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Sodium in PDB 3n82: T244A Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Nadh Complex

Enzymatic activity of T244A Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Nadh Complex

All present enzymatic activity of T244A Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Nadh Complex:
1.2.1.3;

Protein crystallography data

The structure of T244A Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Nadh Complex, PDB code: 3n82 was solved by L.Gonzalez-Segura, T.D.Hurley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 142.216, 150.724, 177.299, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 21.9

Other elements in 3n82:

The structure of T244A Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Nadh Complex also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the T244A Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Nadh Complex (pdb code 3n82). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the T244A Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Nadh Complex, PDB code: 3n82:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 3n82

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Sodium binding site 1 out of 8 in the T244A Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Nadh Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of T244A Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Nadh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na701

b:34.6
occ:1.00
 O A:GLN196 2.3 24.7 1.0
O A:VAL40 2.5 28.3 1.0
OD1 A:ASP109 2.5 25.1 1.0
O A:ASP109 2.6 23.7 1.0
OG1 A:THR39 2.9 29.4 1.0
O A:HOH1975 3.3 35.6 1.0
CG A:ASP109 3.5 24.6 1.0
C A:GLN196 3.5 24.8 1.0
C A:VAL40 3.6 28.3 1.0
C A:ASP109 3.6 23.8 1.0
N A:VAL40 3.6 28.6 1.0
CA A:ASP109 3.9 23.9 1.0
CA A:VAL40 4.2 28.3 1.0
CB A:THR39 4.2 28.9 1.0
OD2 A:ASP109 4.2 26.5 1.0
CB A:ASP109 4.3 24.1 1.0
CA A:GLN196 4.3 24.8 1.0
C A:THR39 4.3 28.6 1.0
CD A:PRO42 4.4 29.6 1.0
N A:THR197 4.5 24.5 1.0
CA A:THR39 4.6 28.8 1.0
N A:ASN41 4.6 28.3 1.0
CA A:THR197 4.7 24.3 1.0
CG2 A:THR197 4.8 24.1 1.0
CB A:GLN196 4.8 24.9 1.0
N A:ASN110 4.8 23.8 1.0
CD1 A:ILE48 4.8 30.3 1.0
CB A:VAL40 4.9 28.2 1.0
O A:VAL345 5.0 27.1 1.0
CG2 A:THR39 5.0 28.9 1.0

Sodium binding site 2 out of 8 in 3n82

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Sodium binding site 2 out of 8 in the T244A Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Nadh Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of T244A Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Nadh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na702

b:25.6
occ:1.00
 O B:GLN196 2.4 20.7 1.0
OD1 B:ASP109 2.4 20.6 1.0
O B:HOH1956 2.5 30.5 1.0
O B:ASP109 2.5 22.0 1.0
O B:VAL40 2.5 25.2 1.0
OG1 B:THR39 3.0 22.7 1.0
O B:HOH1321 3.4 34.8 1.0
C B:ASP109 3.5 21.9 1.0
CG B:ASP109 3.5 21.6 1.0
C B:GLN196 3.6 20.7 1.0
C B:VAL40 3.6 24.9 1.0
N B:VAL40 3.7 24.6 1.0
CA B:ASP109 3.8 21.4 1.0
CA B:VAL40 4.2 24.9 1.0
CB B:ASP109 4.2 21.2 1.0
CB B:THR39 4.3 23.7 1.0
CA B:GLN196 4.4 21.2 1.0
OD2 B:ASP109 4.4 20.7 1.0
C B:THR39 4.4 24.1 1.0
CD B:PRO42 4.4 24.5 1.0
N B:THR197 4.6 20.2 1.0
CG2 B:THR197 4.6 20.2 1.0
N B:ASN110 4.7 22.4 1.0
N B:ASN41 4.7 24.8 1.0
CD1 B:ILE48 4.7 22.8 1.0
CA B:THR197 4.7 19.9 1.0
CA B:THR39 4.7 23.6 1.0
CB B:GLN196 4.8 21.2 1.0
CB B:VAL40 4.9 25.1 1.0
O B:VAL345 5.0 23.2 1.0

Sodium binding site 3 out of 8 in 3n82

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Sodium binding site 3 out of 8 in the T244A Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Nadh Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of T244A Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Nadh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na703

b:23.6
occ:1.00
 O C:HOH1718 2.3 37.2 1.0
O C:GLN196 2.4 20.7 1.0
O C:VAL40 2.4 20.9 1.0
O C:ASP109 2.6 21.7 1.0
OD1 C:ASP109 2.6 22.0 1.0
OG1 C:THR39 3.0 20.9 1.0
O C:HOH1342 3.1 27.1 1.0
C C:VAL40 3.5 21.3 1.0
CG C:ASP109 3.6 22.6 1.0
C C:GLN196 3.6 20.7 1.0
C C:ASP109 3.6 21.3 1.0
N C:VAL40 3.6 21.1 1.0
CA C:ASP109 3.9 21.3 1.0
CA C:VAL40 4.1 20.9 1.0
CB C:THR39 4.3 20.5 1.0
CB C:ASP109 4.3 21.4 1.0
C C:THR39 4.3 20.8 1.0
CA C:GLN196 4.3 20.6 1.0
OD2 C:ASP109 4.3 23.7 1.0
CD C:PRO42 4.5 21.0 1.0
N C:THR197 4.6 20.4 1.0
CA C:THR39 4.6 20.6 1.0
N C:ASN41 4.6 21.0 1.0
O C:HOH1921 4.6 36.2 1.0
CD1 C:ILE48 4.7 20.8 1.0
CA C:THR197 4.7 20.1 1.0
CG2 C:THR197 4.8 19.1 1.0
N C:ASN110 4.8 21.3 1.0
CB C:GLN196 4.8 20.4 1.0
CB C:VAL40 4.9 20.9 1.0
O C:VAL345 5.0 20.2 1.0

Sodium binding site 4 out of 8 in 3n82

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Sodium binding site 4 out of 8 in the T244A Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Nadh Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of T244A Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Nadh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na704

b:33.5
occ:1.00
 O D:GLN196 2.4 25.5 1.0
O D:VAL40 2.4 28.1 1.0
OD1 D:ASP109 2.6 23.1 1.0
O D:ASP109 2.7 23.0 1.0
O D:HOH2424 2.7 28.6 1.0
OG1 D:THR39 3.0 26.6 1.0
C D:VAL40 3.5 28.0 1.0
N D:VAL40 3.5 27.5 1.0
C D:GLN196 3.5 25.3 1.0
CG D:ASP109 3.6 23.6 1.0
C D:ASP109 3.7 23.1 1.0
CA D:ASP109 4.0 22.9 1.0
CA D:VAL40 4.1 27.8 1.0
CA D:GLN196 4.3 25.6 1.0
C D:THR39 4.3 27.1 1.0
CB D:THR39 4.3 26.8 1.0
CB D:ASP109 4.3 23.1 1.0
OD2 D:ASP109 4.3 22.9 1.0
CD D:PRO42 4.5 28.7 1.0
N D:THR197 4.6 24.9 1.0
CA D:THR39 4.6 27.0 1.0
N D:ASN41 4.7 28.2 1.0
CB D:VAL40 4.7 27.8 1.0
CG2 D:THR197 4.7 25.0 1.0
CB D:GLN196 4.8 25.7 1.0
CA D:THR197 4.8 24.7 1.0
CD1 D:ILE48 4.8 23.4 1.0
N D:ASN110 4.9 23.3 1.0
O D:VAL345 4.9 28.9 1.0

Sodium binding site 5 out of 8 in 3n82

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Sodium binding site 5 out of 8 in the T244A Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Nadh Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of T244A Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Nadh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na705

b:33.4
occ:1.00
 O E:HOH1984 2.3 36.5 1.0
O E:VAL40 2.4 26.8 1.0
O E:GLN196 2.5 24.3 1.0
O E:ASP109 2.5 25.7 1.0
OD1 E:ASP109 2.6 26.0 1.0
OG1 E:THR39 3.0 26.8 1.0
O E:HOH782 3.2 26.3 1.0
C E:ASP109 3.5 25.4 1.0
C E:VAL40 3.6 26.9 1.0
CG E:ASP109 3.6 25.3 1.0
N E:VAL40 3.6 27.1 1.0
C E:GLN196 3.7 24.4 1.0
CA E:ASP109 3.9 25.3 1.0
CA E:VAL40 4.2 26.9 1.0
CD E:PRO42 4.3 27.2 1.0
CB E:ASP109 4.3 25.2 1.0
CB E:THR39 4.4 26.8 1.0
CA E:GLN196 4.4 24.4 1.0
C E:THR39 4.5 27.0 1.0
OD2 E:ASP109 4.5 24.4 1.0
N E:ASN41 4.7 26.6 1.0
N E:THR197 4.7 24.3 1.0
O E:VAL345 4.7 27.7 1.0
CA E:THR39 4.7 26.7 1.0
CD1 E:ILE48 4.7 29.4 1.0
N E:ASN110 4.7 25.6 1.0
CB E:VAL40 4.8 27.2 1.0
CG2 E:THR197 4.8 24.5 1.0
CA E:THR197 4.8 24.4 1.0
CB E:GLN196 4.9 24.2 1.0

Sodium binding site 6 out of 8 in 3n82

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Sodium binding site 6 out of 8 in the T244A Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Nadh Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of T244A Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Nadh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na706

b:27.3
occ:1.00
 O F:ASP109 2.4 20.4 1.0
OD1 F:ASP109 2.4 19.3 1.0
O F:GLN196 2.4 19.5 1.0
O F:HOH1585 2.5 30.9 1.0
O F:VAL40 2.5 20.8 1.0
OG1 F:THR39 3.0 21.1 1.0
C F:ASP109 3.4 20.1 1.0
CG F:ASP109 3.4 20.2 1.0
C F:VAL40 3.6 21.4 1.0
O F:HOH934 3.6 20.5 1.0
C F:GLN196 3.7 19.7 1.0
N F:VAL40 3.7 20.9 1.0
CA F:ASP109 3.7 19.8 1.0
CB F:ASP109 4.1 19.4 1.0
CA F:VAL40 4.2 21.1 1.0
OD2 F:ASP109 4.3 18.1 1.0
CD F:PRO42 4.3 21.1 1.0
CB F:THR39 4.3 20.5 1.0
C F:THR39 4.4 20.6 1.0
O F:HOH1141 4.5 30.5 1.0
CA F:GLN196 4.5 20.0 1.0
N F:ASN110 4.6 20.2 1.0
N F:THR197 4.6 19.5 1.0
N F:ASN41 4.6 21.4 1.0
CG2 F:THR197 4.7 18.9 1.0
CA F:THR197 4.7 19.4 1.0
CD1 F:ILE48 4.7 20.8 1.0
CA F:THR39 4.8 20.4 1.0
CA F:ASN41 4.9 21.4 1.0
CB F:VAL40 5.0 21.2 1.0
CB F:GLN196 5.0 20.0 1.0
CG2 F:THR39 5.0 20.5 1.0

Sodium binding site 7 out of 8 in 3n82

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Sodium binding site 7 out of 8 in the T244A Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Nadh Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of T244A Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Nadh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na707

b:33.2
occ:1.00
 O G:VAL40 2.4 29.1 1.0
OD1 G:ASP109 2.4 28.7 1.0
O G:GLN196 2.5 27.6 1.0
O G:ASP109 2.6 25.2 1.0
OG1 G:THR39 2.8 29.1 1.0
O G:HOH2465 3.0 28.6 1.0
C G:VAL40 3.4 29.8 1.0
N G:VAL40 3.4 29.4 1.0
CG G:ASP109 3.5 26.6 1.0
C G:ASP109 3.6 25.6 1.0
C G:GLN196 3.7 27.6 1.0
CA G:ASP109 3.9 25.7 1.0
CA G:VAL40 4.0 29.6 1.0
CB G:THR39 4.1 29.3 1.0
C G:THR39 4.2 29.2 1.0
CB G:ASP109 4.3 26.0 1.0
OD2 G:ASP109 4.3 27.9 1.0
CA G:GLN196 4.4 27.8 1.0
CA G:THR39 4.5 29.2 1.0
CD G:PRO42 4.5 29.9 1.0
N G:ASN41 4.5 29.9 1.0
CD1 G:ILE48 4.6 32.7 1.0
N G:THR197 4.7 26.9 1.0
CB G:VAL40 4.7 29.7 1.0
CG2 G:THR39 4.7 28.5 1.0
CA G:THR197 4.8 26.3 1.0
N G:ASN110 4.8 25.5 1.0
CG2 G:THR197 4.9 25.8 1.0
CB G:GLN196 4.9 27.9 1.0
CA G:ASN41 4.9 30.1 1.0

Sodium binding site 8 out of 8 in 3n82

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Sodium binding site 8 out of 8 in the T244A Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Nadh Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of T244A Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Nadh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na708

b:38.6
occ:1.00
 O H:GLN196 2.4 28.5 1.0
O H:VAL40 2.5 31.1 1.0
OD1 H:ASP109 2.5 29.2 1.0
O H:ASP109 2.6 27.3 1.0
OG1 H:THR39 2.9 30.2 1.0
O H:HOH1571 3.1 23.8 1.0
CG H:ASP109 3.5 28.5 1.0
C H:GLN196 3.5 28.5 1.0
C H:VAL40 3.6 31.2 1.0
N H:VAL40 3.6 30.8 1.0
C H:ASP109 3.6 27.2 1.0
CA H:ASP109 4.0 27.4 1.0
CA H:VAL40 4.1 31.0 1.0
CB H:THR39 4.3 29.9 1.0
OD2 H:ASP109 4.3 27.8 1.0
CA H:GLN196 4.3 28.8 1.0
CB H:ASP109 4.3 27.6 1.0
C H:THR39 4.3 30.5 1.0
CD H:PRO42 4.5 32.1 1.0
N H:THR197 4.5 28.2 1.0
CA H:THR39 4.6 30.2 1.0
N H:ASN41 4.7 31.2 1.0
CG2 H:THR197 4.7 26.5 1.0
CA H:THR197 4.7 27.9 1.0
CD1 H:ILE48 4.7 32.3 1.0
CB H:VAL40 4.8 30.8 1.0
CB H:GLN196 4.8 28.9 1.0
N H:ASN110 4.8 27.2 1.0
O H:VAL345 5.0 30.1 1.0
O H:HOH1196 5.0 26.5 1.0

Reference:

K.-K.Ho, L.Gonzalez-Segura, S.Perez-Miller, H.Weiner, T.D.Hurley. Conformational Selection During Catalysis: the Role of Threonine 244 in ALDH2 To Be Published.
Page generated: Mon Oct 7 11:44:45 2024

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