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Sodium in PDB 3n80: Human Mitochondrial Aldehyde Dehydrogenase, Apo Form

Enzymatic activity of Human Mitochondrial Aldehyde Dehydrogenase, Apo Form

All present enzymatic activity of Human Mitochondrial Aldehyde Dehydrogenase, Apo Form:
1.2.1.3;

Protein crystallography data

The structure of Human Mitochondrial Aldehyde Dehydrogenase, Apo Form, PDB code: 3n80 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 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 141.662, 152.291, 177.282, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 17.5

Other elements in 3n80:

The structure of Human Mitochondrial Aldehyde Dehydrogenase, Apo Form also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Mitochondrial Aldehyde Dehydrogenase, Apo Form (pdb code 3n80). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Human Mitochondrial Aldehyde Dehydrogenase, Apo Form, PDB code: 3n80:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 3n80

Go back to Sodium Binding Sites List in 3n80
Sodium binding site 1 out of 7 in the Human Mitochondrial Aldehyde Dehydrogenase, 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, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na602

b:10.0
occ:1.00
 O B:HOH578 2.2 20.7 1.0
O B:GLN196 2.3 12.5 1.0
O B:ASP109 2.4 7.9 1.0
O B:VAL40 2.4 11.0 1.0
OD1 B:ASP109 2.5 10.4 1.0
O B:HOH1635 2.9 22.9 1.0
OG1 B:THR39 3.0 14.3 1.0
C B:ASP109 3.4 7.4 1.0
CG B:ASP109 3.5 10.5 1.0
C B:GLN196 3.5 10.6 1.0
C B:VAL40 3.5 11.1 1.0
N B:VAL40 3.7 11.9 1.0
CA B:ASP109 3.8 8.2 1.0
CB B:ASP109 4.2 9.4 1.0
CA B:VAL40 4.2 11.4 1.0
CA B:GLN196 4.3 11.5 1.0
O B:HOH1636 4.3 27.9 1.0
OD2 B:ASP109 4.3 12.2 1.0
CB B:THR39 4.4 12.2 1.0
CD B:PRO42 4.4 7.8 1.0
C B:THR39 4.5 11.8 1.0
N B:THR197 4.5 9.3 1.0
N B:ASN41 4.6 10.2 1.0
N B:ASN110 4.6 8.0 1.0
CG2 B:THR197 4.6 11.8 1.0
CA B:THR39 4.7 12.4 1.0
CA B:THR197 4.7 9.6 1.0
CB B:GLN196 4.7 11.4 1.0
CD1 B:ILE48 4.8 10.0 1.0
O B:VAL345 4.9 11.8 1.0
CB B:VAL40 4.9 13.2 1.0
CA B:ASN41 4.9 8.5 1.0

Sodium binding site 2 out of 7 in 3n80

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Sodium binding site 2 out of 7 in the Human Mitochondrial Aldehyde Dehydrogenase, 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, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na603

b:10.9
occ:1.00
 O C:HOH606 2.3 21.7 1.0
O C:GLN196 2.3 12.7 1.0
O C:VAL40 2.4 8.9 1.0
O C:ASP109 2.5 7.4 1.0
OD1 C:ASP109 2.5 12.5 1.0
OG1 C:THR39 3.0 12.1 1.0
O C:HOH942 3.2 16.7 1.0
CG C:ASP109 3.4 11.0 1.0
C C:ASP109 3.5 8.3 1.0
C C:VAL40 3.5 7.9 1.0
C C:GLN196 3.5 10.8 1.0
N C:VAL40 3.7 8.6 1.0
CA C:ASP109 3.8 7.6 1.0
CB C:ASP109 4.2 8.0 1.0
CA C:VAL40 4.2 8.8 1.0
OD2 C:ASP109 4.3 10.2 1.0
CD C:PRO42 4.3 6.5 1.0
CA C:GLN196 4.4 10.9 1.0
CB C:THR39 4.4 10.2 1.0
O C:HOH944 4.5 20.9 1.0
C C:THR39 4.5 8.5 1.0
N C:THR197 4.5 8.8 1.0
CG2 C:THR197 4.6 8.3 1.0
N C:ASN41 4.6 8.1 1.0
CA C:THR197 4.6 9.7 1.0
N C:ASN110 4.7 8.1 1.0
CA C:THR39 4.8 9.2 1.0
CD1 C:ILE48 4.8 8.8 1.0
CB C:VAL40 4.9 10.4 1.0
O C:VAL345 4.9 7.8 1.0
CB C:GLN196 4.9 10.9 1.0
CA C:ASN41 4.9 7.5 1.0

Sodium binding site 3 out of 7 in 3n80

Go back to Sodium Binding Sites List in 3n80
Sodium binding site 3 out of 7 in the Human Mitochondrial Aldehyde Dehydrogenase, 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, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na604

b:10.3
occ:1.00
 O D:VAL40 2.3 10.0 1.0
O D:GLN196 2.3 12.2 1.0
O D:HOH3100 2.4 24.9 1.0
O D:ASP109 2.4 8.3 1.0
OD1 D:ASP109 2.5 11.8 1.0
OG1 D:THR39 3.1 14.3 1.0
C D:ASP109 3.4 8.2 1.0
CG D:ASP109 3.4 12.8 1.0
C D:VAL40 3.4 10.3 1.0
O D:HOH3099 3.5 19.4 1.0
C D:GLN196 3.5 9.8 1.0
N D:VAL40 3.6 10.6 1.0
CA D:ASP109 3.8 8.4 1.0
CA D:VAL40 4.1 10.8 1.0
CB D:ASP109 4.1 8.5 1.0
CA D:GLN196 4.3 10.9 1.0
OD2 D:ASP109 4.3 11.7 1.0
CD D:PRO42 4.3 9.5 1.0
CB D:THR39 4.4 11.6 1.0
C D:THR39 4.4 10.3 1.0
N D:ASN41 4.5 8.9 1.0
N D:THR197 4.6 8.0 1.0
N D:ASN110 4.6 8.2 1.0
CG2 D:THR197 4.7 9.8 1.0
CA D:THR39 4.7 11.8 1.0
CD1 D:ILE48 4.7 8.7 1.0
CA D:THR197 4.8 9.3 1.0
CB D:GLN196 4.8 11.0 1.0
CB D:VAL40 4.8 12.7 1.0
O D:VAL345 4.9 10.4 1.0
CA D:ASN41 4.9 8.1 1.0

Sodium binding site 4 out of 7 in 3n80

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Sodium binding site 4 out of 7 in the Human Mitochondrial Aldehyde Dehydrogenase, 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, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na605

b:9.7
occ:1.00
 O E:VAL40 2.3 9.8 1.0
O E:GLN196 2.4 11.8 1.0
O E:ASP109 2.4 7.8 1.0
O E:HOH3502 2.4 20.1 1.0
OD1 E:ASP109 2.5 11.4 1.0
OG1 E:THR39 3.0 13.0 1.0
C E:ASP109 3.4 7.3 1.0
CG E:ASP109 3.5 10.2 1.0
C E:VAL40 3.5 11.0 1.0
O E:HOH3501 3.5 19.9 1.0
C E:GLN196 3.6 10.8 1.0
N E:VAL40 3.7 11.3 1.0
CA E:ASP109 3.8 7.1 1.0
CA E:VAL40 4.2 12.4 1.0
CB E:ASP109 4.2 8.1 1.0
CD E:PRO42 4.3 7.9 1.0
O E:HOH4638 4.3 29.4 1.0
OD2 E:ASP109 4.3 11.4 1.0
CB E:THR39 4.3 12.1 1.0
CA E:GLN196 4.4 10.6 1.0
C E:THR39 4.4 10.9 1.0
N E:ASN41 4.5 9.2 1.0
N E:THR197 4.6 9.3 1.0
N E:ASN110 4.6 7.2 1.0
CD1 E:ILE48 4.6 10.6 1.0
CA E:THR39 4.7 10.1 1.0
CG2 E:THR197 4.7 10.0 1.0
CA E:THR197 4.7 10.2 1.0
CB E:GLN196 4.9 11.2 1.0
CB E:VAL40 4.9 14.0 1.0
O E:VAL345 4.9 9.7 1.0
CA E:ASN41 4.9 8.5 1.0
CG2 E:THR39 5.0 11.6 1.0

Sodium binding site 5 out of 7 in 3n80

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Sodium binding site 5 out of 7 in the Human Mitochondrial Aldehyde Dehydrogenase, 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, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na606

b:10.8
occ:1.00
 O F:HOH3832 2.2 19.1 1.0
O F:VAL40 2.3 9.1 1.0
O F:GLN196 2.4 12.1 1.0
O F:ASP109 2.5 7.6 1.0
OD1 F:ASP109 2.5 10.9 1.0
OG1 F:THR39 3.0 11.0 1.0
O F:HOH2535 3.3 15.5 1.0
CG F:ASP109 3.4 10.7 1.0
C F:ASP109 3.5 7.0 1.0
C F:VAL40 3.5 8.5 1.0
C F:GLN196 3.6 9.0 1.0
N F:VAL40 3.7 8.6 1.0
CA F:ASP109 3.8 7.0 1.0
CB F:ASP109 4.2 7.7 1.0
CA F:VAL40 4.2 9.1 1.0
CD F:PRO42 4.3 7.6 1.0
OD2 F:ASP109 4.3 9.2 1.0
CB F:THR39 4.4 9.3 1.0
CA F:GLN196 4.4 8.8 1.0
O F:HOH2534 4.5 16.7 1.0
C F:THR39 4.5 8.2 1.0
N F:ASN41 4.5 7.6 1.0
N F:THR197 4.6 7.3 1.0
CG2 F:THR197 4.6 8.8 1.0
N F:ASN110 4.7 6.7 1.0
CA F:THR197 4.7 7.8 1.0
CD1 F:ILE48 4.7 9.0 1.0
CA F:THR39 4.8 8.7 1.0
CB F:VAL40 4.8 8.9 1.0
CB F:GLN196 4.9 9.5 1.0
CA F:ASN41 4.9 6.7 1.0
O F:VAL345 5.0 7.4 1.0

Sodium binding site 6 out of 7 in 3n80

Go back to Sodium Binding Sites List in 3n80
Sodium binding site 6 out of 7 in the Human Mitochondrial Aldehyde Dehydrogenase, 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, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na607

b:13.4
occ:1.00
 O G:HOH2861 2.3 22.7 1.0
O G:VAL40 2.3 14.7 1.0
O G:GLN196 2.4 14.7 1.0
O G:ASP109 2.4 10.1 1.0
OD1 G:ASP109 2.5 13.0 1.0
OG1 G:THR39 3.1 14.9 1.0
O G:HOH2874 3.3 21.2 1.0
C G:ASP109 3.4 11.0 1.0
CG G:ASP109 3.5 14.0 1.0
C G:VAL40 3.5 15.8 1.0
C G:GLN196 3.6 12.9 1.0
N G:VAL40 3.7 15.3 1.0
CA G:ASP109 3.7 11.3 1.0
CA G:VAL40 4.1 16.5 1.0
CB G:ASP109 4.2 12.8 1.0
O G:HOH4802 4.2 36.0 1.0
CD G:PRO42 4.3 12.4 1.0
OD2 G:ASP109 4.3 13.4 1.0
CA G:GLN196 4.4 11.9 1.0
CB G:THR39 4.4 15.3 1.0
C G:THR39 4.5 15.1 1.0
N G:THR197 4.5 11.1 1.0
N G:ASN41 4.6 12.9 1.0
N G:ASN110 4.6 10.7 1.0
CG2 G:THR197 4.6 11.5 1.0
CD1 G:ILE48 4.7 14.7 1.0
CA G:THR197 4.7 10.7 1.0
O G:VAL345 4.8 11.2 1.0
CA G:THR39 4.8 14.4 1.0
CA G:ASN41 4.9 12.5 1.0
CB G:VAL40 4.9 18.0 1.0
CB G:GLN196 5.0 13.4 1.0

Sodium binding site 7 out of 7 in 3n80

Go back to Sodium Binding Sites List in 3n80
Sodium binding site 7 out of 7 in the Human Mitochondrial Aldehyde Dehydrogenase, 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, Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na608

b:10.2
occ:1.00
 O H:GLN196 2.3 10.1 1.0
O H:HOH4243 2.3 24.4 1.0
O H:VAL40 2.4 10.3 1.0
O H:ASP109 2.5 8.6 1.0
OD1 H:ASP109 2.6 10.6 1.0
O H:HOH4242 2.8 22.5 1.0
OG1 H:THR39 3.2 12.2 1.0
C H:ASP109 3.5 7.8 1.0
C H:GLN196 3.5 8.3 1.0
CG H:ASP109 3.5 11.8 1.0
C H:VAL40 3.5 9.9 1.0
N H:VAL40 3.7 9.2 1.0
CA H:ASP109 3.8 7.9 1.0
CA H:VAL40 4.2 10.3 1.0
CB H:ASP109 4.2 8.7 1.0
O H:HOH4244 4.2 25.1 1.0
CA H:GLN196 4.3 8.5 1.0
CD H:PRO42 4.3 7.5 1.0
OD2 H:ASP109 4.4 11.9 1.0
CB H:THR39 4.5 11.3 1.0
N H:THR197 4.5 8.6 1.0
C H:THR39 4.5 9.8 1.0
N H:ASN41 4.6 7.8 1.0
N H:ASN110 4.7 8.5 1.0
CD1 H:ILE48 4.7 9.2 1.0
CB H:GLN196 4.7 9.0 1.0
CG2 H:THR197 4.7 9.1 1.0
CA H:THR197 4.7 8.1 1.0
CA H:THR39 4.8 10.5 1.0
CA H:ASN41 4.9 7.9 1.0
O H:VAL345 4.9 10.8 1.0
CB H:VAL40 4.9 10.7 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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