 4.7 23.5 1.0
CA E:THR39 4.7 28.8 1.0
CA E:ASN41 4.9 26.8 1.0
CB E:VAL40 4.9 32.9 1.0

Sodium binding site 6 out of 12 in 1zum

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Sodium binding site 6 out of 12 in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Apo Form


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, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na3706

b:25.1
occ:1.00
 O F:VAL40 2.3 20.8 1.0
O F:GLN196 2.4 19.2 1.0
OD1 F:ASP109 2.4 20.1 1.0
O F:ASP109 2.5 23.3 1.0
O F:HOH3794 2.6 29.9 1.0
O F:HOH3883 2.8 33.5 1.0
OG1 F:THR39 3.0 26.7 1.0
CG F:ASP109 3.4 18.6 1.0
C F:VAL40 3.4 20.3 1.0
C F:ASP109 3.5 17.9 1.0
C F:GLN196 3.6 18.3 1.0
N F:VAL40 3.7 20.9 1.0
CA F:ASP109 3.8 16.7 1.0
CA F:VAL40 4.1 20.4 1.0
CB F:ASP109 4.2 14.8 1.0
OD2 F:ASP109 4.2 18.8 1.0
CA F:GLN196 4.3 19.0 1.0
CB F:THR39 4.3 27.0 1.0
CD F:PRO42 4.3 16.6 1.0
C F:THR39 4.4 21.4 1.0
O F:HOH3921 4.4 39.3 1.0
N F:ASN41 4.5 18.3 1.0
N F:THR197 4.6 17.9 1.0
CD1 F:ILE48 4.6 18.7 1.0
CA F:THR39 4.7 21.3 1.0
CB F:GLN196 4.7 25.1 1.0
N F:ASN110 4.7 18.9 1.0
CA F:THR197 4.8 17.3 1.0
CB F:VAL40 4.8 19.1 1.0
CG2 F:THR197 4.8 10.8 1.0
CA F:ASN41 4.9 20.4 1.0
CG2 F:THR39 5.0 23.3 1.0

Sodium binding site 7 out of 12 in 1zum

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Sodium binding site 7 out of 12 in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Apo Form


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, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na3707

b:37.1
occ:1.00
 O G:GLN196 2.3 29.4 1.0
O G:VAL40 2.4 38.4 1.0
O G:ASP109 2.5 30.9 1.0
OD1 G:ASP109 2.6 39.3 1.0
O G:HOH3949 2.6 42.8 1.0
OG1 G:THR39 3.0 39.5 1.0
C G:ASP109 3.5 32.3 1.0
CG G:ASP109 3.5 35.8 1.0
C G:GLN196 3.5 33.3 1.0
C G:VAL40 3.5 37.5 1.0
N G:VAL40 3.7 37.0 1.0
CA G:ASP109 3.8 30.5 1.0
CA G:VAL40 4.1 36.8 1.0
CB G:ASP109 4.2 33.3 1.0
CA G:GLN196 4.2 32.5 1.0
CD G:PRO42 4.3 34.7 1.0
OD2 G:ASP109 4.3 37.0 1.0
CB G:THR39 4.3 42.9 1.0
C G:THR39 4.3 40.6 1.0
N G:THR197 4.5 30.9 1.0
N G:ASN41 4.6 31.2 1.0
CA G:THR39 4.7 41.3 1.0
CA G:THR197 4.7 31.1 1.0
N G:ASN110 4.7 32.0 1.0
CG2 G:THR197 4.7 27.6 1.0
CB G:GLN196 4.7 32.6 1.0
CD1 G:ILE48 4.7 38.3 1.0
CB G:VAL40 4.9 35.6 1.0
CA G:ASN41 4.9 33.4 1.0

Sodium binding site 8 out of 12 in 1zum

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Sodium binding site 8 out of 12 in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Apo Form


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, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na3708

b:36.0
occ:1.00
 O H:GLN196 2.3 27.4 1.0
O H:ASP109 2.4 24.2 1.0
O H:VAL40 2.4 36.6 1.0
OD1 H:ASP109 2.5 35.4 1.0
O H:HOH3910 2.5 57.2 1.0
OG1 H:THR39 3.2 32.8 1.0
O H:HOH3861 3.3 48.5 1.0
CG H:ASP109 3.4 31.7 1.0
C H:ASP109 3.4 27.0 1.0
C H:GLN196 3.5 30.3 1.0
C H:VAL40 3.6 37.4 1.0
CA H:ASP109 3.8 26.2 1.0
N H:VAL40 3.8 36.0 1.0
OD2 H:ASP109 4.1 33.6 1.0
CD H:PRO42 4.1 37.7 1.0
CB H:ASP109 4.2 26.6 1.0
CA H:GLN196 4.2 30.5 1.0
CA H:VAL40 4.2 37.3 1.0
CB H:THR39 4.5 36.6 1.0
C H:THR39 4.5 35.8 1.0
N H:THR197 4.5 28.7 1.0
N H:ASN110 4.6 26.6 1.0
N H:ASN41 4.6 34.1 1.0
CG2 H:THR197 4.7 21.7 1.0
CB H:GLN196 4.7 32.7 1.0
CA H:THR197 4.7 27.5 1.0
CD1 H:ILE48 4.8 33.5 1.0
CA H:THR39 4.8 35.4 1.0
O H:VAL345 4.9 36.2 1.0
CA H:ASN41 5.0 31.8 1.0
CB H:VAL40 5.0 36.1 1.0

Sodium binding site 9 out of 12 in 1zum

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Sodium binding site 9 out of 12 in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Apo Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na3709

b:36.2
occ:1.00
 O I:GLN196 2.4 33.9 1.0
O I:VAL40 2.4 30.1 1.0
O I:ASP109 2.5 28.2 1.0
OD1 I:ASP109 2.6 35.8 1.0
O I:HOH3833 2.7 62.9 1.0
O I:HOH3832 2.9 50.2 1.0
OG1 I:THR39 3.1 25.1 1.0
CG I:ASP109 3.4 32.4 1.0
C I:ASP109 3.4 28.1 1.0
C I:VAL40 3.5 30.9 1.0
C I:GLN196 3.5 33.2 1.0
N I:VAL40 3.7 28.8 1.0
CA I:ASP109 3.8 28.7 1.0
CA I:VAL40 4.1 29.9 1.0
CB I:ASP109 4.2 30.9 1.0
OD2 I:ASP109 4.2 30.1 1.0
CA I:GLN196 4.2 35.0 1.0
CD I:PRO42 4.3 28.6 1.0
CB I:THR39 4.4 29.7 1.0
C I:THR39 4.4 29.8 1.0
N I:THR197 4.6 32.3 1.0
N I:ASN41 4.6 28.9 1.0
CD1 I:ILE48 4.6 22.9 1.0
N I:ASN110 4.6 26.1 1.0
CA I:THR39 4.7 27.9 1.0
CG2 I:THR197 4.7 32.9 1.0
CB I:GLN196 4.7 31.1 1.0
CA I:THR197 4.7 28.7 1.0
CB I:VAL40 4.9 33.1 1.0
CA I:ASN41 5.0 28.6 1.0

Sodium binding site 10 out of 12 in 1zum

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Sodium binding site 10 out of 12 in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Apo Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na3710

b:48.1
occ:1.00
 O J:ASP109 2.4 39.0 1.0
O J:GLN196 2.4 50.6 1.0
O J:VAL40 2.4 50.4 1.0
OD1 J:ASP109 2.5 47.0 1.0
O J:HOH3781 2.8 45.5 1.0
C J:ASP109 3.4 42.8 1.0
CG J:ASP109 3.5 46.2 1.0
OG1 J:THR39 3.5 56.2 1.0
C J:GLN196 3.6 48.6 1.0
C J:VAL40 3.6 50.5 1.0
CA J:ASP109 3.9 43.6 1.0
N J:VAL40 3.9 51.4 1.0
CD J:PRO42 4.1 45.1 1.0
CA J:GLN196 4.2 50.1 1.0
CB J:ASP109 4.2 44.0 1.0
CA J:VAL40 4.3 50.3 1.0
OD2 J:ASP109 4.3 46.6 1.0
N J:ASN110 4.6 43.8 1.0
CG2 J:THR197 4.6 41.7 1.0
CB J:GLN196 4.6 49.0 1.0
N J:THR197 4.6 45.1 1.0
N J:ASN41 4.7 49.2 1.0
C J:THR39 4.7 53.8 1.0
O J:VAL345 4.7 39.8 1.0
CB J:THR39 4.8 55.2 1.0
CA J:THR197 4.9 42.2 1.0
N J:PRO42 4.9 47.5 1.0
CA J:ASN41 4.9 49.0 1.0
CB J:VAL40 5.0 52.2 1.0

Reference:

H.N.Larson, H.Weiner, T.D.Hurley. Disruption of the Coenzyme Binding Site and Dimer Interface Revealed in the Crystal Structure of Mitochondrial Aldehyde Dehydrogenase "Asian" Variant J.Biol.Chem. V. 280 30550 2005.
ISSN: ISSN 0021-9258
PubMed: 15983043
DOI: 10.1074/JBC.M502345200
Page generated: Tue Dec 15 05:44:52 2020

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